From 53be49ec9abb1ae8ea47b889fd56777e09680526 Mon Sep 17 00:00:00 2001
From: annefou <annefou@users.noreply.github.com>
Date: Sun, 31 Mar 2024 23:10:03 +0000
Subject: [PATCH] Update tools

---
 tools.md | 2821 +++++++++++++++++++++++++++++++++---------------------
 1 file changed, 1740 insertions(+), 1081 deletions(-)

diff --git a/tools.md b/tools.md
index 1a53d8ace..535d8c86d 100644
--- a/tools.md
+++ b/tools.md
@@ -2,19 +2,22 @@
 layout: default
 ---
 
-# European Galaxy tools (2801 and counting)
+# European Galaxy tools (3449 and counting)
 <hr/>
 <h3>Get Data</h3>
 <a href="https://usegalaxy.eu/root?tool_id=fasterq_dump" title="format from NCBI SRA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Faster Download and Extract Reads in FASTQ</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ncbi_acc_download" title="Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI Accession Download</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=uniprotxml_downloader" title="download proteome as XML or fasta"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UniProt</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=unipept" title="retrieve taxonomy for peptides"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unipept</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=iedb_api" title="MHC Binding prediction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IEDB</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastq_dump" title="format from NCBI SRA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Download and Extract Reads in FASTQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sam_dump" title="format from NCBI SRA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Download and Extract Reads in BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=obis_data" title="retrieve data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OBIS occurences</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=argo_getdata" title="for global ocean in situ observing system"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Argo data access</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mavedb_importer" title="import MAVE data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaveDB</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=iedb_api" title="MHC Binding prediction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IEDB</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dbbuilder" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Protein Database Downloader</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=datasets_download_genome" title="download genome sequence, annotation and metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI Datasets Genomes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ncbi_acc_download" title="Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI Accession Download</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sra_pileup" title="from NCBI SRA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Download and Generate Pileup Format</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spocc_occ" title="from GBIF, ALA, iNAT and others"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get species occurrences data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=uniprotxml_downloader" title="download proteome as XML or fasta"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UniProt</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spocc_occ" title="from GBIF, OBIS, ALA, iNAT and others"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get species occurrences data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=unipept" title="retrieve taxonomy for peptides"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unipept</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_eutils_esearch" title="search NCBI Databases by text query"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI ESearch</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_eutils_egquery" title="Provides the number of records retrieved in all Entrez databases by a single text query."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI EGQuery</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_eutils_ecitmatch" title="search NCBI for citations in PubMed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI ECitMatch</button></a>
@@ -26,6 +29,10 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=uniprot" title="ID mapping and retrieval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UniProt</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=get_sequences" title="using REST API"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get sequences by Ensembl ID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=get_genetree" title="using REST API"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get gene tree by Ensembl ID</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=query_impc" title="query tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IMPC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=iabiodiv_smartbiodiv_med_environ" title="From Copernicus and etopo given geolocalized and timestamped observations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Adds environment variables</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=datasets_download_gene" title="download gene sequences and metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI Datasets Gene</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=datasets_download_genome" title="download genome sequence, annotation and metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI Datasets Genomes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=get_feature_info" title="using REST API"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get features by Ensembl ID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=enasearch_search_data" title="given a query"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Search ENA data</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=enasearch_retrieve_data" title="(other than taxon and project)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Retrieve ENA data</button></a>
@@ -38,8 +45,10 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=pyega3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EGA Download Client</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=upload1" title="from your computer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Upload File</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ds_seek_test" title="Trying to get open files out of SEEK"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SEEK test</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pysradb_search" title="sequence metadata from SRA/ENA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pysradb search</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ucsc_table_direct1" title="table browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UCSC Main</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ucsc_table_direct_archaea1" title="table browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UCSC Archaea</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ncbi_datasets_source" title="import data from the NCBI Datasets Genomes page"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI Datasets Genomes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lftp" title="via lftps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">downloads</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ebi_sra_main" title="ENA SRA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EBI SRA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sra_source" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SRA</button></a>
@@ -63,15 +72,17 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=hbvar" title="Human Hemoglobin Variants and Thalassemias"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HbVar</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=omicsdi" title="Sync dataset's files from OmicsDI"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OmicsDI</button></a>
 <h3>Send Data</h3>
-<a href="https://usegalaxy.eu/root?tool_id=export_remote" title="to remote files source"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Export datasets</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=directory_uri" title="to different data storages"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Export datasets</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ena_upload" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ENA Upload tool</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ena_upload" title="Submission of (meta)data to the European Nucleotide Archive (ENA)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ENA Upload tool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=curl_post" title="send cURL POST requests"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cURL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=send_to_cloud" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Send to cloud</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=export_remote" title="to remote files source"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Export datasets</button></a>
 <h3>Collection Operations</h3>
-<a href="https://usegalaxy.eu/root?tool_id=collapse_dataset" title="into single dataset in order of the collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Collapse Collection</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tp_split_on_column" title="according to the values of a column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split file</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=split_file_to_collection" title="to dataset collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split file</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=unzip" title="Unzip file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unzip</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=collapse_dataset" title="into single dataset in order of the collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Collapse Collection</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pick_value" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pick parameter value</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=__HARMONIZELISTS__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Harmonize two collections</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=unzip" title="Unzip a file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unzip</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=collection_element_identifiers" title="of a list collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract element identifiers</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=collection_column_join" title="on multiple datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Column join</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__UNZIP_COLLECTION__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unzip collection</button></a>
@@ -87,58 +98,57 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=__APPLY_RULES__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Apply rules</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__BUILD_LIST__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build list</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__EXTRACT_DATASET__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract dataset</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=__DUPLICATE_FILE_TO_COLLECTION__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Duplicate file to collection</button></a>
 <h3>Expression Tools</h3>
-<a href="https://usegalaxy.eu/root?tool_id=calculate_numeric_param" title="from parameters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate numeric parameter value</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=compose_text_param" title="from parameters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compose text parameter value</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=calculate_numeric_param" title="from parameters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate numeric parameter value</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=map_param_value" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map parameter value</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=param_value_from_file" title="from dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Parse parameter value</button></a>
 <hr/><h2>General Text Tools</h2>
 <h3>Text Manipulation</h3>
-<a href="https://usegalaxy.eu/root?tool_id=table_compute" title="computes operations on table data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Table Compute</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=diff" title="analyzes two files and generates an unidiff text file with information about the differences and an optional Html report"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">diff</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=histogram_rpy" title="of a numeric column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Histogram</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Add_a_column1" title="an expression on every row"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_awk_tool" title="with awk"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Text reformatting</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tp_cat" title="tail-to-head (cat)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate datasets</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_cut_tool" title="columns from a table (cut)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Advanced Cut</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_easyjoin_tool" title="two files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_find_and_replace" title="parts of text"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_grep_tool" title="(grep)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Search in textfiles</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_head_tool" title="lines from a dataset (head)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select first</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_multijoin_tool" title="(combine multiple files)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Multi-Join</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=nl" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Number lines</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_text_file_with_recurring_lines" title="with recurring lines"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create text file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_replace_in_column" title="in a specific column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace Text</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_replace_in_line" title="in entire line"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace Text</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_sed_tool" title="with sed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Text transformation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_sort_header_tool" title="data in ascending or descending order"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_sort_rows" title="according to their columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort a row</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_uniq_tool" title="assuming sorted input file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unique lines</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_tac" title="reverse a file (reverse cat)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tac</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_tail_tool" title="lines from a dataset (tail)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select last</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_unfold_column_tool" title="columns from a table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unfold</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_sorted_uniq" title="occurrences of each record"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unique</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=histogram_rpy" title="of a numeric column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Histogram</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Add_a_column1" title="on rows"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=diff" title="analyzes two files and generates an unidiff text file with information about the differences and an optional Html report"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">diff</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=replace_column_with_key_value_file" title="by values which are defined in a convert file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace column</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=add_line_to_file" title="writes a line of text at the begining or end of a text file."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add line to file</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_awk_tool" title="with awk"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Text reformatting</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=addName" title="to an existing tabular file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add input name as column</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mergeCols1" title="together"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge Columns</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=imagecoordinates_flipaxis" title="Switches the axes of an image and flips the y axis."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Switch axis coordinates</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_find_and_replace" title="parts of text"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_sort_rows" title="according to their columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort a row</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=table_compute" title="computes operations on table data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Table Compute</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=regexColumn1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Column Regex Find And Replace</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=regex1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Regex Find And Replace</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=join_files_on_column_fuzzy" title="on column allowing a small difference"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join two files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=prinseq" title="to process quality of sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PRINSEQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=query_tabular" title="using sqlite sql"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Query Tabular</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_easyjoin_tool" title="two files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_replace_in_line" title="in entire line"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace Text</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=replace_chromosome_names" title="in a tabular dataset using a mapping table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace chromosome names</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sqlite_to_tabular" title="for SQL query"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SQLite to tabular</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_uniq_tool" title="assuming sorted input file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unique lines</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=filter_tabular" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter Tabular</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_replace_in_column" title="in a specific column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace Text</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=jq" title="process JSON"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cast" title="expand combinations of variables:values to columnar format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cast</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_sort_header_tool" title="data in ascending or descending order"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=melt" title="collapse combinations of variables:values to single lines"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">melt</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gops_basecoverage_1" title="of all intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Base Coverage</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_grep_tool" title="(grep)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Search in textfiles</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_sed_tool" title="with sed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Text transformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_unfold_column_tool" title="columns from a table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unfold</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gops_subtract_1" title="the intervals of two datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Subtract</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gops_complement_1" title="intervals of a dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Complement</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gops_cluster_1" title="the intervals of a dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gff3.rebase" title="against parent features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Rebase GFF3 features</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=column_remove_by_header" title="by heading"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove columns</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=column_order_header_sort" title="by heading"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort Column Order</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_sorted_uniq" title="occurrences of each record"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unique</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_head_tool" title="lines from a dataset (head)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select first</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_multijoin_tool" title="(combine multiple files)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Multi-Join</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_tail_tool" title="lines from a dataset (tail)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select last</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_cut_tool" title="columns from a table (cut)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Advanced Cut</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_text_file_with_recurring_lines" title="with recurring lines"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create text file</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_tac" title="reverse a file (reverse cat)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tac</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gops_coverage_1" title="of a set of intervals on second set of intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Coverage</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=regex_replace" title="Regular Expression replacement using the Python re module"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Regex Replace</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tables_arithmetic_operations" title="on tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Arithmetic Operations</button></a>
@@ -149,6 +159,8 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=subtract_query1" title="from another dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Subtract Whole Dataset</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bg_uniq" title="occurrences of each record"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unique</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=addValue" title="to an existing dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add column</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_split_on_column" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split by group</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cat_multi_datasets" title="tail-to-head by specifying how"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate multiple datasets</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=addValue" title="to an existing dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add column</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cat1" title="tail-to-head"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate datasets</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Cut1" title="columns from a table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cut</button></a>
@@ -163,14 +175,26 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=trimmer" title="leading or trailing characters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trim</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=wc_gnu" title="of a dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Line/Word/Character count</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=secure_hash_message_digest" title="on a dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Secure Hash / Message Digest</button></a>
+<h3>Convert Formats</h3>
+<a href="https://usegalaxy.eu/root?tool_id=ucsc_wigtobigwig" title="bedGraph or Wig to bigWig converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">wigtobigwig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=10x_bamtofastq" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert a 10X BAM file to FASTQ</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=glimmer_glimmer_to_gff" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Glimmer to GFF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=agat" title="GTF/GFF analysis toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AGAT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bed2gff1" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BED-to-GFF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gff2bed1" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF-to-BED</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=MAF_To_BED1" title="Converts a MAF formatted file to the BED format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAF to BED</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=MAF_To_Interval1" title="Converts a MAF formatted file to the Interval format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAF to Interval</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=MAF_To_Fasta1" title="Converts a MAF formatted file to FASTA format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAF to FASTA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Sff_extractor" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SFF converter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bed_to_bigBed" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BED-to-bigBed</button></a>
 <h3>Filter and Sort</h3>
-<a href="https://usegalaxy.eu/root?tool_id=gffcompare" title="compare assembled transcripts to a reference annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GffCompare</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seq_filter_by_id" title="from a tabular file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter sequences by ID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=filter_by_fasta_ids" title="on the headers and/or the sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter FASTA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bg_column_arrange_by_header" title="by header name"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Column arrange</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=xpath" title="compute xpath expressions on XML data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">XPath</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sample_seqs" title="e.g. to reduce coverage"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sub-sample sequences files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seq_filter_by_id" title="from a tabular file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter sequences by ID</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xpath" title="compute xpath expressions on XML data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">XPath</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=find_in_reference" title="filter peptides that are present in proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">find in reference</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gffcompare" title="compare assembled transcripts to a reference annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GffCompare</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Filter1" title="data on any column using simple expressions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sort1" title="data in ascending or descending order"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Grep1" title="lines that match an expression"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select</button></a>
@@ -180,8 +204,8 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=gff_filter_by_feature_count" title="using simple expressions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter GFF data by feature count</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gtf_filter_by_attribute_values_list" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter GTF data by attribute values_list</button></a>
 <h3>Join, Subtract and Group</h3>
-<a href="https://usegalaxy.eu/root?tool_id=collection_column_join" title="on multiple datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Column join</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=datamash_transpose" title="rows/columns in a tabular file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Transpose</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=collection_column_join" title="on multiple datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Column join</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=datamash_reverse" title="columns in a tabular file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Reverse</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=datamash_ops" title="(operations on tabular data)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Datamash</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=datamash_ops" title="(operations on tabular data)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Datamash</button></a>
@@ -191,44 +215,54 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=Grouping1" title="data by a column and perform aggregate operation on other columns."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Group</button></a>
 <hr/><h2>Genomic File Manipulation</h2>
 <h3>Convert Formats</h3>
-<a href="https://usegalaxy.eu/root?tool_id=ucsc-twobittofa" title="Convert all or part of .2bit file to FASTA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">twoBitToFa</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=crossmap_bam" title="Convert genome coordinates or annotation files between genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CrossMap BAM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=GeneBed_Maf_Fasta2" title="given a set of coding exon intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stitch Gene blocks</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ab1_fastq_converter" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ab1 to FASTQ converter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mz_to_sqlite" title="Extract mzIdentML and associated proteomics datasets into a SQLite DB"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mz to sqlite</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=biom_convert" title="between BIOM table formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bioext_bam2msa" title="to FASTA multiple sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_bam_to_cram" title="convert BAM alignments to CRAM format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">samtools BAM to CRAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_montage" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Image Montage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_compare" title="with GraphicsMagick"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare two images</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gffread" title="Filters and/or converts GFF3/GTF2 records"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gffread</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=crossmap_region" title="Convert genome coordinates or annotation files between genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CrossMap region</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_convert" title="with GraphicsMagick"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert image format</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=idpquery" title="Creates text reports from idpDB files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idpQuery</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=thermo_raw_file_converter" title="RAW file converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Thermo</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tab2fasta" title="converts tabular file to FASTA format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tabular-to-FASTA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bax2bam" title="converts PacBio basecall format (bax.h5) into BAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bax2bam</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=crossmap_bed" title="Convert genome coordinates or annotation files between genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CrossMap BED</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=crossmap_gff" title="Convert genome coordinates or annotation files between genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CrossMap GFF</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=crossmap_vcf" title="Convert genome coordinates or annotation files between genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CrossMap VCF</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=crossmap_wig" title="Convert genome coordinates or annotation files between genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CrossMap Wig</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=compress_file" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compress file(s)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fasta2tab" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTA-to-Tabular</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tabular_to_fastq" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tabular to FASTQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gfa_to_fa" title="Convert Graphical Fragment Assembly files to FASTA format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFA to FASTA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=thermo_raw_file_converter" title="RAW file converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Thermo</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=msconvert" title="Convert and/or filter mass spectrometry files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">msconvert</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Interval2Maf1" title="given a set of genomic intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract MAF blocks</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=crossmap_wig" title="Convert genome coordinates or annotation files between genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CrossMap Wig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=crossmap_vcf" title="Convert genome coordinates or annotation files between genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CrossMap VCF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=crossmap_gff" title="Convert genome coordinates or annotation files between genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CrossMap GFF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=crossmap_bed" title="Convert genome coordinates or annotation files between genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CrossMap BED</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=GeneBed_Maf_Fasta2" title="given a set of coding exon intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stitch Gene blocks</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=crossmap_bam" title="Convert genome coordinates or annotation files between genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CrossMap BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mz_to_sqlite" title="Extract mzIdentML and associated proteomics datasets into a SQLite DB"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mz to sqlite</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bed_to_protein_map" title="genomic location of proteins for MVP"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bed to protein map</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gffcompare_to_bed" title="for StringTie results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert gffCompare annotated GTF to BED</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=map_peptides_to_bed" title="for viewing in a genome browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map peptides to a bed file</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=resize_coordinate_window" title="of GFF data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Resize coordinate window</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=msms_extractor" title="Extract MS/MS scans from the mzML file(s) based on PSM report"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">msms_extractor</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_montage" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Image Montage</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_convert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Image Converter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bax2bam" title="converts PacBio basecall format (bax.h5) into BAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bax2bam</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=galaxy_intermine_exchange" title="Dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create InterMine Interchange</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_bam_to_cram" title="convert BAM alignments to CRAM format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">samtools BAM to CRAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bam2fastx" title="PacBio BAM to Fastx"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PacBio bam2fastx</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hictk" title="convert cool to juicebox hic"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hictk</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=idconvert" title="Convert mass spectrometry identification files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idconvert</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=msconvert_subset" title="against list of scan numbers or indices."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">msconvert Subset Peak List</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=idconvert" title="Convert mass spectrometry identification files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idconvert</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gtftobed12" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GTF to BED12</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ucsc-twobittofa" title="Convert all or part of .2bit file to FASTA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">twoBitToFa</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bam_to_scidx" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM to ScIdx</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bigwig_to_bedgraph" title="Convert from bigWig to bedGraph format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bigWigToBedGraph</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=crossmap_region" title="Convert genome coordinates or annotation files between genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CrossMap region</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ab1_fastq_converter" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ab1 to FASTQ converter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=compress_file" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compress file(s)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xmlstarlet" title="convert a metadata XML file in one standard to another"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xmlstarlet</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt2.util.mga_to_gff3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MGA to GFF3</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.external.aragorn-gff3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fix tRNA model</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.genbank.GBKtoFiveCol" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Genbank to Five Column Format</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff.gff2gb" title="convert gff3 to GenBank"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF3 to GenBank</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt2.gff3.splitGff" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split GFF3+Fasta into separate parts</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.customGbkToGff" title="CPT made Biobython-based solution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">(CPT) Genbank to GFF3: </button></a>
 <a href="https://usegalaxy.eu/root?tool_id=axt_to_concat_fasta" title="Converts an AXT formatted file to a concatenated FASTA alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AXT to concatenated FASTA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=axt_to_fasta" title="Converts an AXT formatted file to FASTA format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AXT to FASTA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=axt_to_lav_1" title="Converts an AXT formatted file to LAV format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AXT to LAV</button></a>
@@ -241,27 +275,33 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=wiggle2simple1" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Wiggle-to-Interval</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Sff_extractor" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SFF converter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gtf2bedgraph" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GTF-to-BEDGraph</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=wig_to_bigWig" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Wig/BedGraph-to-bigWig</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bed_to_bigBed" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BED-to-bigBed</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=liftOver1" title="between assemblies and genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert genome coordinates</button></a>
 <h3>FASTA/FASTQ</h3>
-<a href="https://usegalaxy.eu/root?tool_id=cutadapt" title="Remove adapter sequences from FASTQ/FASTA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cutadapt</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastp" title="- fast all-in-one preprocessing for FASTQ files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fastp</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_clipper" title="adapter sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clip</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=umi_tools_whitelist" title="Extract cell barcodes from FASTQ files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools whitelist</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=umi_tools_group" title="Extract UMI from fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools group</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fasta-stats" title="display summary statistics for a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fasta Statistics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=umi_tools_dedup" title="Extract UMI from fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools deduplicate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=umi_tools_count" title="performs quantification of UMIs from BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools count</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=trim_galore" title="Quality and adapter trimmer of reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trim Galore!</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=umi_tools_extract" title="Extract UMI from fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools extract</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rcorrector" title="a kmer-based error correction method for RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA-seq Rcorrector</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastqe" title="visualize fastq files with emoji's 🧬😎"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQE</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastqc" title="Read Quality reports"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastQC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fasplit" title="Split a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">faSplit</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ncbi_fcs_gx" title="detects contamination from foreign organisms in genome sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI FCS GX</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastp" title="fast all-in-one preprocessing for FASTQ files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fastp</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trimmomatic" title="flexible read trimming tool for Illumina NGS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trimmomatic</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqprep" title="Merge and Trim Adapter Sequences from Paired-End Illumina Reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merging paired-end Illumina reads (SeqPrep)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bbtools_bbduk" title="decontamination using kmers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: BBduk</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cutadapt" title="Remove adapter sequences from FASTQ/FASTA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cutadapt</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_comp" title="get the nucleotide composition of FASTA/Q"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_comp</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_cutN" title="cut sequence at long N"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_cutN</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_dropse" title="drop unpaired from interleaved Paired End FASTA/Q"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_dropse</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_fqchk" title="fastq QC (base/quality summary)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_fqchk</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_hety" title="regional heterozygosity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_hety</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_listhet" title="extract the position of each het"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_listhet</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_mergefa" title="merge two FASTA/Q files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_mergefa</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_mergepe" title="interleave two unpaired FASTA/Q files for a paired-end file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_mergepe</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_mutfa" title="point mutate FASTA at specified positions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_mutfa</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_randbase" title="choose a random base from hets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_randbase</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_sample" title="random subsample of fasta or fastq sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_sample</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_seq" title="common transformation of FASTA/Q"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_seq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_subseq" title="extract subsequences from FASTA/Q files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_subseq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_telo" title="find telomeres"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_telo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_trimfq" title="trim FASTQ using the Phred algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_trimfq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seq_filter_by_mapping" title="from SAM/BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter sequences by mapping</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=prinseq" title="to process quality of sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PRINSEQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trim_reads" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select high quality segments</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=filtlong" title="Filtering long reads by quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">filtlong</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=quality_score_distribution" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build base quality distribution</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fasta_compute_length" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute sequence length</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fasta_concatenate0" title="FASTA alignment by species"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate</button></a>
@@ -290,33 +330,33 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=cshl_fasta_formatter" title="formatter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTA Width</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cshl_fasta_nucleotides_changer" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA/DNA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_collapser" title="sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Collapse</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastqe" title="visualize fastq files with emoji's 🧬😎"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQE</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fasta_filter_by_length" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter sequences by length</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fasta2tab" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTA-to-Tabular</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tabular_to_fastq" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tabular to FASTQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tab2fasta" title="converts tabular file to FASTA format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tabular-to-FASTA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_artifacts_filter" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove sequencing artifacts</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=exonerate" title="pairwise sequence comparison"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Exonerate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=trim_galore" title="Quality and adapter trimmer of reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trim Galore!</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=umi_tools_count" title="performs quantification of UMIs from BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools count</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=umi_tools_extract" title="Extract UMI from fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools extract</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sickle" title="windowed adaptive trimming of FASTQ data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sickle</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_sample" title="random subsample of fasta or fastq sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_sample</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bbtools_tadpole" title="Kmer-based assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: Tadpole</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bbtools_bbmerge" title="Merge overlapping mates of a read pair"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: BBMerge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rasusa" title="Randomly subsample reads to a specified coverage"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rasusa</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=umi_tools_group" title="Extract UMI from fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools group</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=umi_tools_whitelist" title="Extract cell barcodes from FASTQ files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools whitelist</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=flash" title="adjust length of short reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FLASH</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_comp" title="get the nucleotide composition of FASTA/Q"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_comp</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_mutfa" title="point mutate FASTA at specified positions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_mutfa</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_hety" title="regional heterozygosity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_hety</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_cutN" title="cut sequence at long N"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_cutN</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_mergefa" title="merge two FASTA/Q files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_mergefa</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_trimfq" title="trim FASTQ using the Phred algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_trimfq</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_fqchk" title="fastq QC (base/quality summary)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_fqchk</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_randbase" title="choose a random base from hets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_randbase</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_subseq" title="extract subsequences from FASTA/Q files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_subseq</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_dropse" title="drop unpaired from interleaved Paired End FASTA/Q"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_dropse</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_mergepe" title="interleave two unpaired FASTA/Q files for a paired-end file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_mergepe</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_seq" title="common transformation of FASTA/Q"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_seq</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_listhet" title="extract the position of each het"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_listhet</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mqc" title="quality control of ribosome profiling mapping results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mQC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fasta-stats" title="display summary statistics for a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fasta Statistics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=filtlong" title="Filtering long reads by quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">filtlong</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_clipper" title="adapter sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clip</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_nucleotides_distribution" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Draw nucleotides distribution chart</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_barcode_splitter" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Barcode Splitter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bctools_extract_crosslinked_nucleotides" title="from full alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get crosslinked nucleotides</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fasplit" title="Split a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">faSplit</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=atactk_trim_adapters" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trim putative adapter sequence</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastqc" title="Read Quality reports"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastQC</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bctools_convert_to_binary_barcode" title="from regular barcodes."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create binary barcodes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bctools_extract_barcodes" title="according to pattern"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract barcodes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bctools_extract_alignment_ends" title="from SAM or BAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract alignment ends</button></a>
@@ -327,175 +367,187 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=je_demultiplex" title="demultiplexes fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Je-Demultiplex</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=je_markdupes" title="to filter BAM files for read duplicates taking UMIs into account"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Je-MarkDuplicates</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=je_demultiplex_illu" title="demultiplexes fastq files using Illumina Index file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Je-Demultiplex-Illu</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=umi_tools_dedup" title="Extract UMI from fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools deduplicate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fasta_merge_files_and_filter_unique_sequences" title="Concatenate FASTA database files together"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTA Merge Files and Filter Unique Sequences</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=align_back_trans" title="Gives a codon aware alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Thread nucleotides onto a protein alignment (back-translation)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seq_filter_by_mapping" title="from SAM/BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter sequences by mapping</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lighter" title="can correct the reads containing sequence errors"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">lighter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fastq_join" title="- Joins two paired-end reads on the overlapping ends"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fastq-join</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rbc_splitfasta" title="files into a collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split Fasta</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rbc_splitfasta" title="files into a collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split Fasta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gfastats" title="the swiss army knife for genome assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gfastats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rcorrector" title="a kmer-based error correction method for RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA-seq Rcorrector</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=iuc_pear" title="Paired-End read merger"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pear</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqcomplexity" title="total and per read"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate sequence complexity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqkit_stats" title="of FASTA/Q files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit statistics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqkit_fx2tab" title="convert FASTA/Q to tabular"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit fx2tab</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=adapter_removal" title="from HTS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AdapterRemoval: remove adapter sequences</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqkit_locate" title="subsequences/motifs, mismatch allowed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit locate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fasta_regex_finder" title="Search in fasta for regexp match"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fasta regular expression finder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.fasta.remove_desc" title="from fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove Description</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.fasta.remove_desc" title="from fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove Description</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=solid2fastq" title="SOLiD output to fastq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=solid_qual_stats" title="for SOLiD data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute quality statistics</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=solid_qual_boxplot" title="for SOLiD data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Draw quality score boxplot</button></a>
 <h3>Quality Control</h3>
 <a href="https://usegalaxy.eu/root?tool_id=multiqc" title="aggregate results from bioinformatics analyses into a single report"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MultiQC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastq_info" title="validates single or paired fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ info</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qualimap_counts" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QualiMap Counts QC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastq_info" title="validates single or paired fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ info</button></a>
 <h3>SAM/BAM</h3>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_coverage" title="computes the depth at each position or region"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools coverage</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bamtools" title="BAM datasets and perform other transformations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert, Merge, Randomize</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bamFilter" title="BAM datasets on a variety of attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bamtools_split_paired" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by Paired/Single End</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bamtools_split_ref" title="into dataset list collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by Reference</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bamtools_split_mapped" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by Mapped</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bamtools_split_tag" title="into dataset list collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by Tag</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_phase" title="call and phase heterozygous SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools phase</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_fastx" title="extract FASTA or FASTQ from alignment files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools fastx</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_view" title="- reformat, filter, or subsample SAM, BAM or CRAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools view</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_stats" title="generate statistics for BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools stats</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_split" title="BAM dataset on readgroups"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools split</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bamtools" title="datasets in various ways"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Operate on and transform BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mosdepth" title="- fast and flexible depth coverage calculation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mosdepth</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_ampliconclip" title="clip primer bases from bam files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools ampliconclip</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pileup_interval" title="condenses pileup format into ranges of bases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pileup-to-Interval</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pileup_parser" title="on coverage and SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter pileup</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sam2interval" title="to interval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sam_merge2" title="merges BAM files together"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge BAM Files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sam_pileup" title="from BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate pileup</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_flagstat" title="tabulate descriptive stats for BAM datset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools flagstat</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_markdup" title="marks duplicate alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools markdup</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_mpileup" title="multi-way pileup of variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools mpileup</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_rmdup" title="remove PCR duplicates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RmDup</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_slice_bam" title="BAM by genomic regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slice</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_idxstats" title="reports stats of the BAM index file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools idxstats</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_sort" title="order of storing aligned sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools sort</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_bedcov" title="calculate read depth for a set of genomic intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools bedcov</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bamutil_diff" title="two coordinate sorted SAM/BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BamUtil diff</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pileup_interval" title="condenses pileup format into ranges of bases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pileup-to-Interval</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_view" title="- reformat, filter, or subsample SAM, BAM or CRAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools view</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_reheader" title="copy SAM/BAM header between datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools reheader</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qualimap_bamqc" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QualiMap BamQC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sam2interval" title="to interval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SAM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sam_pileup" title="from BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate pileup</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qualimap_multi_bamqc" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QualiMap Multi-Sample BamQC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bamtools_split" title="BAM datasets on variety of attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tag_pileup_frequency" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tag pileup frequency</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_mpileup" title="multi-way pileup of variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools mpileup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_calmd" title="recalculate MD/NM tags"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools calmd</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_markdup" title="marks duplicate alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools markdup</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_merge" title="merge multiple sorted alignment files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools merge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_depth" title="compute the depth at each position or region"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools depth</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_fastx" title="extract FASTA or FASTQ from alignment files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools fastx</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_fixmate" title="fill mate coordinates, ISIZE and mate related flags"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools fixmate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_stats" title="generate statistics for BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools stats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_idxstats" title="reports stats of the BAM index file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools idxstats</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtool_filter2" title="files on FLAG MAPQ RG LN or by region"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter SAM or BAM, output SAM or BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_split" title="BAM dataset on readgroups"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools split</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_bedcov" title="calculate read depth for a set of genomic intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools bedcov</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_depth" title="compute the depth at each position or region"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools depth</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_sort" title="order of storing aligned sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools sort</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_coverage" title="computes the depth at each position or region"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools coverage</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ngsutils_bam_filter" title="Removes reads from a BAM file based on criteria"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BAM filter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_rmdup" title="remove PCR duplicates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RmDup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sam_merge2" title="merges BAM files together"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge BAM Files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bamFilter" title="datasets on a variety of attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_calmd" title="recalculate MD/NM tags"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools calmd</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bamtools_split_mapped" title="into a mapped and an unmapped dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by reads mapping status</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bamtools_split_paired" title="reads datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM into paired- and single-end</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bamtools_split_ref" title="into a dataset list collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by reference</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bamtools_split_tag" title="into a dataset list collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by read tag value</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_phase" title="call and phase heterozygous SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools phase</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bamhash" title="Hash BAM and FASTQ files to verify data integrity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BamHash</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=varscan_mpileup" title="mutation caller for targeted, exome, and whole-genome resequencing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan mpileup</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=varscan_somatic" title="somatic mutation caller for cancer genomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan Somatic</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=varscan_somatic" title="somatic mutation caller for cancer genomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan Somatic</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bamutil_diff" title="two coordinate sorted SAM/BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BamUtil diff</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=revertR2orientationInBam" title="Revert the mapped orientation of R2 mates in a bam."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">revertR2orientationInBam</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bamtools_split" title="BAM datasets on variety of attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split</button></a>
 <h3>BED</h3>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_annotatebed" title="annotate coverage of features from multiple files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools AnnotateBed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_bamtobed" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools BAM to BED</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_bed12tobed6" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools BED12 to BED6</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_bedtobam" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools BED to BAM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_bedtoigv" title="create batch script for taking IGV screenshots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools BED to IGV</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_bedpetobam" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools BEDPE to BAM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_closestbed" title="find the closest, potentially non-overlapping interval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools ClosestBed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_clusterbed" title="cluster overlapping/nearby intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools ClusterBed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_complementbed" title="Extract intervals not represented by an interval file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools ComplementBed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_coveragebed" title="of features in file B on the features in file A (bedtools coverage)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools Compute both the depth and breadth of coverage</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bedtools_expandbed" title="replicate lines based on lists of values in columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools ExpandBed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_fisher" title="calculate Fisher statistic between two feature files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools FisherBed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_flankbed" title="create new intervals from the flanks of existing intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools FlankBed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_genomecoveragebed" title="compute the coverage over an entire genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools Genome Coverage</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_getfastabed" title="use intervals to extract sequences from a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools GetFastaBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_nucbed" title="profile the nucleotide content of intervals in a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools NucBed</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bedtools_groupbybed" title="group by common cols and summarize other cols"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools GroupByBed</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bedtools_intersectbed" title="find overlapping intervals in various ways"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools Intersect intervals</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_jaccard" title="calculate the distribution of relative distances between two files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools JaccardBed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_links" title="create a HTML page of links to UCSC locations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools LinksBed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_makewindowsbed" title="make interval windows across a genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools MakeWindowsBed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_map" title="apply a function to a column for each overlapping interval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools MapBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_overlapbed" title="computes the amount of overlap from two intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools OverlapBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_getfastabed" title="use intervals to extract sequences from a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools getfasta</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bedtools_maskfastabed" title="use intervals to mask sequences from a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools MaskFastaBed</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bedtools_mergebed" title="combine overlapping/nearby intervals into a single interval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools MergeBED</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_multicovtbed" title="counts coverage from multiple BAMs at specific intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools MultiCovBed</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bedtools_multiintersectbed" title="identifies common intervals among multiple interval files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools Multiple Intersect</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_nucbed" title="profile the nucleotide content of intervals in a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools NucBed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_overlapbed" title="computes the amount of overlap from two intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools OverlapBed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_randombed" title="generate random intervals in a genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools RandomBed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_reldistbed" title="calculate the distribution of relative distances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools ReldistBed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_shufflebed" title="randomly redistrubute intervals in a genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools ShuffleBed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_slopbed" title="adjust the size of intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools SlopBed</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bedtools_sortbed" title="order the intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools SortBED</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_spacingbed" title="reports the distances between features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools SpacingBed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_subtractbed" title="remove intervals based on overlaps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools SubtractBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_bamtobed" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools BAM to BED</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_complementbed" title="Extract intervals not represented by an interval file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools ComplementBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_windowbed" title="find overlapping intervals within a window around an interval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools WindowBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_annotatebed" title="annotate coverage of features from multiple files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools AnnotateBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_jaccard" title="calculate the distribution of relative distances between two files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools JaccardBed</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bedtools_tagbed" title="tag BAM alignments based on overlaps with interval files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools TagBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_closestbed" title="find the closest, potentially non-overlapping interval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools ClosestBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_spacingbed" title="reports the distances between features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools SpacingBed</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bedtools_unionbedgraph" title="combines coverage intervals from multiple BEDGRAPH files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools Merge BedGraph files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_windowbed" title="find overlapping intervals within a window around an interval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools WindowBed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gffcompare" title="compare assembled transcripts to a reference annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GffCompare</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_bamtofastq" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools Convert from BAM to FastQ</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_genomecoveragebed_bedgraph" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a BedGraph of genome coverage</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_mergebedgraph" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge BedGraph files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedtools_genomecoveragebed_histogram" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a histogram of genome coverage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_makewindowsbed" title="make interval windows across a genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools MakeWindowsBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_coveragebed" title="of features in file B on the features in file A (bedtools coverage)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools Compute both the depth and breadth of coverage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_genomecoveragebed" title="compute the coverage over an entire genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools Genome Coverage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_multicovtbed" title="counts coverage from multiple BAMs at specific intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools MultiCovBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_subtractbed" title="remove intervals based on overlaps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools SubtractBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_clusterbed" title="cluster overlapping/nearby intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools ClusterBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_slopbed" title="adjust the size of intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools SlopBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_flankbed" title="create new intervals from the flanks of existing intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools FlankBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_links" title="create a HTML page of links to UCSC locations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools LinksBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_bed12tobed6" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools BED12 to BED6</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_bedtobam" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools BED to BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_map" title="apply a function to a column for each overlapping interval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools MapBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_bedtoigv" title="create batch script for taking IGV screenshots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools BED to IGV</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_shufflebed" title="randomly redistrubute intervals in a genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools ShuffleBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_reldistbed" title="calculate the distribution of relative distances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools ReldistBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_randombed" title="generate random intervals in a genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools RandomBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_bedpetobam" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools BEDPE to BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_fisher" title="calculate Fisher statistic between two feature files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools FisherBed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_bamtofastq" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools Convert from BAM to FastQ</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_genomecoveragebed_bedgraph" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a BedGraph of genome coverage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_mergebedgraph" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge BedGraph files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedtools_genomecoveragebed_histogram" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a histogram of genome coverage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedops-sort-bed" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedops sort-bed</button></a>
 <h3>VCF/BCF</h3>
-<a href="https://usegalaxy.eu/root?tool_id=vcfanno" title="VCF annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">vcfanno</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=varscan_somatic" title="Call germline/somatic and LOH variants from tumor-normal sample pairs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan somatic</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=varscan_copynumber" title="Determine relative tumor copy number from tumor-normal pileups"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan copynumber</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_csq" title="Haplotype aware consequence predictor"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools csq</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_cnv" title="Call copy number variation from VCF B-allele frequency (BAF) and Log R Ratio intensity (LRR) values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools cnv</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_consensus" title="Create consensus sequence by applying VCF variants to a reference fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools consensus</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_norm" title="Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools norm</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_call" title="SNP/indel variant calling from VCF/BCF"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools call</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfcheck" title="Verify that the reference allele matches the reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFcheck:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcffilter2" title="filter VCF data in a variety of attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFfilter:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfselectsamples" title="Select samples from a VCF dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFselectsamples:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfannotategenotypes" title="Annotate genotypes in a VCF dataset using genotypes from another VCF dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFannotateGenotypes:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfflatten2" title="Removes multi-allelic sites by picking the most common alternate"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFflatten:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfcommonsamples" title="Output records belonging to samples common between two datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFcommonSamples:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfannotate" title="Intersect VCF records with BED annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFannotate:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfvcfintersect" title="Intersect two VCF datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCF-VCFintersect:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfbreakcreatemulti" title="Break multiple alleles into multiple records, or combine overallpoing alleles into a single record"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFbreakCreateMulti:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfcheck" title="Verify that the reference allele matches the reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFcheck:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfaddinfo" title="Adds info fields from the second dataset which are not present in the first dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFaddinfo:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcf2tsv" title="Convert VCF data into TAB-delimited format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFtoTab-delimited:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfleftalign" title="Left-align indels and complex variants in VCF dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFleftAlign:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfcombine" title="Combine multiple VCF datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFcombine:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfsort" title="Sort VCF dataset by coordinate"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFsort:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfhethom" title="Count the number of heterozygotes and alleles, compute het/hom ratio"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFhetHomAlleles:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfrandomsample" title="Randomly sample sites from VCF dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFrandomSample:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfbedintersect" title="Intersect VCF and BED datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCF-BEDintersect:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfgenotypes" title="Convert numerical representation of genotypes to allelic"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFgenotypes:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcffixup" title="Count the allele frequencies across alleles present in each record in the VCF file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFfixup:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfgeno2haplo" title="Convert genotype-based phased alleles into haplotype alleles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFgenotype-to-haplotype:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcfallelicprimitives" title="Split alleleic primitives (gaps or mismatches) into multiple VCF lines"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VcfAllelicPrimitives:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfbreakcreatemulti" title="Break multiple alleles into multiple records, or combine overallpoing alleles into a single record"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFbreakCreateMulti:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfvcfintersect" title="Intersect two VCF datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCF-VCFintersect:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfanno" title="VCF annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">vcfanno</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfannotate" title="Intersect VCF records with BED annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFannotate:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfcommonsamples" title="Output records belonging to samples common between two datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFcommonSamples:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfflatten2" title="Removes multi-allelic sites by picking the most common alternate"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFflatten:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfannotategenotypes" title="Annotate genotypes in a VCF dataset using genotypes from another VCF dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFannotateGenotypes:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfselectsamples" title="Select samples from a VCF dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFselectsamples:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ococo" title="consensus caller on SAM/BAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ococo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=allele_counts_1" title="process variant counts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Variant Annotator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfdistance" title="Calculate distance to the nearest variant"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFdistance:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfdistance" title="Calculate distance to the nearest variant"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFdistance:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcftools_isec" title="multiple VCF datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Intersect</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcftools_merge" title="multiple VCF datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcf2tsv" title="Convert VCF data into TAB-delimited format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFtoTab-delimited:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcf2tsv" title="Convert VCF data into TAB-delimited format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFtoTab-delimited:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcfgeno2haplo" title="Convert genotype-based phased alleles into haplotype alleles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFgenotype-to-haplotype:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcffixup" title="Count the allele frequencies across alleles present in each record in the VCF file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFfixup:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfgenotypes" title="Convert numerical representation of genotypes to allelic"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFgenotypes:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfallelicprimitives" title="Split alleleic primitives (gaps or mismatches) into multiple VCF lines"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VcfAllelicPrimitives:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfannotate" title="Intersect VCF records with BED annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFannotate:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfannotategenotypes" title="Annotate genotypes in a VCF dataset using genotypes from another VCF dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFannotateGenotypes:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcfbedintersect" title="Intersect VCF and BED datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCF-BEDintersect:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfrandomsample" title="Randomly sample sites from VCF dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFrandomSample:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfhethom" title="Count the number of heterozygotes and alleles, compute het/hom ratio"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFhetHomAlleles:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfsort" title="Sort VCF dataset by coordinate"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFsort:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfprimers" title="Extract flanking sequences for each VCF record"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFprimers:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfgenotypes" title="Convert numerical representation of genotypes to allelic"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFgenotypes:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfcheck" title="Verify that the reference allele matches the reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFcheck:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcfcombine" title="Combine multiple VCF datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFcombine:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfleftalign" title="Left-align indels and complex variants in VCF dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFleftAlign:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcf2tsv" title="Convert VCF data into TAB-delimited format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFtoTab-delimited:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfaddinfo" title="Adds info fields from the second dataset which are not present in the first dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFaddinfo:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=varscan" title="for variant detection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=varscan_mpileup" title="for variant detection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan mpileup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcfview" title="Convert, filter, subset VCF/BCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftoolsView</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=freebayes" title="bayesian genetic variant detector"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FreeBayes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfdistance" title="Calculate distance to the nearest variant"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFdistance:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=naive_variant_caller" title="- tabulate variable sites from BAM datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Naive Variant Caller (NVC)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snippy" title="Snippy finds SNPs between a haploid reference genome and your NGS sequence reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snippy</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snippy_core" title="Combine multiple Snippy outputs into a core SNP alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snippy-core</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ococo" title="consensus caller on SAM/BAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ococo</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bamleftalign" title="indels in BAM datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BamLeftAlign</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfcommonsamples" title="Output records belonging to samples commong between two datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFcommonSamples:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcfdistance" title="Calculate distance to the nearest variant"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFdistance:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=allele_counts_1" title="process variant counts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Variant Annotator</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcftools_merge" title="multiple VCF datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcftools_isec" title="multiple VCF datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Intersect</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vt_normalize" title="normalizes variants in a VCF file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VT normalize</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_view" title="Convert, filter, subset VCF/BCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools view</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfbreakcreatemulti" title="Break multiple alleles into multiple records, or combine overallpoing alleles into a single record"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFbreakCreateMulti:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcftools_compare" title="multiple VCF datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcftools_annotate" title="a VCF dataset with custom filters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Annotate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcftools_slice" title="to get data from selected regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slice VCF</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcftools_subset" title="columns from a VCF dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Subset</button></a>
 <h3>Nanopore</h3>
-<a href="https://usegalaxy.eu/root?tool_id=medaka_variant_pipeline" title="via neural networks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">medaka variant pipeline</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ont_fast5_api_multi_to_single_fast5" title="read file(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ont_fast5_api: Multi to single</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ont_fast5_api_compress_fast5" title="multi read file(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ont_fast5_api: Compress</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=nanopolish_polya" title="- Estimate the length of the poly-A tail on direct RNA reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nanopolish polyA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=medaka_variant" title="decodes variant calls from medaka consensus output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">medaka variant tool</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=medaka_consensus" title="Assembly polishing via neural networks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">medaka consensus tool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=flair_correct" title="corrects misaligned splice sites using genome annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FLAIR correct</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=porechop" title="adapter trimmer for Oxford Nanopore reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Porechop</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pycoqc" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pycoqc</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=flair_collapse" title="defines high-confidence isoforms from flair-corrected reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FLAIR collapse</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ngmlr" title="Gap-cost alignMents for Long Reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CoNvex</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=medaka_variant_pipeline" title="via neural networks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">medaka variant pipeline</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=medaka_consensus_pipeline" title="Assembly polishing via neural networks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">medaka consensus pipeline</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=medaka_consensus" title="Assembly polishing via neural networks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">medaka consensus tool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nanocompore_db" title="Process SampComp results database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NanoComporeDB</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ont_fast5_api_fast5_subset" title="of multi read file(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ont_fast5_api: Subset</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ont_fast5_api_single_to_multi_fast5" title="read file(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ont_fast5_api: Single to multi</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nanoplot" title="Plotting suite for Oxford Nanopore sequencing data and alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NanoPlot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=nanopolish_polya" title="- Estimate the length of the poly-A tail on direct RNA reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nanopolish polyA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ont_fast5_api_multi_to_single_fast5" title="read file(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ont_fast5_api: Multi to single</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ont_fast5_api_single_to_multi_fast5" title="read file(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ont_fast5_api: Single to multi</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ont_fast5_api_compress_fast5" title="multi read file(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ont_fast5_api: Compress</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ont_fast5_api_fast5_subset" title="of multi read file(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ont_fast5_api: Subset</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nanopolish_eventalign" title="- Align nanopore events to reference k-mers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nanopolish eventalign</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nanopolish_methylation" title="- Classify nucleotides as methylated or not."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nanopolish methylation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nanopolish_variants" title="- Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nanopolish variants</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nanocompore_sampcomp" title="to compare Nanopolished datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SampComp</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nanopolishcomp_freqmethcalculate" title="calculates methylation frequency at genomic CpG sites"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NanopolishComp: FreqMethCalculate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nanopolishcomp_eventaligncollapse" title="by kmers rather than by event"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NanopolishComp: EventalignCollapse</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=m6anet" title="to detect m6A RNA modifications from nanopore data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">m6anet</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=porechop" title="adapter trimmer for Oxford Nanopore reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Porechop</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=poretools_times" title="and channel information from a set of FAST5 files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract time</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=poretools_nucdist" title="distribution in nanopore sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Show nucleotide</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=poretools_qualdist" title="score distribution in nanopore sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Show quality</button></a>
@@ -509,11 +561,14 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=poretools_qualpos" title="plot of quality score distribution over positions in nanopore reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate box-whisker</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=poretools_winner" title="from a set of FAST5 files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get longest read</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=poretools_events" title="from a set of sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract nanopore events</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pycoqc" title="quality control for Nanopore sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pycoqc</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=clair3" title="germline small variant caller for long-reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clair3</button></a>
 <hr/><h2>Common Genomics Tools</h2>
 <h3>Operate on Genomic Intervals</h3>
+<a href="https://usegalaxy.eu/root?tool_id=gops_basecoverage_1" title="of all intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Base Coverage</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gops_complement_1" title="intervals of a dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Complement</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gops_cluster_1" title="the intervals of a dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gops_basecoverage_1" title="of all intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Base Coverage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gops_subtract_1" title="the intervals of two datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Subtract</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Annotation_Profiler_0" title="for a set of genomic intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Profile Annotations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tbl2gff3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Table to GFF3</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=translate_bed" title="cDNA in 3frames or CDS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Translate BED transcripts</button></a>
@@ -526,6 +581,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=Extract genomic DNA 1" title="using coordinates from assembled/unassembled genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract Genomic DNA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=length_and_gc_content" title="from GTF and FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gene length and GC content</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fraggenescan" title="for finding (fragmented) genes in short reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FragGeneScan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqkit_locate" title="subsequences/motifs, mismatch allowed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit locate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gene2exon1" title="expander"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gene BED To Exon/Intron/Codon BED</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Interval2Maf_pairwise1" title="given a set of genomic intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract Pairwise MAF blocks</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Interval2Maf1" title="given a set of genomic intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract MAF blocks</button></a>
@@ -541,100 +597,91 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=MAF_filter" title="by specified attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter MAF</button></a>
 <hr/><h2>Genomics Analysis</h2>
 <h3>Annotation</h3>
-<a href="https://usegalaxy.eu/root?tool_id=kofamscan" title="gene function annotation based on KEGG orthology and HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">KofamScan</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=maker" title="genome annotation pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Maker</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=interproscan" title="functional annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InterProScan</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=roary" title="the pangenome pipeline - Quickly generate a core gene alignment from gff3 files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Roary</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=progressivemauve" title="constructs multiple genome alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">progressiveMauve</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=transit_hmm" title="- determine essentiality of a genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRANSIT HMM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gff_to_prot" title="to prot_table for TRANSIT"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GFF3</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gecco" title="is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GECCO</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=orthofinder_onlygroups" title="finds orthogroups in a set of proteomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OrthoFinder</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=list_spaln_tables" title="Given a query species, list the spaln settings tables that exist, from closest related species to most different"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">List spaln parameter tables</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spaln" title="Maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Spaln: align cDNA or Protein to genome</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=prokka" title="Prokaryotic genome annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prokka</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=busco" title="assess genome assembly and annotation completeness"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Busco</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hamronize_summarize" title="harmorization reports"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">summarize</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hamronize_tool" title="parse multiple Antimicrobial Resistance Analysis Reports into a common data structure"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hamronize</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=repeatmasker_wrapper" title="screen DNA sequences for interspersed repeats and low complexity regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RepeatMasker</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=homer_findMotifsGenome" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">findMotifsGenome</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=homer_annotatePeaks" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">annotatePeaks</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=funannotate_annotate" title="annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Funannotate functional</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=legsta" title="Legionella pneumophila sequence based typing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">legsta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=krocus" title="Multi-locus sequence typing (MLST) from uncorrected long reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">krocus</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=omark" title="proteome quality assessment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OMArk</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_jackhmmer" title="iteratively search a protein sequence against a protein database (PSIBLAST-like)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">jackhmmer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmemit" title="sample sequence(s) from a profile HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmemit</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmalign" title="align sequences to a profile HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmalign</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=multigsea" title="GSEA-based pathway enrichment analysis for multi-omics data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">multiGSEA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tsebra" title="tanscript selector for BRAKER"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TSEBRA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=annotatemyids" title="annotate a generic set of identifiers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">annotateMyIDs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.fasta.seq_trans" title="Translate fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fasta Translate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=braker3" title="genome annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BRAKER3</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=aegean_locuspocus" title="calculate locus coordinates for the given gene annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn LocusPocus</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bakta" title="Genome annotation via alignment-free sequence identification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bakta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=agat" title="GTF/GFF analysis toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AGAT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=compleasm" title="completeness of genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">compleasm</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mitos2" title="de-novo annotation of metazoan mitochondrial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MITOS2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=genenotebook_build" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build a GeneNoteBook</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=isescan" title="Insertion Sequence Elements detection in prokaryotic genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ISEScan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=funannotate_compare" title="annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Funannotate compare</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=windowmasker_mkcounts" title="Construct WindowMasker unit counts table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WindowMasker mkcounts</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=windowmasker_ustat" title="Mask sequences using a WindowMasker unit counts table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WindowMasker ustat</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_nhmmer" title="search a DNA model or alignment against a DNA database (BLASTN-like)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">nhmmer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deepsig" title="signal peptides predictor"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeepSig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=funannotate_sort" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort assembly</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=funannotate_clean" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Funannotate assembly clean</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=repeatexplorer_clustering" title="repeat discovery and characterization using graph-based sequence clustering"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RepeatExplorer (clustering)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=funannotate_predict" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Funannotate predict annotation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tb_variant_filter" title="M. tuberculosis H37Rv VCF filter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TB Variant Filter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=augustus_training" title="ab-initio gene predictor"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Train Augustus</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=augustus" title="gene prediction for prokaryotic and eukaryotic genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Augustus</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chipseeker" title="for ChIP peak annotation and visualization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChIPseeker</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spotyping" title="fast and accurate in silico Mycobacterium spoligotyping from sequence reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpoTyping</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=lorikeet_spoligotype" title="M. tuberculosis DNA fingerprinting"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">lorikeet spoligotyping</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=busco" title="assess genome assembly and annotation completeness"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Busco</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=optitype" title="HLA genotyping predictions from NGS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OptiType</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=prokka" title="Prokaryotic genome annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prokka</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=roary" title="the pangenome pipeline - Quickly generate a core gene alignment from gff3 files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Roary</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tb_profiler_profile" title="Infer strain types and drug resistance markers from sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TB-Profiler Profile</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmbuild" title="Build a profile HMM from an input multiple alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmbuild</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmscan" title="search protein sequence(s) against a protein profile database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmscan</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=annotatemyids" title="annotate a generic set of identifiers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">annotateMyIDs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tbvcfreport" title="- generate HTML report from SnpEff annotated M.tb VCF(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TB Variant Report</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=goseq" title="tests for overrepresented gene categories"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">goseq</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=maker_map_ids" title="on a Maker annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map annotation ids</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=glimmer_not_knowledge_based" title="Predict ORFs in prokaryotic genomes (not knowlegde-based)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Glimmer3</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=glimmer_knowledge_based" title="Predict ORFs in prokaryotic genomes (knowlegde-based)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Glimmer3</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=glimmer_build_icm" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Glimmer ICM builder</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mitos2" title="de-novo annotation of metazoan mitochondrial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MITOS2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sistr_cmd" title="Salmonella In Silico Typing Resource commandline tool for serovar prediction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sistr_cmd</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hhsearch" title="detecting remote homologues of proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HHsearch</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=abricate_summary" title="Combine ABRicate results into a simple matrix of gene presence/absence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ABRicate Summary</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=optitype" title="HLA genotyping predictions from NGS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OptiType</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_nhmmer" title="search a DNA model or alignment against a DNA database (BLASTN-like)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">nhmmer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hmmer_phmmer" title="search a protein sequence against a protein database (BLASTP-like)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">phmmer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_jackhmmer" title="iteratively search a protein sequence against a protein database (PSIBLAST-like)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">jackhmmer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hmmer_nhmmscan" title="search DNA sequence(s) against a DNA profile database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">nhmmscan</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=repeatmodeler" title="Model repetitive DNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RepeatModeler</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmsearch" title="search profile(s) against a sequence database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmsearch</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kofamscan" title="gene function annotation based on KEGG orthology and HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">KofamScan</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tbl2gff3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Table to GFF3</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=homer_scanMotifGenomeWide" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scanMotifGenomeWide</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmemit" title="sample sequence(s) from a profile HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmemit</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmalign" title="align sequences to a profile HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmalign</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=homer_gtf_to_annotations" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Converts GTF to Annotations file for Homer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=funannotate_clean" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Funannotate assembly clean</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=funannotate_sort" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort assembly</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=funannotate_compare" title="annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Funannotate compare</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmfetch" title="retrieve profile HMM(s) from a file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmfetch</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_alimask" title="append modelmask line to a multiple sequence alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">alimask</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmconvert" title="convert profile file to a HMMER format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmconvert</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mob_recon" title="Type contigs and extract plasmid sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MOB-Recon</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mob_typer" title="Get the plasmid type and mobility given its sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MOB-Typer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seq2hla" title="HLA genotype and expression from RNA-seq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seq2HLA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=transit_gumbel" title="- determine essential genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRANSIT Gumbel</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=transit_resampling" title="- determine per-gene p-values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRANSIT Resampling</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=transit_tn5gaps" title="- determine essential genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRANSIT Tn5Gaps</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mitos" title="de-novo annotation of metazoan mitochondrial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MITOS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ectyper" title="ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ectyper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sistr_cmd" title="Salmonella In Silico Typing Resource commandline tool for serovar prediction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sistr_cmd</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mitos" title="de-novo annotation of metazoan mitochondrial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MITOS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=antismash" title="allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Antismash</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chipseeker" title="for ChIP peak annotation and visualization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChIPseeker</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=progressivemauve" title="constructs multiple genome alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">progressiveMauve</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=xmfa2gff3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert XMFA to gapped GFF3</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mlst_list" title="Lists available schemes for the MLST tool."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MLST List</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mlst" title="Scans genomes against PubMLST schemes."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MLST</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mlst_list" title="Lists available schemes for the MLST tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MLST List</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mlst" title="Scans genomes against PubMLST schemes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MLST</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bp_genbank2gff3" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Genbank to GFF3</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=abricate_list" title="List all of abricate's available databases."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ABRicate List</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=abricate" title="Mass screening of contigs for antimicrobial and virulence genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ABRicate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=exonerate" title="pairwise sequence comparison"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Exonerate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seq2hla" title="HLA genotype and expression from RNA-seq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seq2HLA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fastani" title="fast alignment-free computation of whole-genome Average Nucleotide Identity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastANI</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=transit_tn5gaps" title="- determine essential genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRANSIT Tn5Gaps</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=transit_resampling" title="- determine per-gene p-values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRANSIT Resampling</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=transit_hmm" title="- determine essentiality of a genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRANSIT HMM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=transit_gumbel" title="- determine essential genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRANSIT Gumbel</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tetyper" title="Transposable Element Typer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TETyper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=augustus_training" title="ab-initio gene predictor"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Train Augustus</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=augustus" title="gene prediction for prokaryotic and eukaryotic genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Augustus</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fargene" title="Fragmented antibiotic resistance gene identifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fargene</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=kobas_annotate" title="KEGG Orthology Based Annotation System"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">KOBAS Annotate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=kobas_identify" title="KEGG Orthology Based Annotation System"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">KOBAS Identify</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gff_to_prot" title="to prot_table for TRANSIT"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GFF3</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gprofiler_snpense" title="maps SNP rs-codes to gene names, chromosomal coordinates and variant effects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gProfiler SNPense</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gprofiler_random" title="generates a gene list"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gProfiler Random</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gprofiler_gost" title="performs functional enrichment analysis of gene lists"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gProfiler GOSt</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gprofiler_orth" title="translates gene identifiers between organisms"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gProfiler Orth</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gprofiler_convert" title="converts between various types of namespaces"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gProfiler Convert</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=abricate" title="Mass screening of contigs for antimicrobial and virulence genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ABRicate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=abricate_list" title="List all of abricate's available databases."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ABRicate List</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=blastxml_to_gapped_gff3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BlastXML to gapped GFF3</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=maker" title="genome annotation pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Maker</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Add_a_column1" title="an expression on every row"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=socru" title="Calculate the order and orientation of complete bacterial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">socru</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=goseq" title="tests for overrepresented gene categories"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">goseq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=red" title="repeat masking"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Red</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snap_training" title="ab-initio gene predictor"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Train SNAP</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=maker_map_ids" title="on a Maker annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map annotation ids</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fgsea" title="- fast preranked gene set enrichment analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fgsea</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bg_sortmerna" title="of ribosomal RNAs in metatranscriptomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter with SortMeRNA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spaln" title="Maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Spaln: align cDNA or Protein to genome</button></a>
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 <a href="https://usegalaxy.eu/root?tool_id=goenrichment" title="performs GO enrichment analysis of a set of gene products"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GOEnrichment</button></a>
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-<a href="https://usegalaxy.eu/root?tool_id=hammock_1.0" title="Clusters short peptide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hammock - cluster peptides</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Psortb" title="Determines sub-cellular localisation of bacterial/archaeal protein sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">psortb</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=signalp3" title="Find signal peptides in protein sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SignalP 3.0</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=promoter2" title="Find eukaryotic PolII promoters in DNA sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Promoter 2.0</button></a>
@@ -658,109 +705,152 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=smf_utils_extract-boxed-sequences" title="Extracts boxed sequences from bed_input_file which has to be created with 'find-box', part of this utility"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">extract-boxed-sequences</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=segmentation_fold" title="RNA-Folding including predefined segments including K-turns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">segmentation-fold</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gubbins" title="Recombination detection in Bacteria"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gubbins</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bg_sortmerna" title="of ribosomal RNAs in metatranscriptomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter with SortMeRNA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Probmetab" title="Wrapper function for ProbMetab R package."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProbMetab Tool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lcmsmatching" title="Annotation of MS peaks using matching on a spectra database."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LC/MS matching</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Nucleosome" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nucleosome Predictions</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=orthofinder_onlygroups" title="finds orthogroups in a set of proteomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OrthoFinder</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=miranda" title="finds potential target sites for miRNAs in genomic sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">miRanda</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dotknot" title="pseudoknot prediction in a given RNA sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DotKnot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=blast2go" title="Maps BLAST results to GO annotation terms"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Blast2GO</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_nhmmer" title="search a DNA model or alignment against a DNA database (BLASTN-like)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">nhmmer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmsearch" title="search profile(s) against a sequence database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmsearch</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=repeatmodeler" title="Model repetitive DNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RepeatModeler</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_alimask" title="append modelmask line to a multiple sequence alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">alimask</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=amrfinderplus" title="NCBI Antimicrobial Resistance Gene Finder"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AMRFinderPlus</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=funannotate_annotate" title="annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Funannotate functional</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmconvert" title="convert profile file to a HMMER format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmconvert</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cpat" title="coding potential assessment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CPAT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tapscan_classify" title="Detect Transcription Associated Proteins (TAPs)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TAPScan Classify</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=aegean_canongff3" title="pre-process GFF3 files, removing all features not directly related to protein-coding genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn CanonGFF3</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=aegean_parseval" title="compare two sets of gene annotations for the same sequence."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn ParsEval</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.intersect_and_adjacent" title="Outputs nearby top-level GFF features from two GFF3 files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Intersect and Adjacent</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=helixer" title="gene calling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Helixer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=integron_finder" title="is a program that detects integrons in DNA sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Integron Finder</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmfetch" title="retrieve profile HMM(s) from a file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmfetch</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_jackhmmer" title="iteratively search a protein sequence against a protein database (PSIBLAST-like)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">jackhmmer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_alimask" title="append modelmask line to a multiple sequence alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">alimask</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmscan" title="search sequence(s) against a profile database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmscan</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_nhmmscan" title="search DNA sequence(s) against a DNA profile database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">nhmmscan</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmemit" title="sample sequence(s) from a profile HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmemit</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_phmmer" title="search a protein sequence against a protein database (BLASTP-like)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">phmmer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmalign" title="align sequences to a profile HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmalign</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmbuild" title="Build a profile HMM from an input multiple alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmbuild</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hamronize_summarize" title="Concatenate and summarize AMR detection reports"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hamronize summarize:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hamronize_tool" title="Antimicrobial Resistance Analysis Reports into a common data structure"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hAMRonize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mirmachine" title="A tool to detect miRNA homologs in genome sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MirMachine</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=abritamr" title="AMR gene detection with AMRFinderPlus"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">abriTAMR</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=miniprot" title="align a protein sequence against a genome with affine gap penalty, splicing and frameshift"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Miniprot align</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=miniprot_index" title="build a genome index for miniprot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Miniprot index</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=prodigal" title="A tool for gene prediction in microbial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prodigal Gene Predictor</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=aegean_gaeval" title="compute coverage and integrity scores for gene models using transcript alignments."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn GAEVAL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bg_find_subsequences" title="providing regions in BED format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nucleotide subsequence search</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rbc_gotohscan" title="Find subsequences in db"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GotohScan</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CryptoGenotyper" title="classifies Cryptosporidium species subtypes based on SSU rRNA and gp60 gene markers from Sanger sequencing data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CryptoGenotyper</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=interproscan" title="Interproscan functional predictions of ORFs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interproscan functional predictions of ORFs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dgidb_annotator" title="database info"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Annotate with DGI</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dgidb_annotate" title="database info"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Annotate with DGI</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hhsearch" title="detecting remote homologues of proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HHsearch</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=abricate_summary" title="Combine ABRicate results into a simple matrix of gene presence/absence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ABRicate Summary</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=glimmer_build_icm" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Glimmer ICM builder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=glimmer_knowledge_based" title="Predict ORFs in prokaryotic genomes (knowlegde-based)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Glimmer3</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=glimmer_not_knowledge_based" title="Predict ORFs in prokaryotic genomes (not knowlegde-based)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Glimmer3</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tbvcfreport" title="- generate HTML report from SnpEff annotated M.tb VCF(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TB Variant Report</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tb_variant_filter" title="M. tuberculosis H37Rv VCF filter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TB Variant Filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lorikeet_spoligotype" title="M. tuberculosis DNA fingerprinting"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">lorikeet spoligotyping</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spotyping" title="fast and accurate in silico Mycobacterium spoligotyping from sequence reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpoTyping</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=repeatmasker_wrapper" title="screen DNA sequences for interspersed repeats and low complexity regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RepeatMasker</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=homer_scanMotifGenomeWide" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scanMotifGenomeWide</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=homer_annotatePeaks" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">annotatePeaks</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=homer_findMotifsGenome" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">findMotifsGenome</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=homer_gtf_to_annotations" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Converts GTF to Annotations file for Homer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_geneSets" title="Annotating GeneSets, such as Gene Ontology, KEGG, Reactome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift GeneSets</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=list_spaln_tables" title="Given a query species, list the spaln settings tables that exist, from closest related species to most different"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">List spaln parameter tables</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gecco" title="is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GECCO</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interproscan" title="functional annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InterProScan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=te_finder" title="Transposable element insertions finder"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TEfinder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=netboxr" title="enables automated discovery of biological process modules by network analysis."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">netboxr</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=plasmidfinder" title="Plasmid identification in bacteria."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PlasmidFinder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edta" title="Whole-genome de-novo TE annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">edta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gffcompare" title="compare assembled transcripts to a reference annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GffCompare</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pfamscan" title="search a FASTA sequence against a library of Pfam HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PfamScan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pharokka" title="Rapid standardised annotation tool for bacteriophage genomes and metagenomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pharokka</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=homer_findMotifs" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">findMotifs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=braker" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Braker genome annotation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=get_orfs_or_cdss" title="e.g. to get peptides from ESTs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get open reading frames (ORFs) or coding sequences (CDSs)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.cdsParents" title="is one step of fixing a gene model--adding parent gene features to CDSs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF3 Add Gene to CDS</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.fixsixpack" title="Properly formats naive ORF caller output for Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF3 Add Gene to CDS for Sixpack</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.genbank.shinefind" title="Identify shine-dalgarno sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Shine Find</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.filter_type" title="selects features from a gff3 file based on feature type"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF3 Feature Type Filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.require_phage_start" title="ensures start is ATG, TTG, or GTG"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF3 Filter: Require Phage Start</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.remove_annots" title="that's unused in our GFF tools"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove Annotation Feature</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.prepForApollo" title="by ensuring that CDS features have a wrapping exon feature"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prep GFF3 Input for Apollo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt2.util.glimmer3_to_gff3" title="convert formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Glimmer3 to GFF3</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt2.phage.intron_detection" title="based on nearby protein blast results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interrupted gene detection tool</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.export_seq" title="Export corresponding sequence in genome from GFF3"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF3 Feature Sequence Export</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.fasta.lipory" title="in protein sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Identify Lipoboxes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.genbank.RelabelTags" title="relabels/renumbers GenBank tags according to rules"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Renumber GenBank Genes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.genome_editor" title="allows you to re-arrange a genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Genome Editor</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt2.phage.annotation_validator" title="validate phage annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phage QC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt2.phage.annotation_table" title="from gff3 formatted datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Annotation Table</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gff3.rebase" title="against parent features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Rebase GFF3 features</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.require_sd" title="ensures CDSs have an SD"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gff3 Filter: Require SD</button></a>
 <h3>Multiple Alignments</h3>
-<a href="https://usegalaxy.eu/root?tool_id=mummer_dnadiff" title="Evaluate similarities/differences between two sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DNAdiff</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mummer_nucmer" title="Align two or more sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nucmer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mummer_delta_filter" title="Filters alignment (delta) file from nucmer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delta-Filter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mummer_mummerplot" title="Generate 2-D dotplot of aligned sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Mummerplot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mummer_mummer" title="Align two or more sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Mummer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cd_hit" title="Cluster or compare biological sequence datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cd-hit</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rbc_mafft_add" title="Align a sequence,alignment or fragments to an existing alignment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAFFT add</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rbc_mafft" title="Multiple alignment program for amino acid or nucleotide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAFFT</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mummer_show_coords" title="Parse delta file and report coordinates and other information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Show-Coords</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chromeister" title="ultra-fast pairwise genome comparisons"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Chromeister</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mashmap" title="Fast local alignment boundaries"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mashmap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=maf_stats1" title="Alignment coverage information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAF Coverage Stats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=format_cd_hit_output" title="to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Format cd-hit outputs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=clustalw" title="multiple sequence alignment program for DNA or proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ClustalW</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sina" title="reference based multiple sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SINA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gecko" title="Ungapped genome comparison"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gecko</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=maf_stats1" title="Alignment coverage information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAF Coverage Stats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hammock_1.0" title="Clusters short peptide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hammock - cluster peptides</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chromeister" title="ultra-fast pairwise genome comparisons"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Chromeister</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mummer_mummer" title="Align two or more sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Mummer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mummer_mummerplot" title="Generate 2-D dotplot of aligned sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Mummerplot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mummer_delta_filter" title="Filters alignment (delta) file from nucmer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delta-Filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mummer_nucmer" title="Align two or more sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nucmer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mummer_dnadiff" title="Evaluate similarities/differences between two sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DNAdiff</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mummer_show_coords" title="Parse delta file and report coordinates and other information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Show-Coords</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=kc-align" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kc-Align</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pipelign" title="alignment with pipelign"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Automated multiple sequence</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=selectsequencesfrommsa" title="Tool to select representative sequences from a multiple sequence alignment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select Sequences</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=msaboot" title="Output PHYLIP file with bootstrapped multiple sequence alignment data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSABOOT</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hammock_1.0" title="Clusters short peptide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hammock - cluster peptides</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=format_cd_hit_output" title="to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Format cd-hit outputs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=muscle" title="multiple aligner"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MUSCLE</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=compalignp" title="Fractional identities between alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compalignp</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cd_hit" title="Cluster or compare biological sequence datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cd-hit</button></a>
 <h3>Assembly</h3>
 <a href="https://usegalaxy.eu/root?tool_id=spades_biosyntheticspades" title="biosynthetic gene cluster assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">biosyntheticSPAdes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spades_coronaspades" title="SARS-CoV-2 de novo genome assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">coronaSPAdes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spades_metaplasmidspades" title="extract and assembly plasmids from metagenomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaplasmidSPAdes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spades_metaviralspades" title="extract and assembly viral genomes from metagenomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaviralSPAdes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spades_plasmidspades" title="extract and assembly plasmids from WGS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plasmidSPAdes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spades_rnaviralspades" title="de novo assembler for transcriptomes, metatranscriptomes and metaviromes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rnaviralSPAdes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spades" title="genome assembler for genomes of regular and single-cell projects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SPAdes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metaspades" title="metagenome assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaSPAdes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=quast" title="Genome assembly Quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Quast</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=megahit" title="for metagenomics assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAHIT</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bionano_scaffold" title="automates the scaffolding process"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bionano Hybrid Scaffold</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=abyss-pe" title="de novo sequence assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ABySS</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rnaspades" title="de novo transcriptome assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rnaSPAdes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cactus_cactus" title="whole-genome multiple sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cactus</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=merquryplot" title="evaluate the assembly quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merqury histogram plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hapog" title="genome polishing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hapo-G</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hifiasm" title="haplotype-resolved de novo assembler for PacBio Hifi reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hifiasm</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pretext_map" title="converts SAM or BAM files into genome contact maps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PretextMap</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trycycler_cluster" title="cluster the contigs of your input assemblies into per-replicon groups"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trycycler cluster</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trycycler_consensus" title="generate a consensus contig sequence for each cluster"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trycycler consensus</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trycycler_partition" title="assign the reads to the clusters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trycycler partition</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trycycler_reconcile_msa" title="reconcile the contigs within each cluster and perform a multiple sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trycycler reconcile/msa</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trycycler_subsample" title="make a maximally-independent read subsets of an appropiate depth for your genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trycycler subsample</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=novoplasty" title="de novo assembler for short circular genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NOVOplasty</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=minia" title="Short-read assembler based on a de Bruijn graph"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Minia</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=flye" title="de novo assembler for single molecule sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flye</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hypo" title="super fast and accurate polisher for long read genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPo</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tgsgapcloser" title="fills the N-gap of error-prone long reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TGS-GapCloser</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=salsa" title="scaffold long read assemblies with Hi-C"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SALSA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pretext_map" title="converts SAM or BAM files into genome contact maps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PretextMap</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ragtag" title="reference-guided scaffolding of draft genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RagTag</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=purge_dups" title="and haplotigs in an assembly based on read depth (purge_dups)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Purge overlaps</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=raven" title="De novo assembly of Oxford Nanopore Technologies data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Raven</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hifiasm" title="haplotype-resolved de novo assembler for PacBio Hifi reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hifiasm</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=meryl" title="a genomic k-mer counter and sequence utility"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Meryl</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=genomescope" title="reference-free genome profiling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GenomeScope</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mitohifi" title="assembly mitogenomes from Pacbio HiFi reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MitoHiFi</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bellerophon" title="chimeric reads from Arima Genomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter and merge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=disco" title="to assemble metagenomics data using an overlap-layout-consensus (OLC) approach"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DISCO</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=merqury" title="evaluate the assembly quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merqury</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=miniasm" title="Ultrafast de novo assembly for long noisy reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">miniasm</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=canu" title="Assembler optimized for long error-prone reads such as PacBio, Oxford Nanopore"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Canu assembler</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=racon" title="Consensus module for raw de novo DNA assembly of long uncorrected reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Racon</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=shovill" title="Faster SPAdes assembly of Illumina reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Shovill</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=lordec" title="is a set a programs for correcting sequencing errors in PacBio reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Lordec</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mitobim" title="mitochondrial baiting and iterative mapping"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MITObim</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trimns" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TrimN</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=purge_dups" title="and haplotigs in an assembly based on read depth (purge_dups)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Purge overlaps</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=aegean_parseval" title="compare two sets of gene annotations for the same sequence."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn ParsEval</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=aegean_locuspocus" title="calculate locus coordinates for the given gene annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn LocusPocus</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=aegean_gaeval" title="compute coverage and integrity scores for gene models using transcript alignments."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn GAEVAL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=aegean_canongff3" title="pre-process GFF3 files, removing all features not directly related to protein-coding genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px"> AEGeAn CanonGFF3</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=salsa" title="scaffold long read assemblies with Hi-C"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SALSA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=shasta" title="De novo assembly of long read sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Shasta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lordec" title="is a set a programs for correcting sequencing errors in PacBio reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Lordec</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=novoplasty" title="de novo assembler for short circular genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NOVOplasty</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=megahit" title="for metagenomics assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAHIT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=idba_tran" title="Iterative de Bruijn Graph Assembler for transcriptome data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDBA-TRAN</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=unicycler" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create assemblies with Unicycler</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=shovill" title="Faster SPAdes assembly of Illumina reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Shovill</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=flye" title="de novo assembler for single molecule sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flye</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=racon" title="Consensus module for raw de novo DNA assembly of long uncorrected reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Racon</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=minia" title="Short-read assembler based on a de Bruijn graph"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Minia</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=quast" title="Genome assembly Quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Quast</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=miniasm" title="Ultrafast de novo assembly for long noisy reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">miniasm</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=abyss-pe" title="de novo sequence assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ABySS</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=unicycler" title="pipeline for bacterial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create assemblies with Unicycler</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=idba_ud" title="Iterative de Bruijn Graph Assembler for data with highly uneven depth"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDBA-UD</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=idba_hybrid" title="Iterative de Bruijn Graph Assembler for hybrid sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDBA-HYBRID</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spades" title="genome assembler for genomes of regular and single-cell projects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SPAdes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=velvetoptimiser" title="Automatically optimize Velvet assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VelvetOptimiser</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pilon" title="An automated genome assembly improvement and variant detection tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pilon</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=wtdbg" title="De novo assembler AND consensuser for long noisy sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WTDBG</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=disco" title="to assemble metagenomics data using an overlap-layout-consensus (OLC) approach"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DISCO</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rnaspades" title="de novo transcriptome assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rnaSPAdes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=meryl" title="a genomic k-mer counter and sequence utility"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Meryl</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mira_assembler" title="Takes Sanger, Roche, Illumina, and Ion Torrent data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Assemble with MIRA v3.4</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edena_ass_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Edena (assembling)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edena_ovl_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Edena (overlapping)</button></a>
@@ -768,113 +858,126 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=ssake" title="short DNA sequences assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SSAKE</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=crispr_recognition_tool" title="(CRT)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CRISPR Recognition Tool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=minced" title="(minced)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">detect CRISPR sequences</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=merqury" title="evaluate the assembly quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merqury</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=genomescope" title="reference-free genome profiling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GenomeScope</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bionano_scaffold" title="automates the scaffolding process"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bionano Hybrid Scaffold</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bellerophon" title="chimeric reads from Arima Genomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter and merge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mitohifi" title="assembly mitogenomes from Pacbio HiFi reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MitoHiFi</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=raven" title="De novo assembly of Oxford Nanopore Technologies data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Raven</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ragtag" title="reference-guided scaffolding of draft genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RagTag</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tgsgapcloser" title="fills the N-gap of error-prone long reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TGS-GapCloser</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hypo" title="super fast and accurate polisher for long read genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spades_rnaviralspades" title="de novo assembler for transcriptomes, metatranscriptomes and metaviromes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rnaviralSPAdes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spades_plasmidspades" title="extract and assembly plasmids from WGS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plasmidSPAdes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spades_metaviralspades" title="extract and assembly viral genomes from metagenomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaviralSPAdes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spades_metaplasmidspades" title="extract and assembly plasmids from metagenomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaplasmidSPAdes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spades_coronaspades" title="SARS-CoV-2 de novo genome assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">coronaSPAdes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=links" title="- scaffold genome assemblies with long reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LINKS</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gfastats" title="the swiss army knife for genome assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gfastats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=yahs" title="yet another HI-C scaffolding tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">YAHS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=velvetg" title="Velvet sequence assembler for very short reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">velvetg</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=velveth" title="Prepare a dataset for the Velvet velvetg Assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">velveth</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cap3" title="Sequence Assembly tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cap3</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=smudgeplot" title="inference of ploidy and heterozygosity structure using whole genome sequencing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Smudgeplot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cactus_export" title="whole-genome multiple sequence alignment to other formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cactus: export</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pretext_graph" title="Embed bedgraph formatted data inside a Pretext contact map."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pretextgraph</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=get_organelle_from_reads" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get organelle from reads</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=minipolish" title="polishing miniasm assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">minipolish</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=instagraal" title="Large genome reassembly based on Hi-C data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">instaGRAAL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=necat" title="Error correction and de-novo assembly for ONT Nanopore reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">necat</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biscot" title="Bionano scaffolding correction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BiSCoT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hifiasm_meta" title="for metagenome assembly using Hifi reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hifiasm_meta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=blobtoolkit" title="genome assembly QC"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BlobToolKit</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=nextdenovo" title="string graph-based de novo assembler for long reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NextDenovo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=get_annotated_regions_from_gb" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get annotated regions from genbank files (getorganelle)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=aligned_to_consensus" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Consensus sequence from aligned FASTA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=verkko" title="hybrid genome assembly pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">verkko</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=velvetg" title="Velvet sequence assembler for very short reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">velvetg</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rna_quast" title="A quality assessment tool for De Novo transcriptome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rnaQUAST</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=velveth" title="Prepare a dataset for the Velvet velvetg Assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">velveth</button></a>
 <h3>Mapping</h3>
-<a href="https://usegalaxy.eu/root?tool_id=bowtie2" title="- map reads against reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bowtie2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bbtools_bbmap" title="short-read aligner"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: BBMap</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kma_map" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with KMA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=minimap2" title="A fast pairwise aligner for genomic and spliced nucleotide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with minimap2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bioext_bealign" title="to a reference using a codon alignment algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align sequences</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hisat2" title="A fast and sensitive alignment program"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HISAT2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=winnowmap" title="a mapping tool optimized for repetitive sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Winnowmap</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rna_star" title="Gapped-read mapper for RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA STAR</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bwa_mem" title="- map medium and long reads (> 100 bp) against reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with BWA-MEM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=lastz_wrapper_2" title=": align long sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LASTZ</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pbmm2" title="map PacBio reads to a reference genome."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pbmm2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rna_starsolo" title="mapping, demultiplexing and gene quantification for single cell RNA-seq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA STARSolo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bbtools_bbmap" title="short-read aligner"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: BBMap</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=megablast_xml_parser" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Parse blast XML output</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=megablast_wrapper" title="compare short reads against htgs, nt, and wgs databases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Megablast</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bwameth" title="Fast and accurate aligner of BS-Seq reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bwameth</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lastz_paired_reads_wrapper" title="map short paired reads against reference sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Lastz paired reads</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lastz_wrapper_2" title=": align long sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LASTZ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bowtie_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with Bowtie for Illumina</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bwa_mem2" title="- map medium and long reads (> 100 bp) against reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BWA-MEM2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=lastz_d_wrapper" title=": estimate substitution scores matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LASTZ_D</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=minimap2" title="A fast pairwise aligner for genomic and spliced nucleotide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with minimap2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hisat2" title="A fast and sensitive alignment program"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HISAT2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rna_star" title="Gapped-read mapper for RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA STAR</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bismark_bowtie2" title="Bisulfite reads mapper"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bismark Mapper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kma_map" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with KMA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=star_fusion" title="detect fusion genes in RNA-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">STAR-Fusion</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bismark_deduplicate" title="Deduplicates reads mapped by Bismark"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bismark Deduplicate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bismark_pretty_report" title="Generates a graphical HTML report page from report outputs of Bismark"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bismark Pretty Report</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bismark_methylation_extractor" title="Reports on methylation status of reads mapped by Bismark"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bismark Meth. Extractor</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bowtie2" title="- map reads against reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bowtie2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=segemehl" title="short read mapping with gaps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">segemehl</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bioext_bealign" title="to a reference using a codon alignment algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align sequences</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=graphmap_overlap" title="fast, trimmed overlap pipeline without aligning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Owler</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=graphmap_align" title="for long, error-prone reads, like Nanopore ONT and PacBio"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Mapper</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bismark_bowtie" title="bisulfite mapper (bowtie)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bismark</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bwa" title="- map short reads (< 100 bp) against reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with BWA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bwa_mem" title="- map medium and long reads (> 100 bp) against reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with BWA-MEM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lastz_d_wrapper" title=": estimate substitution scores matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LASTZ_D</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tophat2" title="Gapped-read mapper for RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TopHat</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bowtie_color_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with Bowtie for SOLiD</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=winnowmap" title="a mapping tool optimized for repetitive sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Winnowmap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bwa_mem2" title="- map medium and long reads (> 100 bp) against reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BWA-MEM2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bfast_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with BFAST</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=PerM" title="for SOLiD and Illumina"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with PerM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=srma_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Re-align with SRMA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mosaik_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with Mosaik</button></a>
 <h3>Variant Calling</h3>
+<a href="https://usegalaxy.eu/root?tool_id=cnv_vcf2json" title="Converts 1000hg structural variants VCF file to JSON"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNV VCF2JSON</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfanno" title="VCF annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">vcfanno</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bbtools_callvariants" title="in aligned Bam files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: call variants</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pharmcat" title="Pharmacogenomics Clinical Annotation Tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pharmCAT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=plink" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plink</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqwish" title="Alignment to variation graph inducer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqwish</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_annotate" title="Annotate and edit VCF/BCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools annotate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=freebayes" title="bayesian genetic variant detector"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FreeBayes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bamleftalign" title="indels in BAM datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BamLeftAlign</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_convert_from_vcf" title="Converts VCF/BCF to IMPUTE2/SHAPEIT formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools convert from vcf</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_filter" title="Apply fixed-threshold filters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools filter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_gtcheck" title="Check sample identity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools gtcheck</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_isec" title="Create intersections, unions and complements of VCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools isec</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_reheader" title="Modify header of VCF/BCF files, change sample names"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools reheader</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_view" title="VCF/BCF conversion, view, subset and filter VCF/BCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools view</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_mpileup" title="Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools mpileup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfcheck" title="Verify that the reference allele matches the reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFcheck:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=varscan_somatic" title="Call germline/somatic and LOH variants from tumor-normal sample pairs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan somatic</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=varscan_copynumber" title="Determine relative tumor copy number from tumor-normal pileups"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan copynumber</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=varscan_mpileup" title="for variant detection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan mpileup</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snpEff_build_gb" title="database from Genbank or GFF record"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff build:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=strelka_germline" title="small variant caller for germline variation in small cohorts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Strelka Germline</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sansa_annotate" title="structural variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sansa annotate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=strelka_somatic" title="small variant caller for somatic variation in tumor/normal sample pairs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Strelka Somatic</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=delly_filter" title="somatic or germline structural variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=delly_merge" title="structural variants across/within BCF/VCF file(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly merge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=delly_call" title="and genotype structural variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly call</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=delly_lr" title="optimized calling and genotyping of structural variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly long-read (lr)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_consensus" title="Create consensus sequence by applying VCF variants to a reference fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools consensus</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=delly_classify" title="somatic or germline copy-number variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly classify</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=delly_cnv" title="discover and genotype copy-number variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly cnv</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=control_freec" title="detects copy-number changes and allelic imbalances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Control-FREEC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_stats" title="Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools stats</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gatk4_mutect2" title="- Call somatic SNVs and indels via local assembly of haplotypes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GATK4 Mutect2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deepvariant" title="deep learning-based variant caller"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeepVariant</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snippy_core" title="Combine multiple Snippy outputs into a core SNP alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snippy-core</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snippy" title="Snippy finds SNPs between a haploid reference genome and your NGS sequence reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snippy</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snippy_clean_full_aln" title="Replace any non-standard sequence characters in snippy 'core.full.aln' file."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snippy-clean_full_aln</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=lumpy_sv" title="is a probabilistic framework for structural variant discovery"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LUMPY</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=beagle" title="phasing genotypes and imputing ungenotyped markers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beagle</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_roh" title="HMM model for detecting runs of homo/autozygosity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools roh</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=irissv" title="Refine insertion sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Iris</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=jasminesv" title="Merge structural variants across samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JasmineSV</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sansa_annotate" title="structural variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sansa annotate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=strelka_germline" title="small variant caller for germline variation in small cohorts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Strelka Germline</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=get_hrun" title="Annotate indel variants with homopolymer context"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get homopolymer run length</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=strelka_somatic" title="small variant caller for somatic variation in tumor/normal sample pairs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Strelka Somatic</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_query" title="Extracts fields from VCF/BCF file and prints them in user-defined format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools query</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=lumpy_prep" title="extracts discordant read pairs and split-read alignments from a BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LUMPY preprocessing</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_convert_to_vcf" title="Converts other formats to VCF/BCFk"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools convert to vcf</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_cnv" title="Call copy number variation from VCF B-allele frequency (BAF) and Log R Ratio intensity (LRR) values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools cnv</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=king" title="Kinship-based INference for GWAS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">KING</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vardict_java" title="calls SNVs and indels for tumor-normal pairs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarDict</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=delly_call" title="and genotype structural variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly call</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_concat" title="Concatenate or combine VCF/BCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools concat</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=artic_guppyplex" title="Filter Nanopore reads by read length and (optionally) quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ARTIC guppyplex</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_merge" title="Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools merge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=artic_minion" title="Build consensus sequence and call variants from amplicon-based nanopore sequence data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ARTIC minion</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_consensus" title="Create consensus sequence by applying VCF variants to a reference fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools consensus</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfanno" title="VCF annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">vcfanno</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=irissv" title="Refine insertion sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Iris</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpfreqplot" title="Generates a heatmap of allele frequencies grouped by variant type for SnpEff-annotated SARS-CoV-2 data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Variant Frequency Plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mut2read" title="Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DCS mutations to tags/reads:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_filter" title="Filter variants using arbitrary expressions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mut2sscs" title="Extracts all tags from the single stranded consensus sequence (SSCS) bam file that carry a mutation at the same position a mutation is called in the duplex consensus sequence (DCS) and calculates their frequencies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DCS mutations to SSCS stats:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=read2mut" title="Looks for reads with mutation at known positions and calculates frequencies and stats."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Call specific mutations in reads:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lumpy_sv" title="is a probabilistic framework for structural variant discovery"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LUMPY</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lumpy_prep" title="extracts discordant read pairs and split-read alignments from a BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LUMPY preprocessing</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lofreq_filter" title="called variants posteriorly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Lofreq filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lofreq_call" title="with LoFreq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Call variants</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=artic_minion" title="Build consensus sequence and call variants from amplicon-based nanopore sequence data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ARTIC minion</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cutesv" title="detects long-read-based SVs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cuteSV</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sniffles" title="Structural variation caller using third generation sequencing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sniffles</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vardict_java" title="calls SNVs and indels for tumor-normal pairs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarDict</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=control_freec" title="detects copy-number changes and allelic imbalances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Control-FREEC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gatk4_mutect2" title="- Call somatic SNVs and indels via local assembly of haplotypes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GATK4 Mutect2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_concat" title="Concatenate or combine VCF/BCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools concat</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpeff_sars_cov_2" title="annotate variants for SARS-CoV-2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff eff:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lofreq_viterbi" title="with LoFreq viterbi"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Realign reads</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lofreq_alnqual" title="to aligned read SAM/BAM records"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add LoFreq alignment quality scores</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lofreq_indelqual" title="into a BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Insert indel qualities</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqwish" title="Alignment to variation graph inducer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqwish</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=odgi_viz" title="variation graph visualizations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">odgi viz</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=odgi_build" title="construct a dynamic succinct variation graph"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">odgi build</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vg_view" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">vg view</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vg_deconstruct" title="construct a dynamic succinct variation graph"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">vg deconstruct</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vg_convert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">vg convert</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snippy_core" title="Combine multiple Snippy outputs into a core SNP alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snippy-core</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snippy_clean_full_aln" title="Replace any non-standard sequence characters in snippy 'core.full.aln' file."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snippy-clean_full_aln</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snippy" title="Snippy finds SNPs between a haploid reference genome and your NGS sequence reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snippy</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_merge" title="Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools merge</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcfselectsamples" title="Select samples from a VCF dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFselectsamples:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcfannotategenotypes" title="Annotate genotypes in a VCF dataset using genotypes from another VCF dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFannotateGenotypes:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcfdistance" title="Calculate distance to the nearest variant"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFdistance:</button></a>
@@ -897,122 +1000,169 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=vcfleftalign" title="Left-align indels and complex variants in VCF dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFleftAlign:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcf2tsv" title="Convert VCF data into TAB-delimited format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFtoTab-delimited:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcfaddinfo" title="Adds info fields from the second dataset which are not present in the first dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFaddinfo:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcfcheck" title="Verify that the reference allele matches the reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFcheck:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bcftools_call" title="SNP/indel variant calling from VCF/BCF"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools call</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snpEff_get_chr_names" title="list chromosome names/lengths"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff chromosome-info:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bcftools_norm" title="Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools norm</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bcftools_csq" title="Haplotype aware consequence predictor"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools csq</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bcftools_plugin_frameshifts" title="plugin Annotate frameshift indels"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools frameshifts</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bcftools_plugin_color_chrs" title="plugin Color shared chromosomal segments, requires phased GTs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools color-chrs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_cnv" title="Call copy number variation from VCF B-allele frequency (BAF) and Log R Ratio intensity (LRR) values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools cnv</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snp_dists" title="Compute distance in SNPs between all sequences in a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SNP distance matrix</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tag_pileup_frequency" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tag pileup frequency</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snp_sites" title="from a multi-FASTA alignment file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Finds SNP sites</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=exomedepth" title="Calls copy number variants (CNVs) from targeted sequence data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ExomeDepth</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snpEff_build_gb" title="database from Genbank or GFF record"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff build:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mixcr_analyze" title="immuno clonotyes from sequence data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MiXCR Analyze</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tb_variant_filter" title="M. tuberculosis H37Rv VCF filter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TB Variant Filter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tbvcfreport" title="- generate HTML report from SnpEff annotated M.tb VCF(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TB Variant Report</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snpEff_databases" title="list available databases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff databases:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=freebayes" title="bayesian genetic variant detector"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FreeBayes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=varscan_somatic" title="Call germline/somatic and LOH variants from tumor-normal sample pairs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan somatic</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=basil" title="Breakpoint detection, including large insertions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">basil</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snpEff_download" title="download a pre-built database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff download:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_int" title="Filter variants using intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Intervals</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_rmInfo" title="remove INFO field annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift rmInfo</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snpSift_annotate" title="SNPs from dbSnp"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Annotate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpsift_vartype" title="Annotate with variant type"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Variant Type</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snpSift_annotate" title="SNPs from dbSnp"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Annotate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_caseControl" title="Count samples are in 'case' and 'control' groups."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift CaseControl</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snpEff_get_chr_names" title="list chromosome names/lengths"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff chromosome-info:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_extractFields" title="from a VCF file into a tabular file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Extract Fields</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_vcfCheck" title="basic checks for VCF specification compliance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift vcfCheck</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snpEff" title="annotate variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff eff:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcfview" title="Convert, filter, subset VCF/BCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftoolsView</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bamleftalign" title="indels in BAM datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BamLeftAlign</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vt_normalize" title="normalizes variants in a VCF file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VT normalize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=naive_variant_caller" title="- tabulate variable sites from BAM datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Naive Variant Caller (NVC)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snpEff_databases" title="list available databases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff databases:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_geneSets" title="Annotating GeneSets, such as Gene Ontology, KEGG, Reactome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift GeneSets</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_dbnsfp" title="Add annotations from dbNSFP or similar annotation DBs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift dbNSFP</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_dbnsfp_generic" title="Add Annotations from dbNSFP and similar annotation DBs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift dbNSFP</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snpEff_download" title="download a pre-built database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff download:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snpEff" title="annotate variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff eff:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=manta" title="Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Manta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnv_phenopacket" title="Builds Phenopacket schema for the structural variants metadata from the 1000hg project"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNV Phenopacket</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deepvariant" title="deep learning-based variant caller"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeepVariant</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=varscan_copynumber" title="Determine relative tumor copy number from tumor-normal pileups"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan copynumber</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=varscan" title="for variant detection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=varscan_mpileup" title="for variant detection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan mpileup</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=SnpEff-cds-report" title="Report Variant coding sequence changes for SnpEffects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff Ensembl CDS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpeff_to_peptides" title="to create a Search DB fasta for variant SAP peptides"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff to Peptide fasta</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=naive_variant_caller" title="- tabulate variable sites from BAM datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Naive Variant Caller</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_plugin_split_vep" title="plugin Extracts fields from structured annotations such as INFO/CSQ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools split-vep</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=allele_counts_1" title="process variant counts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Variant Annotator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_int" title="Filter variants using intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Intervals</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_annotate" title="SNPs from dbSnp"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Annotate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_filter" title="Filter variants using arbitrary expressions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_caseControl" title="Count samples are in 'case' and 'control' groups."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift CaseControl</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=get_hrun" title="Annotate indel variants with homopolymer context"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get homopolymer run length</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_mpileup" title="Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools mpileup</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_view" title="VCF/BCF conversion, view, subset and filter VCF/BCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools view</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_stats" title="Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools stats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_roh" title="HMM model for detecting runs of homo/autozygosity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools roh</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_reheader" title="Modify header of VCF/BCF files, change sample names"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools reheader</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_query" title="Extracts fields from VCF/BCF file and prints them in user-defined format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools query</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_isec" title="Create intersections, unions and complements of VCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools isec</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_gtcheck" title="Check sample identity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools gtcheck</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_filter" title="Apply fixed-threshold filters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_convert_to_vcf" title="Converts other formats to VCF/BCFk"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools convert to vcf</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_convert_from_vcf" title="Converts VCF/BCF to IMPUTE2/SHAPEIT formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools convert from vcf</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_annotate" title="Annotate and edit VCF/BCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools annotate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beagle" title="phasing genotypes and imputing ungenotyped markers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beagle</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=king" title="Kinship-based INference for GWAS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">KING</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=artic_guppyplex" title="Filter Nanopore reads by read length and (optionally) quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ARTIC guppyplex</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pharmcat" title="Pharmacogenomics Clinical Annotation Tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pharmCAT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ensembl_vep" title="with VEP"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Predict variant effects</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=breseq" title="find mutations in haploid microbial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">breseq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vcf2maf" title="with vcf2maf"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert VCF to MAF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_plugin_setgt" title="plugin Sets genotypes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools setGT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_plugin_setgt" title="plugin Sets genotypes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools setGT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fatovcf" title="Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">faToVcf</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_access" title="Calculate the sequence-accessible coordinates in chromosomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Access</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_antitarget" title="lists the chromosomal coordinates for targeted resequencing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Antitarget</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_autobin" title="Estimates read counts or depths in a BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Autobin</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_batch" title="Run the CNVkit pipeline on one or more BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Batch</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_call" title="Call copy number variants from segmented log2 ratios"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Call</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_coverage" title="Calculate coverage in the given regions from BAM read depths"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Coverage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_diagram" title="Draw copy number on chromosomes as a diagram"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Diagram</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_fix" title="Adjust raw coverage data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Fix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_heatmap" title="Plot copy number for multiple samples as a heatmap"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Heatmap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_reference" title="Compile a copy-number reference from the given files or directory containing normal samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Reference</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_scatter" title="Plot bin-level log2 coverages and segmentation calls together"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Scatter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_segment" title="Infer copy number segments from the given coverage table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Segment</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_target" title="Prepare a BED file of baited regions for use with CNVkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Target</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=smgu_frameshift_deletions_checks" title="reports on frameshifting indels in consensus sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Frameshift Deletions Checks</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beacon2_csv2xlsx" title="v2 CSV Models to XLSX"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 CSV2XLSX</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beacon2_pxf2bff" title="converts Phenopacket PXF (JSON) to BFF (JSON)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 PXF2BFF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beacon2_vcf2bff" title="converting annotated VCF files to Beacon v2 format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 VCF2BFF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_breaks" title="List the targeted genes with segmentaion breakpoint"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Breaks</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_genemetrics" title="Identify targeted genes with copy number gain or loss"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit genemetrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_segmetrics" title="calculate summary statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Segmetrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_sex" title="Guess samples’ chromosomal sex from the relative coverage of chromosomes X and Y"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Sex</button></a>
 <h3>Genome editing</h3>
 <a href="https://usegalaxy.eu/root?tool_id=crispr_studio" title="facilitate and accelerate CRISPR array visualization from a GFF3 file generated with CRISPRDetect"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CRISPR Studio</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sonneityping" title="for Shigella sonnei and tabulate results into a single tab-delimited file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">parse mykrobe predict</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=amplican" title="analysis tool for genome editing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AmpliCan</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mageck_test" title="- given a table of read counts, perform the sgRNA and gene ranking"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAGeCKs test</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mageck_mle" title="- perform maximum-likelihood estimation of gene essentiality scores"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAGeCK mle</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mageck_gsea" title="- a fast implementation of Gene Set Enrichment Analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAGeCK GSEA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mageck_count" title="- collect sgRNA read counts from read mapping files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAGeCK count</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mageck_pathway" title="- given a ranked gene list, test whether one pathway is enriched"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAGeCK pathway</button></a>
-<h3>RNA-Seq</h3>
-<a href="https://usegalaxy.eu/root?tool_id=blockbuster" title="detects blocks of overlapping reads using a gaussian-distribution approach"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">blockbuster</button></a>
-<h3>RNA Analysis</h3>
-<a href="https://usegalaxy.eu/root?tool_id=trinity_gene_to_trans_map" title="for Trinity assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate gene to transcript map</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=trinotate" title="functional transcript annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trinotate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=edger" title="Perform differential expression of count data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">edgeR</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=limma_voom" title="Perform differential expression with limma-voom or limma-trend"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">limma</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chira_quantify" title="quantify aligned loci to score the alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChiRA qauntify</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chira_merge" title="merge aligned positions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChiRA merge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chira_map" title="map reads to trascriptome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChiRA map</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chira_collapse" title="deduplicate fastq reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChiRA collapse</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=trinity_filter_low_expr_transcripts" title="from a Trinity assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter low expression transcripts</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=trinity_contig_exn50_statistic" title="from a Trinity assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute contig Ex90N50 statistic and Ex90 transcript count</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=trinity_super_transcripts" title="from a Trinity assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate SuperTranscripts</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dexseq" title="Determines differential exon usage from count tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DEXSeq</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=trinity_align_and_estimate_abundance" title="on a de novo assembly of RNA-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align reads and estimate abundance</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dexseq_count" title="Prepare and count exon abundancies from RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DEXSeq-Count</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=plotdexseq" title="Visualization of the per gene DEXSeq results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plotDEXSeq</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=stringtie" title="transcript assembly and quantification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">StringTie</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=stringtie_merge" title="transcripts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">StringTie merge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tximport" title="Summarize transcript-level estimates for gene-level analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tximport</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=trinity" title="de novo assembly of RNA-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trinity</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seurat" title="- toolkit for exploration of single-cell RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Seurat</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=transdecoder" title="finds coding regions within transcripts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TransDecoder</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=infernal_cmalign" title="Align sequences to a covariance model against a sequence database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cmalign</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=infernal_cmbuild" title="Build covariance models from sequence alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cmbuild</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=infernal_cmpress" title="Prepare a covariance model database for cmscan"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cmpress</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=infernal_cmscan" title="Search sequences against collections of covariance models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cmscan</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deseq2" title="Determines differentially expressed features from count tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DESeq2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=infernal_cmsearch" title="Search covariance model(s) against a sequence database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cmsearch</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=infernal_cmstat" title="Summary statistics for covariance model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cmstat</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=alleyoop" title="- post-processing and QC of Slamdunk analyses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Alleyoop</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=slamdunk" title="- streamlining SLAM-seq analysis with ultra-high sensitivity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slamdunk</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cuffmerge" title="merge together several Cufflinks assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cuffmerge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=salmonquantmerge" title="Merge multiple quantification results into a single file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Salmon quantmerge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=featurecounts" title="Measure gene expression in RNA-Seq experiments from SAM or BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">featureCounts</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=egsea" title="easy and efficient ensemble gene set testing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EGSEA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=targetfinder" title="plant small RNA target prediction tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TargetFinder</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=migmap" title="mapper for full-length T- and B-cell repertoire sequencing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MiGMAP</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kallisto_pseudo" title="- run pseudoalignment on RNA-Seq transcripts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kallisto pseudo</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kallisto_quant" title="- quantify abundances of RNA-Seq transcripts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kallisto quant</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ruvseq" title="from RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove Unwanted Variation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=salmon" title="Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Salmon quant</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rna_quast" title="A Quality Assessment Tool for De Novo Transcriptome Assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rnaQUAST</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=genomic_super_signature" title="interpretation of RNAseq experiments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GenomicSuperSignature</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mageck_mle" title="- perform maximum-likelihood estimation of gene essentiality scores"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAGeCK mle</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mageck_gsea" title="- a fast implementation of Gene Set Enrichment Analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAGeCK GSEA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mageck_count" title="- collect sgRNA read counts from read mapping files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAGeCK count</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mageck_pathway" title="- given a ranked gene list, test whether one pathway is enriched"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAGeCK pathway</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sonneityping" title="for Shigella sonnei and tabulate results into a single tab-delimited file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">parse mykrobe predict</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=amplican" title="analysis tool for genome editing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AmpliCan</button></a>
+<h3>RNA-Seq</h3>
+<a href="https://usegalaxy.eu/root?tool_id=blockbuster" title="detects blocks of overlapping reads using a gaussian-distribution approach"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">blockbuster</button></a>
+<h3>RNA Analysis</h3>
+<a href="https://usegalaxy.eu/root?tool_id=cmsearch_deoverlap" title="removes lower scoring overlaps from cmsearch results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CMsearch deoverlap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rbpbench" title="- Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RBPBench</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ribowaltz_plot" title="visual inspection of ribosome profiling data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">riboWaltz-plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=arriba" title="detect gene fusions from STAR aligned RNA-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Arriba</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=filter_combined_via_tracking" title="using tracking file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter Combined Transcripts</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=express" title="Quantify the abundances of a set of target sequences from sampled subsequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eXpress</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chira_extract" title="extrat the chimeras"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChiRA extract</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=masigpro" title="Significant Gene Expression Profile Differences in Time Course Gene Expression Data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">maSigPro</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cuffmerge" title="merge together several Cufflinks assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cuffmerge</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cufflinks" title="transcript assembly and FPKM (RPKM) estimates for RNA-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cufflinks</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cuffdiff" title="find significant changes in transcript expression, splicing, and promoter use"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cuffdiff</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cuffcompare" title="compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cuffcompare</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ruvseq" title="from RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove Unwanted Variation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=feelnc" title="FlExible Extraction of LncRNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FEELnc</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=featurecounts" title="Measure gene expression in RNA-Seq experiments from SAM or BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">featureCounts</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=migmap" title="mapper for full-length T- and B-cell repertoire sequencing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MiGMAP</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scpipe" title="- preprocessing pipeline for single cell RNA-seq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scPipe</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seurat" title="- toolkit for exploration of single-cell RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Seurat</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tetoolkit_tetranscripts" title="annotates reads to genes and transposable elements"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TEtranscripts</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=transdecoder" title="finds coding regions within transcripts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TransDecoder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chira_collapse" title="deduplicate fastq reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChiRA collapse</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chira_merge" title="merge aligned positions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChiRA merge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chira_map" title="map reads to trascriptome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChiRA map</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chira_quantify" title="quantify aligned loci to score the alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChiRA qauntify</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chira_extract" title="extrat the chimeras"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChiRA extract</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=trinotate" title="functional transcript annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trinotate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=footprint" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">footprint</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cuffnorm" title="Create normalized expression levels"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cuffnorm</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cummeRbund" title="visualize Cuffdiff output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cummeRbund</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=htseq_count" title="- Count aligned reads in a BAM file that overlap features in a GFF file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">htseq-count</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=trinity_run_de_analysis" title="using a Trinity assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Differential expression analysis</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=trinity_abundance_estimates_to_matrix" title="for a de novo assembly of RNA-Seq data by Trinity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build expression matrix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=salmon" title="Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Salmon quant</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deseq2" title="Determines differentially expressed features from count tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DESeq2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=stringtie" title="transcript assembly and quantification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">StringTie</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=stringtie_merge" title="transcripts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">StringTie merge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=trinity_align_and_estimate_abundance" title="on a de novo assembly of RNA-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align reads and estimate abundance</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=trinity" title="de novo assembly of RNA-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trinity</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sRNAPipe" title="In-depth study of small RNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sRNAPipe</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=graphprot_predict_profile" title="- Train models and predict RBP binding profiles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GraphProt</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=heinz_visualization" title="the optimal scoring subnetwork"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Visualize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=slamdunk" title="- streamlining SLAM-seq analysis with ultra-high sensitivity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slamdunk</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=alleyoop" title="- post-processing and QC of Slamdunk analyses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Alleyoop</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qualimap_counts" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QualiMap Counts QC</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qualimap_rnaseq" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QualiMap RNA-Seq QC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bg_sortmerna" title="Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter with SortMeRNA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tximport" title="Summarize transcript-level estimates for gene-level analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tximport</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=masigpro" title="Significant Gene Expression Profile Differences in Time Course Gene Expression Data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">maSigPro</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=trinity_super_transcripts" title="from a Trinity assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate SuperTranscripts</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=trinity_abundance_estimates_to_matrix" title="for a de novo assembly of RNA-Seq data by Trinity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build expression matrix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=trinity_contig_exn50_statistic" title="from a Trinity assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute contig Ex90N50 statistic and Ex90 transcript count</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=trinity_filter_low_expr_transcripts" title="from a Trinity assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter low expression transcripts</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=trinity_run_de_analysis" title="using a Trinity assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Differential expression analysis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=salmonquantmerge" title="Merge multiple quantification results into a single file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Salmon quantmerge</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=glassgo" title="sRNA homolog finder"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GLASSgo</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=intarna" title="Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IntaRNA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kallisto_pseudo" title="run pseudoalignment on RNA-Seq transcripts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kallisto pseudo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kallisto_quant" title="quantify abundances of RNA-Seq transcripts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kallisto quant</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edger" title="Perform differential expression of count data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">edgeR</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=crosscontamination_barcode_filter" title="for use in plate-based barcoded analyses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cross-contamination Barcode Filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=limma_voom" title="Perform differential expression with limma-voom or limma-trend"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">limma</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dexseq" title="Determines differential exon usage from count tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DEXSeq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dexseq_count" title="Prepare and count exon abundancies from RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DEXSeq-Count</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=plotdexseq" title="Visualization of the per gene DEXSeq results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plotDEXSeq</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trinity_analyze_diff_expr" title="from a Trinity assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract and cluster differentially expressed transcripts</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=egsea" title="easy and efficient ensemble gene set testing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EGSEA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=selectsequencesfrommsa" title="Tool to select representative sequences from a multiple sequence alignment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select Sequences</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cofold" title="An RNA secondary structure prediction method that takes co-transcriptional folding into account"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cofold</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rnaz_cluster" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAz Cluster</button></a>
@@ -1036,21 +1186,26 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=pipmir" title="a method to identify novel plant miRNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PIPmiR PIPELINE</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nastiseq" title="Identify cis-NATs using ssRNA-seq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NASTIseq</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=flaimapper" title="detects small ncRNA derived fragments in small RNA-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FlaiMapper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=targetfinder" title="plant small RNA target prediction tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TargetFinder</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=AREsite2_REST" title="AREsite2 REST Interface"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get motifs from AREsite2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fuma" title="match detected fusion genes based on gene names (in particular for RNA-Seq)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FuMa</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=RNAlien" title="Unsupervised covariance model construction from a single input sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAlien</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=blockclust" title="efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BlockClust</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=trinity_gene_to_trans_map" title="for Trinity assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate gene to transcript map</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trinity_samples_qccheck" title="for transcript quantification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNASeq samples quality check</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=describe_samples" title="and replicates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Describe samples</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trinity_define_clusters_by_cutting_tree" title="after differential expression analysis using a Trinity assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Partition genes into expression clusters</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_geneBody_coverage" title="Read coverage over gene body."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gene Body Coverage (BAM)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=arriba_draw_fusions" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Arriba Draw Fusions</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=arriba_get_filters" title="to history"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Arriba Get Filters</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ribowaltz_process" title="calculation of optimal P-site offsets and diagnostic analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">riboWaltz</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_geneBody_coverage" title="read coverage over gene body"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gene Body Coverage (BAM)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=heinz_bum" title="with p-values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fit a BUM model</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=heinz" title="using Heinz"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Identify optimal scoring subnetwork</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=heinz_scoring" title="for each node"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate a Heinz score</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sshmm" title="- RNA sequence-structure motif finder"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ssHMM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pizzly" title="- fast fusion detection using kallisto"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pizzly</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rcas" title="- RNA Centric Annotation System"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RCAS</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_geneBody_coverage2" title="Read coverage over gene body"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gene Body Coverage (Bigwig)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_geneBody_coverage2" title="read coverage over gene body"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gene Body Coverage (Bigwig)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rseqc_RPKM_saturation" title="calculates raw count and RPKM values for transcript at exon, intron, and mRNA level"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RPKM Saturation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rseqc_infer_experiment" title="speculates how RNA-seq were configured"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Infer Experiment</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rseqc_RNA_fragment_size" title="calculates the fragment size for each gene/transcript"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA fragment size</button></a>
@@ -1099,13 +1254,18 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=viennarna_rnainverse" title="Calculate RNA sequence from secondary structure"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAinverse</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=viennarna_rnaheat" title="Calculate energies of RNA in a temperature range"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAheat</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=viennarna_rnasubopt" title="Calculates suboptimal secondary structures of RNAs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAsubopt</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=infernal_cmalign" title="Align sequences to a covariance model against a sequence database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cmalign</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=infernal_cmsearch" title="Search covariance model(s) against a sequence database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cmsearch</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=infernal_cmscan" title="Search sequences against collections of covariance models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cmscan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=infernal_cmpress" title="Prepare a covariance model database for cmscan"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cmpress</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=infernal_cmbuild" title="Build covariance models from sequence alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cmbuild</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=infernal_cmstat" title="Summary statistics for covariance model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cmstat</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=remurna" title="Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">remuRNA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rnasnp" title="Efficient detection of local RNA secondary structure changes induced by SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAsnp</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mlocarna" title="Multiple Alignment and Folding of RNAs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LocARNA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=paralyzer" title="A method to map interaction sites between RNA-binding proteins      and their targets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PARalyzer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=circexplorer" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CIRCexplorer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rbc_rnacommender" title="genome-wide recommendation of RNA-protein interactions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAcommender</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_RPKM_count" title="calculates raw count and RPKM values for transcript at exon, intron, and mRNA level"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RPKM Count</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tophat_fusion_post" title="post-processing to identify fusion genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tophat Fusion Post</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=blockbuster" title="detects blocks of overlapping reads using a gaussian-distribution approach"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">blockbuster</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rbc_kinwalker" title="cotranscriptional folding of RNAs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kinwalker</button></a>
@@ -1122,31 +1282,43 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=rsem_prepare_reference" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RSEM prepare reference</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rsem_calculate_expression" title="RNA-Seq by Expectation-Maximization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RSEM calculate expression</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=extract_transcript_to_gene_map_from_trinity" title="extract transcript to gene map from trinity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RSEM trinity fasta to gene map</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=genomic_super_signature" title="interpretation of RNAseq experiments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GenomicSuperSignature</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=barrnap" title="Locate ribosomal RNA's in a fasta file. (GFF output)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">barrnap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circexplorer2" title="circular RNA analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CIRCexplorer2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cemitool" title="gene co-expression network analyses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CEMiTool</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cherri_train" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Train a CheRRI model using RRIs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mirnature" title="Computational detection of canonical microRNAs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">miRNAture</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cherri_eval" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Evaluation of RRIs using CheRRI</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=isoformswitchanalyzer" title="statistical identification of isoform switching"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IsoformSwitchAnalyzeR</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sleuth" title="differential expression analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sleuth</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=trinity_stats" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trinity Stats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=psiclass" title="reference-based transcriptome assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PsiCLASS</button></a>
 <h3>Peak Calling</h3>
-<a href="https://usegalaxy.eu/root?tool_id=peakcalling_ccat" title="Control-based ChIP-seq Analysis Tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CCAT</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=peakcalling_macs" title="Model-based Analysis of ChIP-Seq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=peakcalling_sicer" title="Statistical approach for the Identification of ChIP-Enriched Regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SICER</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=genrich" title="Detecting sites of genomic enrichment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Genrich</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=diffbind" title="differential binding analysis of ChIP-Seq peak data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DiffBind</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=macs2_bdgcmp" title="Deduct noise by comparing two signal tracks in bedGraph"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 bdgcmp</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pileometh" title="A tool for processing bisulfite sequencing alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MethylDackel</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=macs2_bdgbroadcall" title="Call broad peaks from bedGraph output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 bdgbroadcall</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=macs2_refinepeak" title="Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 refinepeak</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=macs2_bdgcmp" title="Deduct noise by comparing two signal tracks in bedGraph"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 bdgcmp</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=macs2_bdgdiff" title="Differential peak detection based on paired four bedgraph files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 bdgdiff</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=macs2_bdgpeakcall" title="Call peaks from bedGraph output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 bdgpeakcall</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=macs2_callpeak" title="Call peaks from alignment results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 callpeak</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=macs2_filterdup" title="Remove duplicate reads at the same position"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 filterdup</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=macs2_predictd" title="Predict 'd' or fragment size from alignment results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 predictd</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=macs2_randsample" title="Randomly sample number or percentage of total reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 randsample</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=macs2_filterdup" title="Remove duplicate reads at the same position"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 filterdup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=macs2_callpeak" title="Call peaks from alignment results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 callpeak</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=macs2_refinepeak" title="Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 refinepeak</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=peakcalling_macs" title="Model-based Analysis of ChIP-Seq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=peakcalling_sicer" title="Statistical approach for the Identification of ChIP-Enriched Regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SICER</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=peakcalling_ccat" title="Control-based ChIP-seq Analysis Tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CCAT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=genrich" title="Detecting sites of genomic enrichment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Genrich</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=peakzilla" title="Identify transcription factor binding sites from ChIP-seq and ChIP-exo experiments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Peakzilla</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=diffbind" title="differential binding analysis of ChIP-Seq peak data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DiffBind</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=peakachu" title="Calls Peaks in CLIP data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PEAKachu</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=zerone" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">zerone</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pureclip" title="- HMM based peak caller designed for eCLIP/iCLIP data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PureCLIP</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=jamm" title="Calls peaks on NGS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JAMM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=piranha" title="peak-caller for CLIP- and RIP-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Piranha</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=piranha" title="peak-caller for CLIP- and RIP-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Piranha</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=p_clip_peaks" title="find CLIP peaks in blockbuster data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CLIP Peakcaller</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=htseq_clip" title="- A toolset for the analysis of eCLIP/iCLIP datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">htseq-clip</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dewseq" title="- A sliding window based peak caller for eCLIP/iCLIP data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DEWSeq</button></a>
 <h3>Epigenetics</h3>
-<a href="https://usegalaxy.eu/root?tool_id=bwameth" title="Fast and accurate aligner of BS-Seq reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bwameth</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pileometh" title="A tool for processing bisulfite sequencing alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MethylDackel</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hifive" title="manipulate, analyze, and plot HiC and 5C chromatin interaction data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hifive</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcf_filter" title="a VCF file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=seacr" title="for sparse enrichment analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SEACR</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=moabs" title="MOdel based Analysis of Bisulfite Sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MOABS</button></a>
@@ -1173,42 +1345,39 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=hicup_deduplicator" title="removes duplicated di-tags (retaining one copy of each) from the data set."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hicup Deduplicator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=epicseg_segment" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EpiCSeg - Chromatin segmentation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicup_mapper" title="aligns paired reads independently to a reference genome and retains reads where both partners align."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hicup Mapper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cooler_makebins" title="Generate fixed-width genomic bins."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cooler_makebins</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cooler_csort_tabix" title="Sort and index a contact list."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cooler csort with tabix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cooler_cload_tabix" title="Create a cool file from a tabix-indexed contact file and a list of genomic bins."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cooler_cload_tabix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cooler_balance" title="Copy and balance a cool file."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cooler_balance</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicup2juicer" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hicup to juicer converter</button></a>
 <h3>Phylogenetics</h3>
-<a href="https://usegalaxy.eu/root?tool_id=pangolin" title="Phylogenetic Assignment of Outbreak Lineages"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pangolin</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=nextalign" title="Viral genome sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NextAlign</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=nextclade" title="Viral genome clade assignment, mutation calling, and sequence quality checks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nextclade</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=raxml" title="Maximum Likelihood based inference of large phylogenetic trees"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RAxML</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hyphy_prime" title="Property Informed Models of Evolution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-PRIME</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hyphy_busted" title="Branch-site Unrestricted Statistical Test for Episodic Diversification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-BUSTED</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hyphy_bgm" title="- Detecting coevolving sites via Bayesian graphical models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-BGM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hyphy_gard" title="Genetic Algorithm for Recombination Detection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-GARD</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hyphy_absrel" title="adaptive Branch Site Random Effects Likelihood"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-aBSREL</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snp_dists" title="Compute distance in SNPs between all sequences in a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SNP distance matrix</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hyphy_summary" title="generate summary report of HyPhy analyses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-Summary</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hyphy_relax" title="Detect relaxed selection in a codon-based    phylogenetic framework"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-RELAX</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hyphy_strike_ambigs" title="in a multiple alignment using HyPhy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace ambiguous codons</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hyphy_fubar" title="Fast Unconstrained Bayesian AppRoximation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-FUBAR</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hyphy_gard" title="Genetic Algorithm for Recombination Detection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-GARD</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hyphy_fel" title="Fixed Effects Likelihood"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-FEL</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hyphy_slac" title="Single Likelihood Ancestor Counting"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-SLAC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hyphy_meme" title="Mixed Effects Model of Evolution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-MEME</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hyphy_prime" title="Property Informed Models of Evolution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-PRIME</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hyphy_bgm" title="- Detecting coevolving sites via Bayesian graphical models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-BGM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hyphy_cfel" title="Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-CFEL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hyphy_fade" title=": FUBAR* Approach to Directional Evolution (*Fast    Unconstrained Bayesian Approximation)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-FADE</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hyphy_sm19" title="Partition Tree using Modified Slatkin-Maddison Test"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-SM2019</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hyphy_conv" title="translate an in-frame codon alignment to proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-Conv</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hyphy_annotate" title="a newick tree with HyPhy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Annotate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hyphy_meme" title="Mixed Effects Model of Evolution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-MEME</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hyphy_slac" title="Single Likelihood Ancestor Counting"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-SLAC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hyphy_fel" title="Fixed Effects Likelihood"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-FEL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=t_coffee" title="multiple sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">T-Coffee</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hyphy_relax" title="Detect relaxed selection in a codon-based    phylogenetic framework"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-RELAX</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=usher_matutils" title="analyze, edit, and manipulate mutation annotated tree files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UShER matUtils</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=usher" title="ultrafast sample placement on existing trees"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UShER</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sarscov2formatter" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sarscov2formatter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=t_coffee" title="multiple sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">T-Coffee</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=raxml" title="- Maximum Likelihood based inference of large phylogenetic trees"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyogenetic reconstruction with RAxML</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gstf_preparation" title="converts data for the workflow"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GeneSeqToFamily preparation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=phyml" title="Phylogeny software based on the maximum-likelihood method."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PhyML</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phyml" title="Phylogeny software based on the maximum-likelihood method"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PhyML</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sarscov2summary" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sarscov2summary</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pangolin" title="Phylogenetic Assignment of Outbreak Lineages"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pangolin</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ete_gene_csv_finder" title="from a genetree using the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gene Copy Number Finder</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hcluster_sg_parser" title="converts hcluster_sg 3-column output into lists of IDs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hcluster_sg parser</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ete_lineage_generator" title="from a list of species/taxids using the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ETE lineage generator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ete_species_tree_generator" title="from a list of species using the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ETE species tree generator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ete_genetree_splitter" title="from a genetree using the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ETE GeneTree splitter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ete_homology_classifier" title="from a genetree utilising the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Homology Classifier and Filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ete_homology_classifier" title="from a genetree using the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Homology Classifier and Filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ete_init_taxdb" title="generates the ETE sqlite DB from the NCBI taxdump.tar.gz"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ETE taxa DB generator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ete3_mod" title="manipulates tree topology by rooting, pruning or sorting branches"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ETE mod</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=treebest_best" title="Generate a phylogenetic tree using CDS alignment and species tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TreeBeST best</button></a>
@@ -1218,6 +1387,24 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=fasta_header_converter" title="to append species information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTA header converter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hcluster_sg" title="Hierarchically clustering on a sparse graph"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hcluster_sg</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=blast_parser" title="Convert 12- or 24-column BLAST output into 3-column hcluster_sg input"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BLAST parser</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=nextalign" title="Viral genome sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NextAlign</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=nextclade" title="Viral genome clade assignment, mutation calling, and sequence quality checks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nextclade</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hyphy_conv" title="translate an in-frame codon alignment to proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-Conv</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hyphy_annotate" title="a newick tree with HyPhy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Annotate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hyphy_strike_ambigs" title="in a multiple alignment using HyPhy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace ambiguous codons</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hyphy_cfel" title="Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-CFEL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hyphy_summary" title="generate summary report of HyPhy analyses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-Summary</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snp_dists" title="Compute distance in SNPs between all sequences in a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SNP distance matrix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picrust2_add_descriptions" title="column to a function abundance table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PICRUSt2 Add descriptions</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picrust2_hsp" title="to predict gene family abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PICRUSt2 Hidden state prediction (HSP)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picrust2_metagenome_pipeline" title="to generate per-sample metagenome functional profiles based on the predicted functions for each study sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PICRUSt2 Metagenome prediction</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picrust2_pathway_pipeline" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PICRUSt2 Pathway abundance inference</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picrust2_pipeline" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PICRUSt2 Full pipeline</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picrust2_place_seqs" title="into reference tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PICRUSt2 Sequence placement</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picrust2_shuffle_predictions" title="for a specified number of replicates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PICRUSt2 Generation of shuffled predictions</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.blast.relatedness.nuc" title="based on nucleotide blast results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Related Genomes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.blast.relatedness.prot" title="based on protein blast results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Related Genomes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xmfa2tbl" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert XMFA to percent identity table</button></a>
 <h3>Phenotype Association</h3>
 <a href="https://usegalaxy.eu/root?tool_id=vcf2pgSnp" title="Convert from VCF to pgSnp format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCF to pgSnp</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hgv_snpFreq" title="significant SNPs in case-control data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snpFreq</button></a>
@@ -1225,8 +1412,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=hgv_hilbertvis" title="visualization of genomic data with the Hilbert curve"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HVIS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dividePgSnp" title="into columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Separate pgSnp alleles</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctdBatch_1" title="analysis of chemicals, diseases, or genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CTD</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hgv_codingSnps" title="amino-acid changes caused by a set of SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">aaChanges</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hgv_add_scores" title="interspecies conservation scores"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">phyloP</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hgv_sift" title="predictions of functional sites"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SIFT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hgv_linkToGProfile" title="tools for functional profiling of gene lists"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">g:Profiler</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hgv_david" title="functional annotation for a list of genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DAVID</button></a>
@@ -1237,72 +1422,93 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=hgv_lps" title="LASSO-Patternsearch algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LPS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=master2pgSnp" title="Convert from MasterVar to pgSnp format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MasterVar to pgSnp</button></a>
 <h3>Single-cell</h3>
-<a href="https://usegalaxy.eu/root?tool_id=music_construct_eset" title="Create an ExpressionSet object from tabular and textual data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Construct Expression Set Object</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=music_deconvolution" title="estimate cell type proportions in bulk RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MuSiC Deconvolution</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=music_compare" title="estimate and compare cell type proportions in multiple sets of bulk RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MuSiC Compare</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=raceid_inspectclusters" title="examines gene expression within clusters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster Inspection using RaceID</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=raceid_filtnormconf" title="performs filtering, normalisation, and confounder removal to generate a normalised and filtered count matrix of single-cell RNA data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Initial processing using RaceID</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=raceid_clustering" title="performs clustering, outlier detection, dimensional reduction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clustering using RaceID</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=raceid_trajectory" title="generates lineage from prior clustering"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Lineage computation using StemID</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=raceid_inspecttrajectory" title="inspects branches of a lineage tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Lineage Branch Analysis using StemID</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scater_plot_pca" title="cell-level reduced dimension of a normalised SCE"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: PCA plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scater_filter" title="with user-defined parameters or PCA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: filter SCE</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scater_plot_tsne" title="of two components"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: t-SNE plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scater_create_qcmetric_ready_sce" title="from single-cell expression matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: calculate QC metrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scater_plot_dist_scatter" title="to visualise library size, feature counts and mito gene expression"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: plot library QC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=alevin" title="Quantification and analysis of 3’ tagged-end single-cell sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Alevin</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dropletutils" title="Utilities for handling droplet-based single-cell RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DropletUtils</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_plot" title="with scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_inspect" title="with scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Inspect and manipulate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_cluster_reduce_dimension" title="with scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster, infer trajectories and embed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=anndata_import" title="from different format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Import Anndata and loom</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=anndata_export" title="Interconvert AnnData and Loom formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Export AnnData and loom files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=anndata_manipulate" title="object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Manipulate AnnData</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=music_inspect_eset" title="Inspect an ExpressionSet object by a variety of attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Inspect Expression Set Object</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_filter" title="with scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_normalize" title="with scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Normalize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scanpy_cluster_reduce_dimension" title="with scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster, infer trajectories and embed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sceasy_convert" title="Convert between common single cell formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SCEasy Converter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=baredsc_1d" title="Compute distribution for a single gene"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">baredSC 1d</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scanpy_normalize" title="and impute with scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Normalize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scanpy_inspect" title="with scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Inspect and manipulate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=anndata_inspect" title="object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Inspect AnnData</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=anndata_export" title="Interconvert AnnData and Loom formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Export AnnData and loom files</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_remove_confounders" title="with scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove confounders</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=baredsc_combine_2d" title="from baredSC"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Combine multiple 2D Models</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=baredsc_combine_1d" title="from baredSC"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Combine multiple 1D Models</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=anndata_import" title="from different format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Import Anndata and loom</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=anndata_manipulate" title="object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Manipulate AnnData</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=modify_loom" title="Add layers, or row/column attributes to a loom file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Manipulate loom object</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dropletutils" title="Utilities for handling droplet-based single-cell RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DropletUtils</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dropletutils_read_10x" title="into SingleCellExperiment object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DropletUtils Read10x</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dropletutils_empty_drops" title="Distinguish between droplets containing cells and ambient RNA in a droplet-based single-cell RNA sequencing experiment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DropletUtils emptyDrops</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=alevin" title="Quantification and analysis of 3-prime tagged-end single-cell sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Alevin</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=music_deconvolution" title="estimate cell type proportions in bulk RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MuSiC Deconvolution</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_slice_image" title="into smaller patches"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slice Image</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_parameter_iterator" title="produce an iteration over a defined parameter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy ParameterIterator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scater_plot_tsne" title="of two components"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: t-SNE plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scater_plot_pca" title="cell-level reduced dimension of a normalised SCE"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: PCA plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scater_plot_exprs_freq" title="Plot the frequency of expression against the mean expression level for SCE"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: plot expression frequency</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scater_plot_dist_scatter" title="to visualise library size, feature counts and mito gene expression"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: plot library QC</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scater_normalize" title="Compute normalised expression values for SCE"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: normalize SCE</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scater_filter" title="with user-defined parameters or PCA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: filter SCE</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scater_create_qcmetric_ready_sce" title="from single-cell expression matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: calculate QC metrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=baredsc_2d" title="Compute distribution for a pair of genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">baredSC 2d</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=velocyto_cli" title="pre-process data for the analysis of RNA velocity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">velocyto CLI</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=raceid_inspectclusters" title="examines gene expression within clusters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster Inspection using RaceID</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=raceid_filtnormconf" title="performs filtering, normalisation, and confounder removal to generate a normalised and filtered count matrix of single-cell RNA data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Initial processing using RaceID</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=raceid_clustering" title="performs clustering, outlier detection, dimensional reduction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clustering using RaceID</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=raceid_trajectory" title="generates lineage from prior clustering"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Lineage computation using StemID</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=raceid_inspecttrajectory" title="inspects branches of a lineage tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Lineage Branch Analysis using StemID</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=music_construct_eset" title="Create an ExpressionSet object from tabular and textual data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Construct Expression Set Object</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=music_inspect_eset" title="Inspect an ExpressionSet object by a variety of attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Inspect Expression Set Object</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=music_compare" title="estimate and compare cell type proportions in multiple sets of bulk RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MuSiC Compare</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scran_normalize" title="Normalize raw counts expression values using deconvolution size factors"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scran_normalize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cite_seq_count" title="Count CMO/HTO"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CITE-seq-Count</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sinto_barcode" title="add cell barcodes to FASTQ read names"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sinto barcode</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sinto_fragments" title="Create an ATAC-seq fragment file from a BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sinto fragments</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=episcanpy_build_matrix" title="with EpiScanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build count matrix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=episcanpy_preprocess" title="with EpiScanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scATAC-seq Preprocessing</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=episcanpy_cluster_embed" title="with EpiScanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster, embed and annotate</button></a>
+<h3>Spatial Omics</h3>
+<a href="https://usegalaxy.eu/root?tool_id=mesmer" title="with Mesmer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform segmentation of multiplexed tissue data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=basic_illumination" title="ImageJ BaSiC shading correction for use with Ashlar"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BaSiC Illumination</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ashlar" title="Alignment by Simultaneous Harmonization of Layer/Adjacency Registration"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ASHLAR</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=unet_coreograph" title="TMA core detection and dearraying"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UNetCoreograph</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=unmicst" title="Image segmentation - probability map generation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UnMicst</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=s3segmenter" title="single cell (nuclei and cytoplasm) label masks."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">s3segmenter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=quantification" title="a module for single-cell data extraction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MCQUANT</button></a>
 <hr/><h2>Genomics Toolkits</h2>
 <h3>Picard</h3>
-<a href="https://usegalaxy.eu/root?tool_id=picard_FastqToSam" title="convert Fastq data into unaligned BAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastqToSam</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_CollectBaseDistributionByCycle" title="charts the nucleotide distribution per cycle in a SAM or BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectBaseDistributionByCycle</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_AddCommentsToBam" title="add comments to BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AddCommentsToBam</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=picard_AddOrReplaceReadGroups" title="add or replaces read group information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AddOrReplaceReadGroups</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_MeanQualityByCycle" title="chart distribution of base qualities"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MeanQualityByCycle</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_RevertOriginalBaseQualitiesAndAddMateCigar" title="revert the original base qualities and add the mate cigar tag"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RevertOriginalBaseQualitiesAndAddMateCigar</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_CollectHsMetrics" title="compute metrics about datasets generated through hybrid-selection (e.g. exome)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectHsMetrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_SortSam" title="sort SAM/BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SortSam</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_RevertSam" title="revert SAM/BAM datasets to a previous state"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RevertSam</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_FixMateInformation" title="ensure that all mate-pair information is in sync between each read and it's mate pair"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FixMateInformation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_BedToIntervalList" title="convert coordinate data into picard interval list format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BedToIntervalList</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_CleanSam" title="perform SAM/BAM grooming"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CleanSam</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=picard_CASM" title="writes a file containing summary alignment metrics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Collect Alignment Summary Metrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_NormalizeFasta" title="normalize fasta datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NormalizeFasta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_CollectBaseDistributionByCycle" title="charts the nucleotide distribution per cycle in a SAM or BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectBaseDistributionByCycle</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_CollectGcBiasMetrics" title="charts the GC bias metrics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectGcBiasMetrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_CollectHsMetrics" title="compute metrics about datasets generated through hybrid-selection (e.g. exome)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectHsMetrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_CollectInsertSizeMetrics" title="plots distribution of insert sizes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectInsertSizeMetrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_CollectRnaSeqMetrics" title="collect metrics about the alignment of RNA to various functional classes of loci in the genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectRnaSeqMetrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_artifact_metrics" title="Collect metrics to quantify single-base sequencing artifacts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Picard Collect Sequencing Artifact Metrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_CollectWgsMetrics" title="compute metrics for evaluating of whole genome sequencing experiments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectWgsMetrics</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=picard_DownsampleSam" title="Downsample a file to retain a subset of the reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Downsample SAM/BAM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_MergeBamAlignment" title="merge alignment data with additional info stored in an unmapped BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MergeBamAlignment</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_EstimateLibraryComplexity" title="assess sequence library complexity from read sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EstimateLibraryComplexity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_FastqToSam" title="convert Fastq data into unaligned BAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastqToSam</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_FilterSamReads" title="include or exclude aligned and unaligned reads and read lists"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FilterSamReads</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_FixMateInformation" title="ensure that all mate-pair information is in sync between each read and it's mate pair"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FixMateInformation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_MarkDuplicates" title="examine aligned records in BAM datasets to locate duplicate molecules"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MarkDuplicates</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=picard_MarkDuplicatesWithMateCigar" title="examine aligned records in BAM datasets to locate duplicate molecules"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MarkDuplicatesWithMateCigar</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_CleanSam" title="perform SAM/BAM grooming"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CleanSam</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_ReplaceSamHeader" title="replace header in a SAM/BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ReplaceSamHeader</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_MeanQualityByCycle" title="chart distribution of base qualities"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MeanQualityByCycle</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_MergeBamAlignment" title="merge alignment data with additional info stored in an unmapped BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MergeBamAlignment</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=picard_MergeSamFiles" title="merges multiple SAM/BAM datasets into one"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MergeSamFiles</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_MarkDuplicates" title="examine aligned records in BAM datasets to locate duplicate molecules"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MarkDuplicates</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_ValidateSamFile" title="assess validity of SAM/BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ValidateSamFile</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_NormalizeFasta" title="normalize fasta datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NormalizeFasta</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=picard_QualityScoreDistribution" title="chart quality score distribution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QualityScoreDistribution</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_CollectRnaSeqMetrics" title="collect metrics about the alignment of RNA to various functional classes of loci in the genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectRnaSeqMetrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_BedToIntervalList" title="convert coordinate data into picard interval list format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BedToIntervalList</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_CollectWgsMetrics" title="compute metrics for evaluating of whole genome sequencing experiments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectWgsMetrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_artifact_metrics" title="Collect metrics to quantify single-base sequencing artifacts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Picard Collect Sequencing Artifact Metrics</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=picard_ReorderSam" title="reorder reads to match ordering in reference sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ReorderSam</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_CollectGcBiasMetrics" title="charts the GC bias metrics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectGcBiasMetrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_FilterSamReads" title="include or exclude aligned and unaligned reads and read lists"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FilterSamReads</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_AddCommentsToBam" title="add comments to BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AddCommentsToBam</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_ReplaceSamHeader" title="replace header in a SAM/BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ReplaceSamHeader</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_RevertOriginalBaseQualitiesAndAddMateCigar" title="revert the original base qualities and add the mate cigar tag"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RevertOriginalBaseQualitiesAndAddMateCigar</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_RevertSam" title="revert SAM/BAM datasets to a previous state"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RevertSam</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=picard_SamToFastq" title="extract reads and qualities from SAM/BAM dataset and convert to fastq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SamToFastq</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_EstimateLibraryComplexity" title="assess sequence library complexity from read sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EstimateLibraryComplexity</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_CollectInsertSizeMetrics" title="plots distribution of insert sizes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectInsertSizeMetrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_SortSam" title="sort SAM/BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SortSam</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_ValidateSamFile" title="assess validity of SAM/BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ValidateSamFile</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=PicardASMetrics" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SAM/BAM Alignment Summary Metrics</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=picard_BamIndexStats" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BAM Index Statistics</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=picard_ARRG" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add or Replace Groups</button></a>
@@ -1311,161 +1517,156 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=rgPicFixMate" title="for paired data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Paired Read Mate Fixer</button></a>
 <h3>deepTools</h3>
 <a href="https://usegalaxy.eu/root?tool_id=deeptools_bam_compare" title="normalizes and compares two BAM or CRAM files to obtain the ratio, log2ratio or difference between them"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bamCompare</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deeptools_bam_pe_fragmentsize" title="Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bamPEFragmentSize</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deeptools_multi_bam_summary" title="calculates average read coverages for a list of two or more BAM/CRAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">multiBamSummary</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deeptools_compute_matrix" title="prepares data for plotting a heatmap or a profile of given regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">computeMatrix</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deeptools_plot_enrichment" title="plots read/fragment coverage over sets of regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plotEnrichment</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=deeptools_bam_coverage" title="generates a coverage bigWig file from a given BAM or CRAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bamCoverage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deeptools_bam_pe_fragmentsize" title="Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bamPEFragmentSize</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=deeptools_bigwig_compare" title="normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bigwigCompare</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=deeptools_plot_heatmap" title="creates a heatmap for score distributions across genomic regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plotHeatmap</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=deeptools_correct_gc_bias" title="uses the output from computeGCBias to generate GC-corrected BAM/CRAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">correctGCBias</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deeptools_alignmentsieve" title="Filter BAM/CRAM files according to specified parameters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">alignmentsieve</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deeptools_compute_matrix_operations" title="Modify or combine the output of computeMatrix in a variety of ways."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">computeMatrixOperations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deeptools_plot_fingerprint" title="plots profiles of BAM files; useful for assessing ChIP signal strength"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plotFingerprint</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deeptools_plot_coverage" title="assesses the sequencing depth of BAM/CRAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plotCoverage</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deeptools_plot_correlation" title="Create a heatmap or scatterplot of correlation scores between different samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plotCorrelation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deeptools_plot_profile" title="creates a profile plot for score distributions across genomic regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plotProfile</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deeptools_multi_bigwig_summary" title="calculates average scores for a list of two or more bigwig files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">multiBigwigSummary</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deeptools_compute_gc_bias" title="Determine the GC bias of your sequenced reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">computeGCBias</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deeptools_multi_bam_summary" title="calculates average read coverages for a list of two or more BAM/CRAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">multiBamSummary</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=deeptools_plot_pca" title="Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plotPCA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deeptools_compute_matrix" title="prepares data for plotting a heatmap or a profile of given regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">computeMatrix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deeptools_compute_gc_bias" title="Determine the GC bias of your sequenced reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">computeGCBias</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deeptools_multi_bigwig_summary" title="calculates average scores for a list of two or more bigwig files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">multiBigwigSummary</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deeptools_plot_profile" title="creates a profile plot for score distributions across genomic regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plotProfile</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deeptools_plot_correlation" title="Create a heatmap or scatterplot of correlation scores between different samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plotCorrelation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deeptools_plot_coverage" title="assesses the sequencing depth of BAM/CRAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plotCoverage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deeptools_plot_fingerprint" title="plots profiles of BAM files; useful for assessing ChIP signal strength"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plotFingerprint</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deeptools_compute_matrix_operations" title="Modify or combine the output of computeMatrix in a variety of ways."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">computeMatrixOperations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deeptools_alignmentsieve" title="Filter BAM/CRAM files according to specified parameters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">alignmentsieve</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deeptools_plot_enrichment" title="plots read/fragment coverage over sets of regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plotEnrichment</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=deeptools_estimatereadfiltering" title="estimates the number of reads that would be filtered given certain criteria"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">estimateReadFiltering</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicup_deduplicator" title="removes duplicated di-tags (retaining one copy of each) from the data set."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hicup Deduplicator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deeptools_bigwig_average" title="normalizes and average multiple bigWig files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bigwigAverage</button></a>
 <h3>Gemini</h3>
 <a href="https://usegalaxy.eu/root?tool_id=gemini_query" title="Querying the GEMINI database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI query</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gemini_annotate" title="the variants in an existing GEMINI database with additional information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI annotate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gemini_load" title="Loading a VCF file into GEMINI"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI load</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gemini_db_info" title="Retrieve information about tables, columns and annotation data stored in a GEMINI database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI database info</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gemini_load" title="Loading a VCF file into GEMINI"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI load</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gemini_pathways" title="Map genes and variants to KEGG pathways"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI pathways</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gemini_windower" title="Compute sliding window statistics from variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI windower</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gemini_inheritance" title="based identification of candidate genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI inheritance pattern</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gemini_interactions" title="Find genes among variants that are interacting partners"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI interactions</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gemini_qc" title="Quality control tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI qc</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gemini_set_somatic" title="Tag somatic mutations in a GEMINI database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI set_somatic</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gemini_roh" title="Identifying runs of homozygosity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI roh</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gemini_fusions" title="Identify somatic fusion genes from a GEMINI database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI fusions</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gemini_lof_sieve" title="Filter LoF variants by transcript position and type"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI lof_sieve</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gemini_actionable_mutations" title="Retrieve genes with actionable somatic mutations via COSMIC and DGIdb"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI actionable_mutations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gemini_annotate" title="the variants in an existing GEMINI database with additional information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI annotate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gemini_amend" title="Amend an already loaded GEMINI database."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI amend</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gemini_stats" title="Compute useful variant statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI stats</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gemini_gene_wise" title="Discover per-gene variant patterns across families"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI gene_wise</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gemini_burden" title="perform sample-wise gene-level burden calculations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI burden</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gemini_stats" title="Compute useful variant statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI stats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gemini_actionable_mutations" title="Retrieve genes with actionable somatic mutations via COSMIC and DGIdb"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI actionable_mutations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gemini_lof_sieve" title="Filter LoF variants by transcript position and type"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI lof_sieve</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gemini_fusions" title="Identify somatic fusion genes from a GEMINI database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI fusions</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gemini_roh" title="Identifying runs of homozygosity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI roh</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gemini_set_somatic" title="Tag somatic mutations in a GEMINI database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI set_somatic</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gemini_qc" title="Quality control tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI qc</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gemini_interactions" title="Find genes among variants that are interacting partners"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI interactions</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gemini_inheritance" title="based identification of candidate genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMINI inheritance pattern</button></a>
 <h3>EMBOSS</h3>
-<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: pepwheel72" title="Shows protein sequences as helices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pepwheel</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: wordcount109" title="Counts words of a specified size in a DNA sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">wordcount</button></a>
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+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: pepinfo69" title="Plots simple amino acid properties in parallel"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pepinfo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: megamerger53" title="Merge two large overlapping nucleic acid sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">megamerger</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: trimseq103" title="Trim ambiguous bits off the ends of sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">trimseq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: showfeat85" title="Show features of a sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">showfeat</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: palindrome65" title="Looks for inverted repeats in a nucleotide sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">palindrome</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: pasteseq66" title="Insert one sequence into another"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pasteseq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: lindna48" title="Draws linear maps of DNA constructs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">lindna</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: plotorf76" title="Plot potential open reading frames"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plotorf</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: etandem33" title="Looks for tandem repeats in a nucleotide sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">etandem</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: cai6" title="CAI codon adaptation index"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cai</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: dreg27" title="Regular expression search of a nucleotide sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dreg</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: syco96" title="Synonymous codon usage Gribskov statistic plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">syco</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: compseq14" title="Count composition of dimer/trimer/etc words in a sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">compseq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: sixpack90" title="Display a DNA sequence with 6-frame translation and ORFs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sixpack</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: btwisted5" title="Calculates the twisting in a B-DNA sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">btwisted</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: prettyseq80" title="Output sequence with translated ranges"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">prettyseq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: diffseq22" title="Find differences between nearly identical sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">diffseq</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: newseq59" title="Type in a short new sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">newseq</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: chaos7" title="Create a chaos game representation plot for a sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chaos</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: plotcon75" title="Plot quality of conservation of a sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plotcon</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: dottup26" title="Displays a wordmatch dotplot of two sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dottup</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: pepnet70" title="Displays proteins as a helical net"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pepnet</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: textsearch98" title="Search sequence documentation. Slow, use SRS and Entrez!"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">textsearch</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: chips10" title="Codon usage statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chips</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: prettyplot79" title="Displays aligned sequences, with colouring and boxing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">prettyplot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: fuzzpro38" title="Protein pattern search"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fuzzpro</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: primersearch81" title="Searches DNA sequences for matches with primer pairs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">primersearch</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: wobble108" title="Wobble base plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">wobble</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: vectorstrip106" title="Strips out DNA between a pair of vector sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">vectorstrip</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: seqmatchall83" title="All-against-all comparison of a set of sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqmatchall</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: wordcount109" title="Counts words of a specified size in a DNA sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">wordcount</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: shuffleseq87" title="Shuffles a set of sequences maintaining composition"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">shuffleseq</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: garnier40" title="Predicts protein secondary structure"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">garnier</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: trimest102" title="Trim poly-A tails off EST sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">trimest</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: cusp17" title="Create a codon usage table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cusp</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: dotpath25" title="Non-overlapping wordmatch dotplot of two sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dotpath</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: matcher52" title="Finds the best local alignments between two sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matcher</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: descseq21" title="Alter the name or description of a sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">descseq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: hmoment44" title="Hydrophobic moment calculation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmoment</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: einverted28" title="Finds DNA inverted repeats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">einverted</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: cirdna11" title="Draws circular maps of DNA constructs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cirdna</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: tmap99" title="Displays membrane spanning regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tmap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: nthseq62" title="Writes one sequence from a multiple set of sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">nthseq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: checktrans9" title="Reports STOP codons and ORF statistics of a protein"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">checktrans</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: cpgreport16" title="Reports all CpG rich regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cpgreport</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: polydot77" title="Displays all-against-all dotplots of a set of sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">polydot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: dan19" title="Calculates DNA RNA/DNA melting temperature"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dan</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: sirna89" title="Finds siRNA duplexes in mRNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sirna</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: pepcoil68" title="Predicts coiled coil regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pepcoil</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: isochore47" title="Plots isochores in large DNA sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">isochore</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: est2genome32" title="Align EST and genomic DNA sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">est2genome</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: epestfind29" title="Finds PEST motifs as potential proteolytic cleavage sites"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">epestfind</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: coderet13" title="Extract CDS, mRNA and translations from feature tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">coderet</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: fuzznuc37" title="Nucleic acid pattern search"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fuzznuc</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: charge8" title="Protein charge plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">charge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: freak36" title="Residue/base frequency table or plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">freak</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: biosed4" title="Replace or delete sequence sections"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">biosed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: twofeat104" title="Finds neighbouring pairs of features in sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">twofeat</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: wordmatch110" title="Finds all exact matches of a given size between 2 sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">wordmatch</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: backtranseq2" title="Back translate a protein sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">backtranseq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: antigenic1" title="Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">antigenic</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: dotmatcher24" title="Displays a thresholded dotplot of two sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dotmatcher</button></a>
 <h3>NCBI Blast</h3>
-<a href="https://usegalaxy.eu/root?tool_id=bbtools_bbduk" title="decontamination using kmers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: BBduk</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bg_diamond" title="alignment tool for short sequences against a protein database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diamond</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bg_diamond_makedb" title="Build database from a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diamond makedb</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bg_diamond_view" title="generate formatted output from DAA files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diamond view</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=taxonomy_krona_chart" title="from taxonomic profile"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krona pie chart</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bbtools_bbmap" title="short-read aligner"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: BBMap</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bbtools_callvariants" title="in aligned Bam files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: call variants</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=blastxml_to_tabular" title="Convert BLAST XML output to tabular"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BLAST XML to tabular</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=get_species_taxids" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI get species taxids</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_blastdbcmd_info" title="Show BLAST database information from blastdbcmd"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI BLAST+ database info</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_blastdbcmd_wrapper" title="Extract sequence(s) from BLAST database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI BLAST+ blastdbcmd entry(s)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_blastn_wrapper" title="Search nucleotide database with nucleotide query sequence(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI BLAST+ blastn</button></a>
@@ -1480,49 +1681,50 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_segmasker_wrapper" title="low-complexity regions in protein sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI BLAST+ segmasker</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_tblastn_wrapper" title="Search translated nucleotide database with protein query sequence(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI BLAST+ tblastn</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_tblastx_wrapper" title="Search translated nucleotide database with translated nucleotide query sequence(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI BLAST+ tblastx</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kraken-translate" title="convert taxonomy IDs to names"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken-translate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kraken-filter" title="filter classification by confidence score"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken-filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bg_diamond_view" title="generate formatted output from DAA files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diamond view</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bg_diamond" title="alignment tool for short sequences against a protein database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diamond</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bg_diamond_makedb" title="Build database from a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diamond makedb</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=magicblast" title="against a whole genome or transcriptome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Magic-BLAST: map large RNA or DNA sequences</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=blast_reciprocal_best_hits" title="from two FASTA files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BLAST Reciprocal Best Hits (RBH)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sample_seqs" title="e.g. to reduce coverage"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sub-sample sequences files</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=blastxml_to_top_descr" title="Make a table from BLAST output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BLAST top hit descriptions</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bbtools_callvariants" title="in aligned Bam files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: call variants</button></a>
 <h3>HiCExplorer</h3>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hictransform" title="transform a matrix to obs/exp, pearson and covariance matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicTransform</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hictadclassifier" title="TAD detection based on ML models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicTADClassifier</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicquickqc" title="get a first quality estimate of Hi-C data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicQuickQC</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicplotviewpoint" title="plot interactions around a viewpoint"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPlotViewpoint</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicplotmatrix" title="plot a Hi-C contact matrix heatmap"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPlotMatrix</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicfindtads" title="identify TAD boundaries by computing the degree of separation of each Hi-C matrix bin"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicFindTADs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hiccomparematrices" title="normalize and compare two Hi-C contact matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicCompareMatrices</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicaggregatecontacts" title="allow plotting of aggregated Hi-C contacts between regions specified in a file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicAggregateContacts</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicplotsvl" title="plots the relation of short vs long range contacts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPlotSVL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicplotaverageregions" title="plot the average regions from hicAverageRegions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPlotAverageRegions</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicnormalize" title="normalizes a matrix to norm range or smallest read count"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicNormalize</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicsummatrices" title="combine Hi-C matrices of the same size"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicSumMatrices</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicconvertformat" title="Convert between different file formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicConvertFormat</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicadjustmatrix" title="adjust the shape of a Hi-C matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicAdjustMatrix</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicinfo" title="get information about the content of a Hi-C matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicInfo</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hichyperoptDetectLoops" title="optimizes parameters for hicDetectLoops"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicHyperoptDetectLoops</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicdetectloops" title="searches for enriched regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicDetectLoops</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hiccorrelate" title="compute pairwise correlations between multiple Hi-C contact matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicCorrelate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hiccompartmentspolarization" title="compute pairwise correlations between multiple Hi-C contact matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicCompartmentalization</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicdifferentialtest" title="computes differential interactions of viewpoints"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicDifferentialTest</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=schicexplorer_schicqualitycontrol" title="quality control for single-cell Hi-C interaction matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scHicQualityControl</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicplotviewpoint" title="creates plots for viewpoints"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicPlotViewpoint</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicdifferentialtest" title="computes differential interactions of viewpoints"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicDifferentialTest</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicaggregatestatistic" title="computes with a target file the to be tested regions for chicDifferentialTest"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicAggregateStatistic</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicsignificantinteractions" title="computes viewpoints with the given reference points and a background model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicSignificantInteractions</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicviewpoint" title="computes viewpoints with the given reference points and a background model."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicViewpoint</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicdifferentialtad" title="searches for differential TADs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicDifferentialTAD</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicmergedomains" title="Merges TAD domains"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicMergeDomains</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicqualitycontrol" title="generates an estimate of the quality of each viewpoint"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicQualityControl</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicfindrestrictionsites" title="identify restriction enzyme sites"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicFindRestSite</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicviewpointbackgroundmodel" title="compute a background model for cHi-C / HiChIP data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicViewpointBackgroundModel</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicquickqc" title="get a first quality estimate of Hi-C data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicQuickQC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicbuildmatrix" title="create a contact matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicBuildMatrix</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicmergematrixbins" title="merge adjacent bins from a Hi-C contact matrix to reduce its resolution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicMergeMatrixBins</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hictransform" title="transform a matrix to obs/exp, pearson and covariance matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicTransform</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hiccompartmentspolarization" title="compute pairwise correlations between multiple Hi-C contact matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicCompartmentalization</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hiccorrelate" title="compute pairwise correlations between multiple Hi-C contact matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicCorrelate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicdetectloops" title="searches for enriched regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicDetectLoops</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicmergeloops" title="merge detected loops of different resolutions."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicMergeLoops</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicvalidatelocations" title="validate detected loops with protein peaks."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicValidateLocations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hiccorrectmatrix" title="run a Hi-C matrix correction algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicCorrectMatrix</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicpca" title="compute the principal components for A / B compartment analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPCA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicplotaverageregions" title="plot the average regions from hicAverageRegions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPlotAverageRegions</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicplotmatrix" title="plot a Hi-C contact matrix heatmap"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPlotMatrix</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicplotdistvscounts" title="compute distance vs Hi-C counts plot per chromosome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPlotDistVsCounts</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicpca" title="compute the principal components for A / B compartment analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPCA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicfindtads" title="identify TAD boundaries by computing the degree of separation of each Hi-C matrix bin"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicFindTADs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicvalidatelocations" title="validate detected loops with protein peaks."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicValidateLocations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicmergeloops" title="merge detected loops of different resolutions."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicMergeLoops</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hiccomparematrices" title="normalize and compare two Hi-C contact matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicCompareMatrices</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicaverageregions" title="sums Hi-C contacts around given reference points and computes their average."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicAverageRegions</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicplotsvl" title="plots the relation of short vs long range contacts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPlotSVL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicaggregatecontacts" title="allow plotting of aggregated Hi-C contacts between regions specified in a file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicAggregateContacts</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hiccorrectmatrix" title="run a Hi-C matrix correction algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicCorrectMatrix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicsummatrices" title="combine Hi-C matrices of the same size"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicSumMatrices</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicmergematrixbins" title="merge adjacent bins from a Hi-C contact matrix to reduce its resolution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicMergeMatrixBins</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicconvertformat" title="Convert between different file formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicConvertFormat</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicadjustmatrix" title="adjust the shape of a Hi-C matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicAdjustMatrix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicbuildmatrix" title="create a contact matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicBuildMatrix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicfindrestrictionsites" title="identify restriction enzyme sites"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicFindRestSite</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicinfo" title="get information about the content of a Hi-C matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicInfo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicviewpointbackgroundmodel" title="compute a background model for cHi-C / HiChIP data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicViewpointBackgroundModel</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicqualitycontrol" title="generates an estimate of the quality of each viewpoint"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicQualityControl</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=schicexplorer_schiccorrectmatrices" title="correct with KR algorithm single-cell Hi-C interaction matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scHicCorrectMatrices</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=schicexplorer_schicplotconsensusmatrices" title="plot single-cell Hi-C interaction matrices cluster consensus matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scHicPlotConsensusMatrices</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=schicexplorer_schicplotclusterprofiles" title="plot single-cell Hi-C interaction matrices cluster profiles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scHicPlotClusterProfiles</button></a>
@@ -1538,23 +1740,28 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=schicexplorer_schicclustercompartments" title="clusters single-cell Hi-C interaction matrices with A/B compartments dimension reduction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scHicClusterCompartments</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=schicexplorer_schiccluster" title="clusters single-cell Hi-C interaction matrices on the raw data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scHicCluster</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=schicexplorer_schicadjustmatrix" title="clusters single-cell Hi-C interaction matrices on the raw data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scHicAdjustMatrix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicexportdata" title="exports data of hdf to txt based files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicExportData</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicdifferentialtad" title="searches for differential TADs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicDifferentialTAD</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicinterintratad" title="computes the ratio of inter TAD-scores vs. intra TADs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicInterIntraTAD</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicmergedomains" title="Merges TAD domains"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicMergeDomains</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hictraintadclassifier" title="train a TAD detection ML model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicTrainTADClassifier</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicplottads" title="plot Hi-C contact matrices heatmaps alongside other data tracks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPlotTADs</button></a>
 <h3>RAD-seq</h3>
+<a href="https://usegalaxy.eu/root?tool_id=BayeScan" title="Detecting natural selection from population-based genetic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BayeScan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=stacks_assembleperead" title="run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks: assemble read pairs by locus</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=stacks_cstacks" title="build a catalogue of loci"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks: cstacks</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=stacks2_shortreads" title="fast cleaning of randomly sheared genomic or transcriptomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks2: process shortreads</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=stacks2_kmerfilter" title="Identify PCR clones"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks2: kmer filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=stacks2_clonefilter" title="Identify PCR clones"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks2: clone filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=stacks2_tsv2bam" title="Sort reads by RAD locus"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks2: tsv2bam</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=stacks2_refmap" title="the Stacks pipeline with a reference genome (ref_map.pl)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks2: reference map</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=stacks2_denovomap" title="the Stacks pipeline without a reference genome (denovo_map.pl)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks2: de novo map</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=stacks2_procrad" title="the Stacks demultiplexing script"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks2: process radtags</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=stacks2_populations" title="Calculate population-level summary statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks2: populations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=stacks2_gstacks" title="Call variants, genotypes and haplotype"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks2: gstacks</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=stacks2_ustacks" title="Identify unique stacks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks2: ustacks</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=stacks2_kmerfilter" title="Identify PCR clones"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks2: kmer filter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=stacks2_clonefilter" title="Identify PCR clones"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks2: clone filter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=stacks2_tsv2bam" title="Sort reads by RAD locus"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks2: tsv2bam</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=stacks2_sstacks" title="Match samples to the catalog"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks2: sstacks</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=BayeScan" title="Detecting natural selection from population-based genetic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BayeScan</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=stacks_assembleperead" title="run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks: assemble read pairs by locus</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=stacks_cstacks" title="build a catalogue of loci"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks: cstacks</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=stacks2_cstacks" title="Generate catalog of loci"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks2: cstacks</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=stacks2_ustacks" title="Identify unique stacks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks2: ustacks</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=stacks_populations" title="analyze a population of individual samples ('populations' program)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks: populations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=stacks_clonefilter" title="Identify PCR clones"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks: clone filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=stacks_stats" title="on stacks found for multiple samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks: statistics</button></a>
@@ -1601,104 +1808,71 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=mimodd_sort" title="takes a SAM/BAM dataset and generates a coordinate/name-sorted copy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MiModD Sort</button></a>
 <hr/><h2>Metagenomics</h2>
 <h3>Metagenomic Analysis</h3>
-<a href="https://usegalaxy.eu/root?tool_id=drep_compare" title="compare a list of genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dRep compare</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=lotus2" title="fast OTU processing pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LotuS2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=customize_metaphlan_database" title="from the MetaPhlAn database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Customize the marker sequences and metadata</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=merge_metaphlan_tables" title="MetaPhlAn abundance tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=metabat2_jgi_summarize_bam_contig_depths" title="for MetaBAT2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate contig depths</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=last_al" title="finds local alignments between query sequences, and reference sequences."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LASTal</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=malt_run" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MALT analyzer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=maaslin2" title="Microbiome Multivariable Association with Linear Models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaAsLin 2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=est_abundance" title="Bayesian Reestimation of Abundance with KrakEN"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Estimate Abundance at Taxonomic Level</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=metaeuk_easy_predict" title="High-throughput gene discovery and annotation for large-scale eukaryotic metagenomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaEuk Easy Predict</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kraken2" title="assign taxonomic labels to sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kraken" title="assign taxonomic labels to sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kraken-report" title="view sample report of a classification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken-report</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kraken-mpa-report" title="view report of classification for multiple samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken-mpa-report</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=megan_sam2rma" title="from a DIAMOND or MALT sam file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAN: Generate a MEGAN rma6 file</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=megan_blast2rma" title="from BLAST output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAN: Generate RMA files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=megan_blast2lca" title="to produce a taxonomic classification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAN Blast2LCA: apply LCA alignment</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=metaphlan" title="to profile the composition of microbial communities"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaPhlAn</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bigscape" title="Construct sequence similarity networks of BGCs and group them into GCF"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BiG-SCAPE</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phyloseq_plot_ordination" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq: plot ordination</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_otu_network" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 OTU network plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_frequency" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 frequency plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kraken_taxonomy_report" title="view report of classification for multiple samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken taxonomic report</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recentrifuge" title="Robust comparative analysis and contamination removal for metagenomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Recentrifuge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=das_tool" title="for genome-resolved metagenomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DAS Tool</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_core" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 core community analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=extract_metaphlan_database" title="from the MetaPhlAn database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract the marker sequences and metadata</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=drep_dereplicate" title="De-replicate a list of genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dRep dereplicate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=metabat2" title="metagenome binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaBAT2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Kraken2Tax" title="data to Galaxy taxonomy representation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Kraken</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kraken-translate" title="convert taxonomy IDs to names"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken-translate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kraken-filter" title="filter classification by confidence score"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken-filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lotus2" title="fast OTU processing pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LotuS2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=maxbin2" title="clusters metagenomic contigs into bins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaxBin2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=polypolish" title="Short-read polishing of long-read bacterial genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Polypolish</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_alpha_diversity" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 alpha diversity</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=taxonomy_krona_chart" title="from taxonomic profile"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krona pie chart</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kraken_taxonomy_report" title="view report of classification for multiple samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken taxonomic report</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=instrain_profile" title="Creates an inStrain profile (microdiversity analysis) from a mapping file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InStrain Profile</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kraken-filter" title="filter classification by confidence score"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken-filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kraken-translate" title="convert taxonomy IDs to names"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken-translate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=semibin_generate_cannot_links" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Contig annotations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kleborate" title="screen genome assemblies of Klebsiella pneumoniae"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kleborate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kraken2" title="assign taxonomic labels to sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dada2_makeSequenceTable" title="construct a sequence table (analogous to OTU table)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: makeSequenceTable</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dada2_plotQualityProfile" title="plot a visual summary of the quality scores"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: plotQualityProfile</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dada2_mergePairs" title="Merge denoised forward and reverse reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: mergePairs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dada2_assignTaxonomyAddspecies" title="Learn Error rates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: assignTaxonomy and addSpecies</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dada2_makeSequenceTable" title="construct a sequence table (analogous to OTU table)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: makeSequenceTable</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dada2_learnErrors" title="Learn Error rates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: learnErrors</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dada2_removeBimeraDenovo" title="Remove bimeras from collections of unique sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: removeBimeraDenovo</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dada2_dada" title="Remove sequencing errors"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: dada</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dada2_filterAndTrim" title="Filter and trim short read data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: filterAndTrim</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann_strain_profiler" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make strain profiles</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann_split_stratified_table" title="into 2 tables (one stratified and one unstratified)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split a HUMAnN table</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann_rename_table" title="of a HUMAnN generated table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Rename features</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann_join_tables" title="gene, pathway, or taxonomy HUMAnN/MetaPhlAn tables into a single table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join (merge)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann_associate" title="on HUMAnN generated table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform metadata association</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann_regroup_table" title="HUMAnN table features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Regroup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann" title="to profile presence/absence and abundance of microbial pathways and gene families"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HUMAnN</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann_split_table" title="a merged HUMAnN table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann_renorm_table" title="a HUMAnN generated table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Renormalize</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann_barplot" title="stratified HUMAnN features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Barplot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bio_hansel" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Salmonella Subtyping</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=jellyfish" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">jellyfish</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann2" title="to profile presence/absence and abundance of microbial pathways and gene families"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HUMAnN2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=last_db" title="prepares sequences for subsequent comparison and alignment using lastal."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LASTdb</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=last_split" title="finds 'split alignments' (typically for DNA) or 'spliced alignments' (typically for RNA)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LAST-split</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=last_train" title="finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LAST-train</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=last_maf_convert" title="read MAF-format alignments and write them in another format."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAF-convert</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=khmer_abundance_distribution_single" title="Calculate abundance distribution of k-mers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">khmer: Abundance Distribution (all-in-one)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=khmer_partition" title="Load, partition, and annotate sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">khmer: Sequence partition all-in-one</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=khmer_count_median" title="Count the median/avg k-mer abundance for each sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">khmer: Count Median</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=khmer_abundance_distribution" title="Calculate abundance distribution of k-mers using pre-made k-mer countgraphs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">khmer: Abundance Distribution</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=khmer_filter_below_abundance_cutoff" title="below k-mer abundance of 50"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">khmer: Filter reads</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=khmer_filter_abundance" title="by minimal k-mer abundance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">khmer: Filter reads</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=staramr_search" title="Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">staramr</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scoary" title="calculates the assocations between all genes in the accessory genome and the traits"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scoary</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=khmer_extract_partitions" title="Separate sequences that are annotated with partitions into grouped files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">khmer: Extract partitions</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=khmer_normalize_by_median" title="Filter reads using digital normalization via k-mer abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">khmer: Normalize By Median</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann_reduce_table" title="a joined HUMAnN table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Reduce</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann_rna_dna_norm" title="combined meta'omic sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Normalize</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann_unpack_pathways" title="to show the genes for each"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unpack pathway abundances</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mash_screen" title="determines how well query sequences are contained within a pool of sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mash screen</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dada2_seqCounts" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: sequence counts</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dada2_plotComplexity" title="Plot sequence complexity profile"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: plotComplexity</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=instrain_compare" title="Compares multiple inStrain profiles (popANI, coverage_overlap, etc.)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InStrain Compare</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dada2_learnErrors" title="Learn Error rates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: learnErrors</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dada2_dada" title="Remove sequencing errors"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: dada</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dada2_removeBimeraDenovo" title="Remove bimeras from collections of unique sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: removeBimeraDenovo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dada2_filterAndTrim" title="Filter and trim short read data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: filterAndTrim</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=metaeuk_easy_predict" title="High-throughput gene discovery and annotation for large-scale eukaryotic metagenomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaEuk Easy Predict</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=staramr_search" title="Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">staramr</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=last_train" title="finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LAST-train</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mt2mq" title="Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MT2MQ</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann2_join_tables" title="HUMAnN2 generated tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vsearch_search" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VSearch search</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann2_associate" title="HUMAnN2 functions with metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Associate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann2_barplot" title="stratified HUMAnN2 features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Barplot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann2_genefamilies_genus_level" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a genus level gene families file</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann2_reduce_table" title="a HUMAnN2 generated table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Reduce</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann2_regroup_table" title="a HUMAnN2 generated table by features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Regroup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann2_rename_table" title="features of a HUMAnN2 generated table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Rename</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann2_renorm_table" title="a HUMAnN2 generated table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Renormalize</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann2_rna_dna_norm" title="combined meta'omic sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Normalize</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann2_split_stratified_table" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split stratified table</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann2_split_table" title="a HUMAnN2 generated table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann2_strain_profiler" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make strain profiles</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=humann2_unpack_pathways" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unpack pathway abundances to show genes included</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=last_al" title="finds local alignments between query sequences, and reference sequences."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LASTal</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=drep_dereplicate" title="De-replicate a list of genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dRep dereplicate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=drep_compare" title="compare a list of genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dRep compare</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=last_db" title="prepares sequences for subsequent comparison and alignment using lastal."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LASTdb</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=last_split" title="finds 'split alignments' (typically for DNA) or 'spliced alignments' (typically for RNA)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LAST-split</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=last_maf_convert" title="read MAF-format alignments and write them in another format."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAF-convert</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mash_screen" title="determines how well query sequences are contained within a pool of sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mash screen</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metagene_annotator" title="gene-finding program for prokaryote and phage (used by sixgill)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaGeneAnnotator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mash_sketch" title="Create a reduced representation of a sequence or set of sequences, based on min-hashes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mash sketch</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sixgill_merge" title="metapeptide databases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sixgill merge</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sixgill_filter" title="a metapeptide database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sixgill filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sixgill_build" title="a metapeptide database from metagenome fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sixgill build</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sixgill_makefasta" title="from a metapeptide database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sixgill makefasta</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cat_contigs" title="annotate with taxonomic classification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CAT contigs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=srst2" title="Short Read Sequence Typing for Bacterial Pathogens"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SRST2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cat_bins" title="annotate with taxonomic classification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CAT bins</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cat_contigs" title="annotate with taxonomic classification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CAT contigs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=khmer_filter_abundance" title="by minimal k-mer abundance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">khmer: Filter reads</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=khmer_filter_below_abundance_cutoff" title="below k-mer abundance of 50"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">khmer: Filter reads</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=khmer_extract_partitions" title="Separate sequences that are annotated with partitions into grouped files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">khmer: Extract partitions</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=khmer_abundance_distribution" title="Calculate abundance distribution of k-mers using pre-made k-mer countgraphs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">khmer: Abundance Distribution</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=khmer_count_median" title="Count the median/avg k-mer abundance for each sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">khmer: Count Median</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=khmer_partition" title="Load, partition, and annotate sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">khmer: Sequence partition all-in-one</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=khmer_normalize_by_median" title="Filter reads using digital normalization via k-mer abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">khmer: Normalize By Median</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=khmer_abundance_distribution_single" title="Calculate abundance distribution of k-mers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">khmer: Abundance Distribution (all-in-one)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kraken" title="assign taxonomic labels to sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kraken-report" title="view sample report of a classification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken-report</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cat_add_names" title="annotate with taxonomic names"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CAT add_names</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cat_summarise" title="the number of contigs or bins assigned to each taxonomic name"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CAT summarise</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cat_prepare" title="a database for CAT - Contig Annotation Tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CAT prepare</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=maxbin2" title="clusters metagenomic contigs into bins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaxBin2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=group_humann2_uniref_abundances_to_go" title="of UniRef50 gene families obtained (HUMAnN2 output) to Gene Ontology (GO) slim terms"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Group abundances</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=PlasFlow" title="Prediction of plasmid sequences in metagenomic contigs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PlasFlow</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kraken-mpa-report" title="view report of classification for multiple samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken-mpa-report</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vegan_diversity" title="index"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Vegan Diversity</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vegan_fisher_alpha" title="index"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Vegan Fisher Alpha</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vegan_rarefaction" title="curve and statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Vegan Rarefaction</button></a>
@@ -1709,16 +1883,111 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=vsearch_alignment" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VSearch alignment</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vsearch_dereplication" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VSearch dereplication</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vsearch_shuffling" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VSearch shuffling</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=compare_humann2_output" title="and extract similar and specific information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare outputs of HUMAnN2 for several samples</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=combine_metaphlan2_humann2" title="to relate genus/species abundances and gene families/pathways abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Combine MetaPhlAn2 and HUMAnN2 outputs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=format_metaphlan2_output" title="output to extract abundance at different taxonomic levels"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Format MetaPhlAn2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=valet" title="to detect mis-assemblies in metagenomic assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VALET</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=data_source_gdcwebapp" title="an intuitive interface to filter, extract, and convert Genomic Data Commons experiments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDCWebApp</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bio_hansel" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Salmonella Subtyping</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nonpareil" title="to estimate average coverage and generate Nonpareil curves"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nonpareil</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=metaphlan2" title="to profile the composition of microbial communities"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaPhlAn2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metaphlan2krona" title="output for Krona"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Format MetaPhlAn2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=merge_metaphlan_tables" title="MetaPhlAn abundance tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metaphlan_hclust_heatmap" title="with hierarchical clustering of both samplesand microbial clades for MetaPhlAn2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate heatmap</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metagenomeseq_normalizaton" title="Cumulative sum scaling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metagenomeSeq Normalization</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Kraken2Tax" title="data to Galaxy taxonomy representation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Kraken</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scoary" title="calculates the assocations between all genes in the accessory genome and the traits"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scoary</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=jellyfish" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">jellyfish</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=humann" title="to profile presence/absence and abundance of microbial pathways and gene families"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HUMAnN</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=humann_associate" title="on HUMAnN generated table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform metadata association</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=humann_barplot" title="stratified HUMAnN features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Barplot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=humann_join_tables" title="gene, pathway, or taxonomy HUMAnN/MetaPhlAn tables into a single table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join (merge)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=humann_reduce_table" title="a joined HUMAnN table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Reduce</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=humann_regroup_table" title="HUMAnN table features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Regroup</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=humann_rename_table" title="of a HUMAnN generated table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Rename features</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=humann_renorm_table" title="a HUMAnN generated table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Renormalize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=humann_rna_dna_norm" title="combined meta'omic sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Normalize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=humann_split_stratified_table" title="into 2 tables (one stratified and one unstratified)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split a HUMAnN table</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=humann_split_table" title="a merged HUMAnN table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=humann_strain_profiler" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make strain profiles</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=humann_unpack_pathways" title="to show the genes for each"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unpack pathway abundances</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=metaphlan" title="to profile the composition of microbial communities"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaPhlAn</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=customize_metaphlan_database" title="from the MetaPhlAn database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Customize the marker sequences and metadata</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=metabat2" title="metagenome binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaBAT2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_boxplot" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 boxplot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_export_fasta" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 export fasta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_heatmap" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 heatmap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_load" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 load</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_merge_ampvis2" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 merge ampvis2 data sets</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_mergereplicates" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 merge replicates</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_octave" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 octave plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_ordinate" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 ordination plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_rankabundance" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 rank abundance plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_rarecurve" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 rarefaction curve</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_setmetadata" title="types"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 set metadata</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_subset_samples" title="by sample metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 subset samples</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_subset_taxa" title="by taxonomy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 subset data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_timeseries" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 timeseries plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_venn" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 venn diagram</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqsero2" title="Salmonella serotype prediction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqSero2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=est_abundance" title="to re-estimate abundance at a taxonomic level from kraken output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bracken</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=coverm_contig" title="Calculate read coverage per contig"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CoverM contig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=coverm_genome" title="Calculate coverage of individual genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CoverM genome</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Fasta_to_Contig2Bin" title="to scaffolds-to-bin table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Converts genome bins in fasta format</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phyloseq_from_dada2" title="from dada2 sequence and taxonomy tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create phyloseq object</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phyloseq_from_biom" title="from a BIOM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create phyloseq object</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=virannot_blast2tsv" title="convert XML blast results to tabular file with taxonomic informations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virAnnot Blast2tsv</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=virannot_otu" title="create viral OTUs based on RPS and Blast annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virAnnot OTU</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=virAnnot_rps2tsv" title="Convert xml rpstblast results to tab file with taxonomic informations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virAnnot Rps2tsv</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phyloseq_plot_richness" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq: plot alpha diverstiy measure</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=metabat2_jgi_summarize_bam_contig_depths" title="for MetaBAT2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate contig depths</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=semibin" title="for Semi-supervised Metagenomic Binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=semibin_bin" title="into bins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Group the contigs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=semibin_concatenate_fasta" title="for multi-sample binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Concatenate fasta files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=semibin_generate_sequence_features" title="(kmer and abundance) as training data for semi-supervised deep learning model training"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Generate sequence features</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=semibin_train" title="the semi-supervised deep learning model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Train</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=instrain_profile" title="Creates an inStrain profile (microdiversity analysis) from a mapping file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InStrain Profile</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=instrain_compare" title="Compares multiple inStrain profiles (popANI, coverage_overlap, etc.)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InStrain Compare</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=maaslin2" title="Microbiome Multivariable Association with Linear Models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaAsLin 2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=malt_run" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MALT analyzer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=megan_sam2rma" title="from a DIAMOND or MALT sam file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAN: Generate a MEGAN rma6 file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=megan_blast2rma" title="from BLAST output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAN: Generate RMA files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=megan_blast2lca" title="to produce a taxonomic classification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAN Blast2LCA: apply LCA alignment</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bin_refiner" title="refines metagenome bins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Binning refiner</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=concoct" title="for metagenome binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CONCOCT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=concoct_coverage_table" title="for CONCOCT"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CONCOCT: Generate the input coverage table</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=concoct_cut_up_fasta" title="in non-overlapping or overlapping parts of equal length"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CONCOCT: Cut up contigs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=concoct_extract_fasta_bins" title="for each cluster"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CONCOCT: Extract a fasta file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=concoct_merge_cut_up_clustering" title="and assign concensus clusters for the original contigs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CONCOCT: Merge cut clusters</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=megan_daa2info" title="about a DIAMOND file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAN: Get information</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=megan_daa2rma" title="from a DIAMOND daa file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAN: Generate a MEGAN rma6 file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=megan_daa_meganizer" title="for use with MEGAN"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAN: meganize a DIAMOND file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=megan_read_extractor" title="by classification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAN: Extract reads</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=itsx" title="identifies ITS sequences and extracts the ITS region"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ITSx</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=aldex2" title="differential abundance analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ALDEx2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ancombc" title="differential abundance analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ANCOM-BC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=checkm_taxonomy_wf" title="Analyze all genome bins with the same marker set"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM taxonomy_wf</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=checkm_tree" title="Place bins in the genome tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM tree</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=checkm_lineage_wf" title="Assessing the completeness and contamination of genome bins using lineage-specific marker sets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM lineage_wf</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=checkm_tree_qa" title="Assess phylogenetic markers in the genome tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM tree_qa</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=checkm_analyze" title="Identify marker genes in bins and calculate genome statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM analyze</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=checkm_tetra" title="Calculate tetranucleotide signature of sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM tetra</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=checkm_qa" title="Assess bins for contamination and completeness"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM qa</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=checkm_taxon_set" title="Generate taxonomic-specific marker set"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM taxon_set</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=checkm_plot" title="for assessing the quality of genome bins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=checkm_lineage_set" title="Infer lineage-specific marker sets for each bin"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM lineage_set</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kraken_biom" title="Create BIOM-format tables from kraken output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken-biom</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vapor" title="Classify Influenza samples from short reads sequence data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VAPOR</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dram_strainer" title="down to genes of interest"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DRAM strain annotations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dram_distill" title="metagenome-assembled-genomes (MAGs)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DRAM distill</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dram_annotate" title="metagenome-assembled-genomes (MAGs)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DRAM annotate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dram_merge_annotations" title="into a single set"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DRAM merge multiple annotations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dram_neighborhoods" title="around genes of interest"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DRAM find neighborhoods</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=krakentools_kreport2krona" title="to krona text file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krakentools: Convert kraken report file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=krakentools_beta_diversity" title="from Kraken, Krona and Bracken files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krakentools: calculates beta diversity (Bray-Curtis dissimilarity)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=krakentools_alpha_diversity" title="from the Bracken abundance estimation file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krakentools: Calculates alpha diversity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=krakentools_kreport2mpa" title="to MetaPhlAn-style"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krakentools: Convert kraken report file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=krakentools_combine_kreports" title="into a combined report file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krakentools: Combine multiple Kraken reports</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=krakentools_extract_kraken_reads" title="Extract reads that were classified by the Kraken family at specified taxonomic IDs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krakentools: Extract Kraken Reads By ID</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=combine_metaphlan_humann" title="to relate genus/species abundances and gene families/pathways abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Combine MetaPhlAn and HUMAnN outputs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mapseq" title="sequence read classification designed to assign taxonomy and OTU classifications"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAPseq</button></a>
 <h3>Qiime</h3>
 <a href="https://usegalaxy.eu/root?tool_id=qiime_collapse_samples" title="Collapse samples in a BIOM table and mapping file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Collapse samples</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime_make_otu_table" title="Make an OTU table from an OTU map and a taxonomy assignment file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make OTU table</button></a>
@@ -1890,6 +2159,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=mothur_get_coremicrobiome" title="fraction of OTUs for samples or abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get.coremicrobiome</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mothur_chimera_uchime" title="Find putative chimeras using uchime"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Chimera.uchime</button></a>
 <h3>DNA Metabarcoding</h3>
+<a href="https://usegalaxy.eu/root?tool_id=obi_tab" title="converts sequence file to a tabular file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">obitab</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=obi_stat" title="computes basic statistics for attribute values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">obistat</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=obi_sort" title="sorts sequence records according to the value of a given attribute"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">obisort</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=obi_convert" title="converts sequence files to different output formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">obiconvert</button></a>
@@ -1897,98 +2167,91 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=obi_uniq" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">obiuniq</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=obi_grep" title="Filters sequence file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">obigrep</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=obi_annotate" title="Adds/Edits sequence record annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">obiannotate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=obi_illumina_pairend" title="Construct consensus reads from Illumina pair-end reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Illuminapairedend</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=obi_ngsfilter" title="Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NGSfilter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=obi_tab" title="converts sequence file to a tabular file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">obitab</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=obi_illumina_pairend" title="Construct consensus reads from Illumina pair-end reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Illuminapairedend</button></a>
+<h3>Data and Metadata Management</h3>
+<a href="https://usegalaxy.eu/root?tool_id=raster_template" title="attributes for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates for raster files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eal_table_template" title="attributes and categorical variables for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates for data tables</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eal_templates" title="for core features of a data package for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=makeeml" title="Create EML from EAL templates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make EML</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eml2eal" title="Create EAL templates from EML metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EML to EAL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=geo_cov_template" title="for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make geographic coverage template</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=taxo_cov_template" title="for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make taxonomic coverage template</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vector_template" title="attributes for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates for vector files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=entities_template" title="for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make entities templates for raster, vector and other entities files</button></a>
 <h3>Virology</h3>
-<a href="https://usegalaxy.eu/root?tool_id=read_it_and_keep" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Read It and Keep</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lineagespot" title="identifies SARS-CoV-2 lineages contributing to metagenomic samples from per-sample variant files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">lineagespot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snipit" title="Summarise snps relative to a reference sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snipit</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=varvamp" title="design primers for highly diverse viruses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">varVAMP</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ivar_consensus" title="Call consensus from aligned BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ivar consensus</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ivar_removereads" title="Remove reads from trimmed BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ivar removereads</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ivar_trim" title="Trim reads in aligned BAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ivar trim</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ivar_getmasked" title="Detect primer mismatches and get primer indices for the amplicon to be masked"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ivar getmasked</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ivar_variants" title="Call variants from aligned BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ivar variants</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ivar_filtervariants" title="Filter variants across replicates or multiple samples aligned using the same reference"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ivar filtervariants</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ivar_consensus" title="Call consensus from aligned BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ivar consensus</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ivar_getmasked" title="Detect primer mismatches and get primer indices for the amplicon to be masked"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ivar getmasked</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=read_it_and_keep" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Read It and Keep</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=freyja_variants" title="and get sequencing depth information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Freyja: Call variants</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=freyja_demix" title="lineage abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Freyja: Demix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=freyja_boot" title="method"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Freyja: Bootstrapping</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=freyja_aggregate_plot" title="demixed results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Freyja: Aggregate and visualize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cooc_mutbamscan" title="scans an alignment file for mutation co-occurrences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cojac: mutbamscan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cooc_pubmut" title="pretty-prints cojac mutbamscan co-occurrence results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cojac: pubmut</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cooc_tabmut" title="exports co-occurrence results from mutbamscan as a table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cojac: tabmut</button></a>
 <hr/><h2>Proteomics, Metabolomics, Chemistry</h2>
 <h3>Proteomics</h3>
-<a href="https://usegalaxy.eu/root?tool_id=eggnog_mapper" title="functional sequence annotation by orthology"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eggNOG Mapper</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=proteinortho_summary" title="summaries the orthology-pairs/RBH files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteinortho summary</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=OpenPepXL" title="Tool for protein-protein cross-linking identification using labeled linkers."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenPepXL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=XFDR" title="Calculates false discovery rate estimates on crosslink identifications"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">XFDR</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=PercolatorAdapter" title="Facilitate input to Percolator and reintegrate."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PercolatorAdapter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=metaquantome_sample" title="by specifying the experiment's groups and associated column names"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaQuantome: create samples file</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fasta_cli" title="Appends decoy sequences to FASTA files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastaCLI</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ident_params" title="Sets the identification parameters to be used in SearchGUI and PeptideShaker apps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Identification Parameters</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=maxquant_mqpar" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaxQuant (using mqpar.xml)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=search_gui" title="Perform protein identification using various search engines and prepare results for input to Peptide Shaker"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Search GUI</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=XMLValidator" title="Validates XML files against an XSD schema."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">XMLValidator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=OpenSwathConfidenceScoring" title="Compute confidence scores for OpenSwath results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathConfidenceScoring</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=PeakPickerIterative" title="Finds mass spectrometric peaks in profile mass spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PeakPickerIterative</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=RNPxlXICFilter" title="Remove MS2 spectra from treatment based on the fold change between control and treatment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNPxlXICFilter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=MassTraceExtractor" title="Detects mass traces in centroided LC-MS data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MassTraceExtractor</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ERPairFinder" title="Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ERPairFinder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=FileMerger" title="Merges several MS files into one file."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FileMerger</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=FeatureFinderMRM" title="Detects two-dimensional features in LC-MS data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureFinderMRM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ConsensusID" title="Computes a consensus of peptide identifications of several identification engines."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ConsensusID</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=SpectraFilterMarkerMower" title="Applies thresholdfilter to peak spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpectraFilterMarkerMower</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=BaselineFilter" title="Removes the baseline from profile spectra using a top-hat filter."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BaselineFilter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=TextExporter" title="Exports various XML formats to a text file."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TextExporter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=proteinortho_summary" title="summaries the orthology-pairs/RBH files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteinortho summary</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=proteinortho_grab_proteins" title="finds genes/proteins in a given fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteinortho grab proteins</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=proteinortho" title="detects orthologous proteins/genes within different species"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteinortho</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=proteomiqon_labeledproteinquantification" title="estimates protein abundances using quantified peptide ions."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteomiqon LabeledProteinQuantification</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=proteomiqon_joinquantpepionswithproteins" title="combines the results from ProteinInference and PSMBasedQuantification."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteomiqon JoinQuantPepIonsWithProteins</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=proteomiqon_psmbasedquantification" title="allows label-free quantification as well as quantification of full metabolic labeled samples."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteomiqon PSMBasedQuantification</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cardinal_combine" title="combine several mass spectrometry imaging datasets into one"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI combine</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cardinal_spectra_plots" title="mass spectrometry imaging mass spectra plots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI plot spectra</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cardinal_preprocessing" title="mass spectrometry imaging preprocessing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI preprocessing</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cardinal_quality_report" title="mass spectrometry imaging QC"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI Qualitycontrol</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cardinal_mz_images" title="mass spectrometry imaging m/z heatmaps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI mz images</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cardinal_data_exporter" title="exports imzML and Analyze7.5 to tabular files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI data exporter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cardinal_segmentations" title="mass spectrometry imaging spatial clustering"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI segmentation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cardinal_filtering" title="tool for filtering mass spectrometry imaging data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI filtering</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=proteomiqon_psmstatistics" title="utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProteomIQon PSMStatistics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=msstats" title="statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSstats</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=proteomiqon_proteininference" title="uses identified peptides to infere proteins explaining their presence in the sample."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProteomIQon ProteinInference</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=msstatstmt" title="protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSstatsTMT</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=peptide_shaker" title="Perform protein identification using various search engines based on results from SearchGUI"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Peptide Shaker</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=proteomiqon_peptidedb" title="creates a peptide database in the SQLite format."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProteomIQon PeptideDB</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=diann" title="is a software for DIA/SWATH data processing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DIA-NN</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pepquery2_show_sets" title="PepQueryDB datasets, Parameters, PTMs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PepQuery2 Show Sets</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pepquery2" title="Peptide-centric search engine for novel peptide identification and validation."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PepQuery2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=maxquant" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaxQuant</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=proteomiqon_mzmltomzlite" title="converts mzML files to mzLite files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProteomIQon MzMLToMzLite</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=diffacto" title="Comparative Protein Abundance from Covariation of Peptide Abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diffacto</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cardinal_classification" title="spatial classification of mass spectrometry imaging data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI classification</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=msstatstmt" title="protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSstatsTMT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=msstats" title="statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSstats</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metaquantome_viz" title="taxonomic analysis, functional analysis, and function-taxonomy analysis results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaQuantome: visualize</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metaquantome_stat" title="differential analysis of functional expression and taxonomic abundance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaQuantome: stat</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=metaquantome_filter" title="for quality, redundancy, and sample coverage"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaQuantome: filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metaquantome_expand" title="a set of functional or taxonomy annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaQuantome: expand</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=idpassemble" title="Merge IDPicker databases from single files into a merged database, and filters the result at PSM/spectrum/peptide/protein/gene levels."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idpAssemble</button></a>
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-<a href="https://usegalaxy.eu/root?tool_id=idpqonvert" title="Prepare identification results for IDPicker"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idpQonvert</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=encyclopedia_fasta_to_prosit_csv" title="Create Prosit CSV Input From a Protein FASTA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ConvertFastaToPrositCSV</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=encyclopedia_quantify" title="samples from Data-Independent Acquisition (DIA) MS/MS Data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EncyclopeDIA Quantify</button></a>
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-<a href="https://usegalaxy.eu/root?tool_id=encyclopedia_library_to_blib" title="Convert EncyclopeDIA Library to BLIB for Skyline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ConvertLibraryToBlib</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pepquery" title="Peptide-centric search engine for novel peptide identification and validation."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PepQuery</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=peptide_genomic_coordinate" title="Get Peptide's genomic coordinate using mzsqlite DB and genomic mapping sqlite DB"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Peptide Genomic Coordinate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ConsensusID" title="Computes a consensus of peptide identifications of several identification engines."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ConsensusID</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=encyclopedia_prosit_csv_to_library" title="Convert Prosit/Spectronaut CSV to EncyclopeDIA DLIB library"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ConvertPrositCSVToLibrary</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=myrimatch" title="Identify peptides in tandem mass spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MyriMatch</button></a>
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 <a href="https://usegalaxy.eu/root?tool_id=metaquantome_db" title="download the GO, EC, and NCBI databases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaQuantome: database</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=maxquant_mqpar" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaxQuant (using mqpar.xml)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=metaquantome_filter" title="for quality, redundancy, and sample coverage"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaQuantome: filter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=proteomiqon_peptidespectrummatching" title="iterates across all MS/MS scans in an MS run, determines precursor charge states and possible peptide spectrum matches."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProteomIQon PeptideSpectrumMatching</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=proteinortho_grab_proteins" title="finds genes/proteins in a given fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteinortho grab proteins</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=orthofinder_onlygroups" title="finds orthogroups in a set of proteomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OrthoFinder</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=validate_fasta_database" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Validate FASTA Database</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=proteomiqon_labelfreeproteinquantification" title="estimates protein abundances using quantified peptide ions."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteomiqon LabelFreeProteinQuantification</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=feature_alignment" title="integrates information from all available runs via a graph-based alignment strategy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRIC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eggnog_mapper" title="functional sequence annotation by orthology"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eggNOG Mapper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cardinal_combine" title="combine several mass spectrometry imaging datasets into one"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI combine</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=PSMFeatureExtractor" title="Computes extra features for each input PSM."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PSMFeatureExtractor</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=meta_proteome_analyzer" title="functional and taxonomic characterization of proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaProteomeAnalyzer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=metaquantome_sample" title="by specifying the experiment's groups and associated column names"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaQuantome: create samples file</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mztab2tsv" title="convert mztab to tabular"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pyteomics</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dialignr" title="for retention time alignment of targeted mass spectrometric data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DIAlignR</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fastg2protlib-peptides" title="Generate FASTA from FASTG"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTG2Protlib-Peptides</button></a>
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-<a href="https://usegalaxy.eu/root?tool_id=NovorAdapter" title="Template for Tool creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NovorAdapter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=NovorAdapter" title="Performs de novo sequencing of peptides from MS/MS data with Novor."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NovorAdapter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=LuciphorAdapter" title="Modification site localisation using LuciPHOr2."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LuciphorAdapter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=AssayGeneratorMetabo" title="Assay library generation from DDA data (Metabolomics)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AssayGeneratorMetabo</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=SiriusAdapter" title="Tool for metabolite identification using single and tandem mass spectrometry"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SiriusAdapter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=MSFraggerAdapter" title="Peptide Identification with MSFragger"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSFraggerAdapter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=MSFraggerAdapter" title="Peptide Identification with MSFragger.Important note:The Regents of the University of Michigan (“Michigan”) grants us permission to redistribute    the MS Fragger application developed by Michigan within the OpenMS Pipeline and make available for use on related service offerings supported by the University of Tubingen and the Center forIntegrative Bioinformatics.                                                                    Per the license agreement the use of the pipeline and associated materials is for academic     research, non-commercial or educational purposes. Any commercial use inquiries                 must be directed to the University of Michigan Technology Transfer Office at                   techtransfer@umich.edu. All right title and interest in MS Fragger shall remain with the       University of Michigan.For details, please see the supplied license file or                                           https://raw.githubusercontent.com/OpenMS/THIRDPARTY/master/All/MSFragger/License.txt"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSFraggerAdapter</button></a>
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+<a href="https://usegalaxy.eu/root?tool_id=cardinal_spectra_plots" title="mass spectrometry imaging mass spectra plots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI plot spectra</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cardinal_mz_images" title="mass spectrometry imaging m/z heatmaps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI mz images</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cardinal_preprocessing" title="mass spectrometry imaging preprocessing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI preprocessing</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=PeakPickerHiRes" title="Finds mass spectrometric peaks in profile mass spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PeakPickerHiRes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=RNAMassCalculator" title="Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAMassCalculator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=QualityControl" title="Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QualityControl</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=RNPxlXICFilter" title="Remove MS2 spectra from treatment based on the fold change between control and treatment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNPxlXICFilter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=OpenSwathConfidenceScoring" title="Compute confidence scores for OpenSwath results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathConfidenceScoring</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MultiplexResolver" title="Completes peptide multiplets and resolves conflicts within them."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MultiplexResolver</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=psmvalidator" title="Validate PSMs against Ion Fragmentation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PSM-Fragment Validator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_remove_protonation_state" title="of every atom"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove protonation state</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=idpquery" title="Creates text reports from idpDB files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idpQuery</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=OpenSwathFeatureXMLToTSV" title="Converts a featureXML to a mProphet tsv."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathFeatureXMLToTSV</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=OpenSwathDIAPreScoring" title="Scoring spectra using the DIA scores."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathDIAPreScoring</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MapStatistics" title="Extract extended statistics on the features of a map for quality control."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MapStatistics</button></a>
@@ -2005,7 +2268,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=MRMTransitionGroupPicker" title="Picks peaks in SRM/MRM chromatograms."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MRMTransitionGroupPicker</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MapAlignerIdentification" title="Corrects retention time distortions between maps based on common peptide identifications."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MapAlignerIdentification</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=IsobaricAnalyzer" title="Calculates isobaric quantitative values for peptides"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IsobaricAnalyzer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ERPairFinder" title="Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ERPairFinder</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ClusterMassTraces" title="Creates pseudo spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ClusterMassTraces</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ClusterMassTracesByPrecursor" title="Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ClusterMassTracesByPrecursor</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CometAdapter" title="Annotates MS/MS spectra using Comet."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CometAdapter</button></a>
@@ -2017,69 +2279,64 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=QCExporter" title="Will extract several qp from several run/sets in a tabular format."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCExporter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=SpectraFilterNormalizer" title="Normalizes intensity of peak spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpectraFilterNormalizer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=InternalCalibration" title="Applies an internal mass recalibration."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InternalCalibration</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=MassTraceExtractor" title="Detects mass traces in centroided LC-MS data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MassTraceExtractor</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=PepNovoAdapter" title="Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PepNovoAdapter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Digestor" title="Digests a protein database in-silico."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Digestor</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=PepNovoAdapter" title="Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PepNovoAdapter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=PeptideIndexer" title="Refreshes the protein references for all peptide hits."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PeptideIndexer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MapRTTransformer" title="Applies retention time transformations to maps."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MapRTTransformer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=OpenSwathAssayGenerator" title="Generates assays according to different models for a specific TraML"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathAssayGenerator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=DTAExtractor" title="Extracts spectra of an MS run file to several files in DTA format."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DTAExtractor</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=SequenceCoverageCalculator" title="Prints information about idXML files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SequenceCoverageCalculator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=OpenSwathAssayGenerator" title="Generates assays according to different models for a specific TraML"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathAssayGenerator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MetaProSIP" title="Performs proteinSIP on peptide features for elemental flux analysis."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaProSIP</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=SequenceCoverageCalculator" title="Prints information about idXML files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SequenceCoverageCalculator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ProteinQuantifier" title="Compute peptide and protein abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProteinQuantifier</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=IDConflictResolver" title="Resolves ambiguous annotations of features with peptide identifications"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDConflictResolver</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=PeakPickerWavelet" title="Finds mass spectrometric peaks in profile mass spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PeakPickerWavelet</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ProteinQuantifier" title="Compute peptide and protein abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProteinQuantifier</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=PeakPickerIterative" title="Finds mass spectrometric peaks in profile mass spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PeakPickerIterative</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Decharger" title="Decharges and merges different feature charge variants of the same peptide."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Decharger</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FuzzyDiff" title="Compares two files, tolerating numeric differences."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FuzzyDiff</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Decharger" title="Decharges and merges different feature charge variants of the same peptide."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Decharger</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MzMLSplitter" title="Splits an mzML file into multiple parts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MzMLSplitter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FileConverter" title="Converts between different MS file formats."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FileConverter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=MassCalculator" title="Calculates masses and mass-to-charge ratios of peptide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MassCalculator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=SpectraFilterNLargest" title="Applies thresholdfilter to peak spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpectraFilterNLargest</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=MassCalculator" title="Calculates masses and mass-to-charge ratios of peptide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MassCalculator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=SpectraFilterThresholdMower" title="Applies thresholdfilter to peak spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpectraFilterThresholdMower</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MapAlignerPoseClustering" title="Corrects retention time distortions between maps using a pose clustering approach."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MapAlignerPoseClustering</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=QCEmbedder" title="Attaches a table or an image to a given qc parameter."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCEmbedder</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Epifany" title="Runs a Bayesian protein inference."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Epifany</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=SpectraFilterThresholdMower" title="Applies thresholdfilter to peak spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpectraFilterThresholdMower</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=SpectraMerger" title="Merges spectra (each MS level separately), increasing S/N ratios."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpectraMerger</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=OpenSwathDecoyGenerator" title="Generates decoys according to different models for a specific TraML"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathDecoyGenerator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=PTModel" title="Trains a model for the prediction of proteotypic peptides from a training set."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PTModel</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=OpenSwathDecoyGenerator" title="Generates decoys according to different models for a specific TraML"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathDecoyGenerator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ProteinInference" title="Protein inference based on an aggregation of the scores of the identified peptides."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProteinInference</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=TargetedFileConverter" title="Converts different transition files for targeted proteomics / metabolomics analysis."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TargetedFileConverter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=TextExporter" title="Exports various XML formats to a text file."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TextExporter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=TOFCalibration" title="Applies time of flight calibration."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TOFCalibration</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=TransformationEvaluation" title="Applies a transformation to a range of values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TransformationEvaluation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=XMLValidator" title="Validates XML files against an XSD schema."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">XMLValidator</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ProteinInference" title="Protein inference based on an aggregation of the scores of the identified peptides."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProteinInference</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=IDRipper" title="Split protein/peptide identification file into several files according to identification run and annotated file origin."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDRipper</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=SvmTheoreticalSpectrumGeneratorTrainer" title="Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SvmTheoreticalSpectrumGeneratorTrainer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=IDRipper" title="Split protein/peptide identification file into several files according to annotated file origin."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDRipper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=MascotAdapterOnline" title="Annotates MS/MS spectra using Mascot."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MascotAdapterOnline</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=SpectraSTSearchAdapter" title="Interface to the SEARCH Mode of the SpectraST executable"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpectraSTSearchAdapter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=SpectraFilterSqrtMower" title="Applies thresholdfilter to peak spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpectraFilterSqrtMower</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=SpectraFilterMarkerMower" title="Applies thresholdfilter to peak spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpectraFilterMarkerMower</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=SemanticValidator" title="SemanticValidator for semantically validating certain XML files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemanticValidator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=SpecLibSearcher" title="Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpecLibSearcher</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=MascotAdapterOnline" title="Annotates MS/MS spectra using Mascot."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MascotAdapterOnline</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=LabeledEval" title="Evaluation tool for isotope-labeled quantitation experiments."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LabeledEval</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MapAlignerSpectrum" title="Corrects retention time distortions between maps by spectrum alignment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MapAlignerSpectrum</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=SpecLibCreator" title="Creates an MSP formatted spectral library."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpecLibCreator</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=SemanticValidator" title="SemanticValidator for semantically validating certain XML files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemanticValidator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=MaRaClusterAdapter" title="Facilitate input to MaRaCluster and reintegrate."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaRaClusterAdapter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=SimpleSearchEngine" title="Annotates MS/MS spectra using SimpleSearchEngine."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SimpleSearchEngine</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=LabeledEval" title="Evaluation tool for isotope-labeled quantitation experiments."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LabeledEval</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=PrecursorIonSelector" title="PrecursorIonSelector"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PrecursorIonSelector</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=SeedListGenerator" title="Generates seed lists for feature detection."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeedListGenerator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=RTModel" title="Trains a model for the retention time prediction of peptides from a training set."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RTModel</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=MaRaClusterAdapter" title="Facilitate input to MaRaCluster and reintegrate."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaRaClusterAdapter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=RNPxlSearch" title="Annotate RNA/DNA-peptide cross-links in MS/MS spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNPxlSearch</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=PrecursorIonSelector" title="PrecursorIonSelector"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PrecursorIonSelector</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FeatureFinderCentroided" title="Detects two-dimensional features in LC-MS data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureFinderCentroided</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=RNPxlSearch" title="Annotate RNA/DNA-peptide cross-links in MS/MS spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNPxlSearch</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=SpectraFilterParentPeakMower" title="Applies thresholdfilter to peak spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpectraFilterParentPeakMower</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=TICCalculator" title="Calculates the TIC from a mass spectrometric raw file (useful for benchmarking)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TICCalculator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=IDFilter" title="Filters results from protein or peptide identification engines based on different criteria."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDFilter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=NucleicAcidSearchEngine" title="Annotate nucleic acid identifications to MS/MS spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NucleicAcidSearchEngine</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MRMMapper" title="MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MRMMapper</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=OMSSAAdapter" title="Annotates MS/MS spectra using OMSSA."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OMSSAAdapter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EICExtractor" title="Extracts intensities from dedicates positions in a LC/MS map"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EICExtractor</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MyriMatchAdapter" title="Annotates MS/MS spectra using MyriMatch."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MyriMatchAdapter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=IDFilter" title="Filters results from protein or peptide identification engines based on different criteria."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDFilter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=MSSimulator" title="A highly configurable simulator for mass spectrometry experiments."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSSimulator</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=BaselineFilter" title="Removes the baseline from profile spectra using a top-hat filter."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BaselineFilter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=NucleicAcidSearchEngine" title="Annotate nucleic acid identifications to MS/MS spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NucleicAcidSearchEngine</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=SpectraFilterBernNorm" title="Applies thresholdfilter to peak spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpectraFilterBernNorm</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CVInspector" title="A tool for visualization and validation of PSI mapping and CV files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CVInspector</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=MSSimulator" title="A highly configurable simulator for mass spectrometry experiments."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSSimulator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=RNADigestor" title="Digests an RNA sequence database in-silico."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNADigestor</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CVInspector" title="A tool for visualization and validation of PSI mapping and CV files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CVInspector</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cardinal_quality_report" title="mass spectrometry imaging QC"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI Qualitycontrol</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=DecoyDatabase" title="Create decoy sequence database from forward sequence database."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DecoyDatabase</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ExternalCalibration" title="Applies an external mass recalibration."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ExternalCalibration</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FalseDiscoveryRate" title="Estimates the false discovery rate on peptide and protein level using decoy searches."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FalseDiscoveryRate</button></a>
@@ -2087,7 +2344,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=FeatureFinderIsotopeWavelet" title="Detects two-dimensional features in LC-MS data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureFinderIsotopeWavelet</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FeatureFinderMetabo" title="Assembles metabolite features from centroided (LC-)MS data using the mass trace approach."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureFinderMetabo</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FeatureFinderMetaboIdent" title="Detects features in MS1 data based on metabolite identifications."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureFinderMetaboIdent</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=FeatureFinderMRM" title="Detects two-dimensional features in LC-MS data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureFinderMRM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FeatureFinderMultiplex" title="Determination of peak ratios in LC-MS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureFinderMultiplex</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FeatureLinkerUnlabeled" title="Groups corresponding features from multiple maps."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureLinkerUnlabeled</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FeatureLinkerUnlabeledKD" title="Groups corresponding features from multiple maps."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureLinkerUnlabeledKD</button></a>
@@ -2096,16 +2352,19 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=FidoAdapter" title="Runs the protein inference engine Fido."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FidoAdapter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FileFilter" title="Extracts or manipulates portions of data from peak, feature or consensus-feature files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FileFilter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FileInfo" title="Shows basic information about the file, such as data ranges and file type."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FileInfo</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=FileMerger" title="Merges several MS files into one file."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FileMerger</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=GNPSExport" title="Tool to export consensus features into MGF format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GNPSExport</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=GNPSExport" title="Tool to export representative consensus MS/MS scan per consensusElement into a .MGF file format.See the documentation on https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-openms"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GNPSExport</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=AccurateMassSearch" title="Match MS signals to molecules from a database by mass."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AccurateMassSearch</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=DatabaseFilter" title="Filters a protein database (FASTA format) based on identified proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DatabaseFilter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=DeMeanderize" title="Orders the spectra of MALDI spotting plates correctly."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeMeanderize</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FeatureFinderSuperHirn" title="Finds mass spectrometric features in mass spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureFinderSuperHirn</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cardinal_classification" title="spatial classification of mass spectrometry imaging data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI classification</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=OpenSwathMzMLFileCacher" title="This tool caches the spectra and chromatogram data of an mzML to disk."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathMzMLFileCacher</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=OpenSwathRewriteToFeatureXML" title="Combines featureXML and mProphet tsv to FDR filtered featureXML."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathRewriteToFeatureXML</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=IDPosteriorErrorProbability" title="Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDPosteriorErrorProbability</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=IDFileConverter" title="Converts identification engine file formats."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDFileConverter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cardinal_data_exporter" title="exports imzML and Analyze7.5 to tabular files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI data exporter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cardinal_segmentations" title="mass spectrometry imaging spatial clustering"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI segmentation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cardinal_filtering" title="tool for filtering mass spectrometry imaging data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI filtering</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=IDScoreSwitcher" title="Switches between different scores of peptide or protein hits in identification data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDScoreSwitcher</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MapAlignerTreeGuided" title="Tree guided correction of retention time distortions between maps."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MapAlignerTreeGuided</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MapNormalizer" title="Normalizes peak intensities in an MS run."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MapNormalizer</button></a>
@@ -2115,11 +2374,18 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=MSstatsConverter" title="Converter to input for MSstats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSstatsConverter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MzTabExporter" title="Exports various XML formats to an mzTab file."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MzTabExporter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=NoiseFilterGaussian" title="Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NoiseFilterGaussian</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=encyclopedia_encyclopedia" title="Library Searching Directly from Data-Independent Acquisition (DIA) MS/MS Data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EncyclopeDIA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=NoiseFilterSGolay" title="Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NoiseFilterSGolay</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=encyclopedia_fasta_to_prosit_csv" title="Create Prosit CSV Input From a Protein FASTA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ConvertFastaToPrositCSV</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=encyclopedia_quantify" title="samples from Data-Independent Acquisition (DIA) MS/MS Data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EncyclopeDIA Quantify</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=OpenPepXLLF" title="Tool for protein-protein cross linking with label-free linkers."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenPepXLLF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=encyclopedia_walnut" title="PeCAn-based Peptide Detection Directly from Data-Independent Acquisition (DIA) MS/MS Data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Walnut</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=encyclopedia_prosit_csv_to_library" title="Convert Prosit/Spectronaut CSV to EncyclopeDIA DLIB library"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ConvertPrositCSVToLibrary</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=OpenSwathChromatogramExtractor" title="Extract chromatograms (XIC) from a MS2 map file."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathChromatogramExtractor</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=OpenSwathAnalyzer" title="Picks peaks and finds features in an SWATH-MS or SRM experiment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathAnalyzer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=encyclopedia_searchtolib" title="Build a Chromatogram Library from Data-Independent Acquisition (DIA) MS/MS Data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SearchToLib</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=OpenSwathFileSplitter" title="Splits SWATH files into n files, each containing one window."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathFileSplitter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=encyclopedia_library_to_blib" title="Convert EncyclopeDIA Library to BLIB for Skyline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ConvertLibraryToBlib</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=OpenSwathRTNormalizer" title="This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathRTNormalizer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=PhosphoScoring" title="Scores potential phosphorylation sites in order to localize the most probable sites."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PhosphoScoring</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=HighResPrecursorMassCorrector" title="Corrects the precursor mass and charge determined by the instrument software."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HighResPrecursorMassCorrector</button></a>
@@ -2127,15 +2393,22 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=QCCalculator" title="Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCCalculator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CruxAdapter" title="Identifies MS/MS spectra using Crux."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CruxAdapter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ConsensusMapNormalizer" title="Normalizes maps of one consensusXML file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ConsensusMapNormalizer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=QCShrinker" title="This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCShrinker</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=QCImporter" title="Imports tables with quality control parameters into qcml files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCImporter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=SpectraFilterScaler" title="Applies thresholdfilter to peak spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpectraFilterScaler</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=QCShrinker" title="This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCShrinker</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=IDExtractor" title="Extracts 'n' peptides randomly or best 'n' from idXML files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDExtractor</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=QCExtractor" title="Extracts a table attachment to a given qc parameter."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCExtractor</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ProteinResolver" title="protein inference"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProteinResolver</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=IDExtractor" title="Extracts 'n' peptides randomly or best 'n' from idXML files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDExtractor</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=LowMemPeakPickerHiRes" title="Finds mass spectrometric peaks in profile mass spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LowMemPeakPickerHiRes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=LowMemPeakPickerHiResRandomAccess" title="Finds mass spectrometric peaks in profile mass spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LowMemPeakPickerHiResRandomAccess</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=maxquant_mqpar" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaxQuant (using mqpar.xml)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mt2mq" title="Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MT2MQ</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pepquery" title="Peptide-centric search engine for novel peptide identification and validation."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PepQuery</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=myrimatch" title="Identify peptides in tandem mass spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MyriMatch</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=idpqonvertEmbedder" title="Embed human/mouse gene metadata into IDPicker files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idpEmbedder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=idpqonvert" title="Prepare identification results for IDPicker"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idpQonvert</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=idpassemble" title="Merge IDPicker databases from single files into a merged database, and filters the result at PSM/spectrum/peptide/protein/gene levels."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idpAssemble</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pepquery2_index" title="MS/MS data for faster search"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PepQuery2 index</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pyprophet_export" title="Export tabular files, optional swath2stats export"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyProphet export</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=proteomics_moff" title="extracts MS1 intensities from spectrum files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">moFF</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=unipept" title="retrieve taxonomy for peptides"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unipept</button></a>
@@ -2150,12 +2423,15 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=pyprophet_subsample" title="Subsample OpenSWATH file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyProphet subsample</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=flashlfq" title="ultrafast label-free quantification for mass-spectrometry proteomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FlashLFQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=quantwiz_iq" title="Isobaric Quantitation using QuantWiz-IQ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QuantWiz-IQ</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=peptide_genomic_coordinate" title="Get Peptide's genomic coordinate using mzsqlite DB and genomic mapping sqlite DB"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Peptide Genomic Coordinate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=reactome_pathwaymatcher" title="PathwayMatcher is a software tool to search for pathways related to a list of proteins in Reactome."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pathway Matcher</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=peptide_shaker" title="Perform protein identification using various search engines based on results from SearchGUI"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Peptide Shaker</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rawtools" title="Perform scan data parsing, quantification and quality control analysis of Thermo Orbitrap raw mass spectrometer files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Raw Tools</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dia_umpire_se" title="DIA signal extraction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DIA_Umpire_SE</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=custom_pro_db" title="Generate protein FASTAs from exosome or transcriptome data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CustomProDB</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=quantp" title="Correlation between protein and transcript abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QuanTP</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=maldi_quant_preprocessing" title="Preprocessing of mass-spectrometry imaging data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MALDIquant preprocessing</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=search_gui" title="Perform protein identification using various search engines and prepare results for input to Peptide Shaker"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Search GUI</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pep_pointer" title="classify genomic location of peptides"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PepPointer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=megahit_contig2fastg" title="for converting MEGAHIT's contigs (.fa) to assembly graphs (.fastg)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">megahit contig2fastg</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=percolator_input_converters" title="to create Percolator input files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Search engine output to Pin converter</button></a>
@@ -2174,22 +2450,65 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=IDDecoyProbability" title="Estimates peptide probabilities using a decoy search strategy.WARNING: This util is deprecated."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDDecoyProbability</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=RNPxl" title="Tool for RNP cross linking experiment analysis."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNPxl</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=AdditiveSeries" title="Computes an additive series to quantify a peptide in a set of samples."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AdditiveSeries</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=idpquery" title="Creates text reports from idpDB files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idpQuery</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=TopPerc" title="Facilitate input to Percolator and reintegrate."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TopPerc</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=eden_protease_prediction" title="based on cleavage sites"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Protease prediction</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=decoyfasta" title="Creates a decoy search database by adding reverse    sequences to an existing database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create Decoy Database (reverse)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=morpheus" title="database search algorithm for high-resolution tandem mass spectra"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Morpheus</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fasta_cli" title="Appends decoy sequences to FASTA files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastaCLI</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ident_params" title="Sets the identification parameters to be used in SearchGUI and PeptideShaker apps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Identification Parameters</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=diffacto" title="Comparative Protein Abundance from Covariation of Peptide Abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diffacto</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=proteomiqon_mzmltomzlite" title="converts mzML files to mzLite files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProteomIQon MzMLToMzLite</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=proteomiqon_peptidedb" title="creates a peptide database in the SQLite format."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProteomIQon PeptideDB</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=proteomiqon_peptidespectrummatching" title="iterates across all MS/MS scans in an MS run, determines precursor charge states and possible peptide spectrum matches."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProteomIQon PeptideSpectrumMatching</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=proteomiqon_psmstatistics" title="utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProteomIQon PSMStatistics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=proteomiqon_proteininference" title="uses identified peptides to infere proteins explaining their presence in the sample."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProteomIQon ProteinInference</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=validate_fasta_database" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Validate FASTA Database</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=proteomiqon_psmbasedquantification" title="allows label-free quantification as well as quantification of full metabolic labeled samples."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteomiqon PSMBasedQuantification</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=proteomiqon_joinquantpepionswithproteins" title="combines the results from ProteinInference and PSMBasedQuantification."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteomiqon JoinQuantPepIonsWithProteins</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=proteomiqon_labeledproteinquantification" title="estimates protein abundances using quantified peptide ions."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteomiqon LabeledProteinQuantification</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=proteomiqon_labelfreeproteinquantification" title="estimates protein abundances using quantified peptide ions."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteomiqon LabelFreeProteinQuantification</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=feature_alignment" title="integrates information from all available runs via a graph-based alignment strategy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRIC</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=proteomics_search_tandem_1" title="Run an X!Tandem Search"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">X!Tandem MSMS Search</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cardinal_single_ion_segmentation" title="mass spectrometry imaging spatial DGMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI single ion segmentation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cardinal_colocalization" title="mass spectrometry imaging colocalization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI colocalization</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=metanovo" title="Produce targeted databases for mass spectrometry analysis."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaNovo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=prot_scriber" title="Protein annotation of short human readable descriptions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">prot-scriber</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=syndiva" title="diversity analysis of synthetic libraries of a Fibronectin domain"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">syndiva</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=proteomics_search_tandem_2" title="Run an X!Tandem Search - test"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">X!Tandem MSMS Search</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mqppep_preproc" title="Prep phosphoproteomic MaxQuant output for statistical anlaysis."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaxQuant Phosphopeptide Preprocessing</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mqppep_anova" title="Runs ANOVA and KSEA for phosphopeptides."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaxQuant Phosphopeptide ANOVA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qupath_roi_splitter" title="Split ROI coordinates of QuPath TMA annotation by cell type (classification)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QuPath ROI Splitter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=calisp" title="Estimate isotopic composition of peptides from proteomics mass spectrometry data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">calisp</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eggnog_mapper_annotate" title="annotation phase"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eggNOG Mapper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eggnog_mapper_search" title="search phase"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eggNOG Mapper</button></a>
 <h3>Metabolomics</h3>
-<a href="https://usegalaxy.eu/root?tool_id=metams_runGC" title="GC-MS data preprocessing using metaMS package"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaMS.runGC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=isoplot" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Isoplot: Generate plots from isocor output</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=abims_xcms_refine" title="Remove or merge chromatographic peaks based on specific criteria."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xcms refineChromPeaks (refine)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=w4mclassfilter" title="Filter W4M data by values or metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">W4m Data Subset</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_add_key" title="Set metadata key in MSP to static value"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms add key</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dimet_timecourse_analysis" title="Differential analysis of tracer metabolomics data comparing consecutive time-points (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet timecourse analysis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dimet_pca_analysis" title="Principal Component Analysis for tracer metabolomics data, producing tables (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet pca analysis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dimet_metabologram" title="Integration of transcriptomics and (tracer) metabolomics differential data (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet metabologram</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dimet_differential_analysis" title="Differential analysis of tracer metabolomics data comparing two groups (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet differential analysis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_metadata_match" title="matchms metadata match calculation for numeric fields based on tolerance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms metadata match</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dimet_bivariate_analysis" title="Computation of the correlation of MDV profiles, or the metabolite time course profiles (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet bivariate analysis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dimet_pca_plot" title="Figures of Principal Component Analysis for tracer metabolomics (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet pca plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dimet_enrichment_plot" title="Figures of mean enrichment by metabolite, as line-plots (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet enrichment plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dimet_abundance_plot" title="Figures of metabolites total abundance as barplots (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet abundance plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_subsetting" title="Extract spectra from a library given unique metadata identifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms subsetting</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_metadata_export" title="extract all metadata from mass spectra file to tabular format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms metadata export</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_msfinder" title="Annotation of fragment peaks in mass spectral libraries."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RECETOX MsFinder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_filtering" title="filter and normalize mass spectrometry data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms filtering</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_formatter" title="reformat scores object of matchms to long format table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms scores formatter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_metadata_merge" title="Merge metadata csv into MSP by a specified column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms metadata merge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Transformation" title="Transforms the dataMatrix intensity values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Transformation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=abims_anova" title="N-way anova. With ou Without interactions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Anova</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Multivariate" title="PCA, PLS and OPLS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Multivariate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biosigner" title="Molecular signature discovery from omics data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Biosigner</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Univariate" title="Univariate statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Univariate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mzmine_batch" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MZMine batch</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimspy_align_samples" title="- Align peaks across Peaklists"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align Samples</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimspy_replicate_filter" title="- Remove peaks that fail to appear in at least x-out-of-n (technical) replicates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replicate Filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimspy_process_scans" title="- Read, filter and average MS scans"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Process Scans (and SIM-Stitch)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metfrag_vis" title="Visualisation for MetFrag results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetFrag Vis</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=w4mcorcov" title="OPLS-DA Contrasts of Univariate Results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OPLS-DA_Contrasts</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimspy_get_peaklists" title="or an average peaklist from a Peak Intensity Matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get peaklists</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimspy_hdf5_to_txt" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert DIMSpy-based HDF5 to tsv</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimspy_missing_values_sample_filter" title="- Remove samples with a high percentage of missing values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Missing Values Sample Filter</button></a>
@@ -2208,6 +2527,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=mspurity_frag4feature" title="Assign fragmentation spectra to XCMS features using msPurity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">msPurity.frag4feature</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mspurity_puritya" title="Assess acquired precursor ion purity of MS/MS spectra"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">msPurity.purityA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mspurity_flagremove" title="Tool to flag and remove XCMS grouped peaks from the xcmsSet object based on various thresholds        (e.g. RSD of intensity and retention time)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">msPurity.flagRemove</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=w4mclassfilter" title="Filter W4M data by values or metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">W4m Data Subset</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Heatmap" title="Heatmap of the dataMatrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Heatmap</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=genform" title="Generation of molecular formulas by high-resolution MS and MS/MS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">genform</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=NmrAnnotation" title="Annotation of complex mixture NMR spectra and metabolite proportion estimation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NMR_Annotation</button></a>
@@ -2235,9 +2555,11 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=abims_xcms_xcmsSet" title="Chromatographic peak detection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xcms findChromPeaks (xcmsSet)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=msnbase_readmsdata" title="Imports mass-spectrometry data files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSnbase readMSData</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lipidmaps" title=": search on LIPID MAPS Structure Database (LMSD) online with masses and its Text/Ontology-based search engine."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Lipidmaps </button></a>
+<a href="https://usegalaxy.eu/root?tool_id=w4mcorcov" title="OPLS-DA Contrasts of Univariate Results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OPLS-DA_Contrasts</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=w4mjoinpn" title="Join positive and negative ionization-mode W4M datasets for the same samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join +/- Ions</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=generic_filter" title="Removes elements according to numerical or qualitative values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generic_Filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=quality_metrics" title="Metrics and graphics to check the quality of the data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Quality Metrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=metams_runGC" title="GC-MS data preprocessing using metaMS package"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaMS.runGC</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mixomics_multilevel" title="Data transformation: Within matrix decomposition for repeated measurements (cross-over design) with mixOmics package"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Multilevel</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=checkFormat" title="Checking/formatting the sample and variable names of the dataMatrix, sampleMetadata, and variableMetadata files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Check Format</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Determine_BC" title="to choose between linear, lowess and loess methods"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Determine_batch_correction</button></a>
@@ -2249,43 +2571,55 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=NmrBucketing" title="Bucketing and integration of NMR Bruker raw data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NMR_Bucketing</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=NmrNormalization" title="Normalization of NMR bucketed and integrated spectra"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NMR_Normalization</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=NmrAlignment" title="based on the Cluster-based Peak Alignment (CluPA) algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NMR spectra alignment</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=NmrAlignment" title="based on the Cluster-based Peak Alignment (CluPA) algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NMR spectra alignment</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_convert" title="convert between mass spectral library formats (.mgf/.msp/.json) using matchms"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms convert</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_fingerprint_similarity" title="calculate similarity between molecular fingerprints calculated from structural spectrum metadata descriptors"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms fingerprint similarity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_networking" title="create similarity network graph from matchms similarity scores"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms networking</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_spectral_similarity" title="matchms spectral similarity calculation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms spectral similarity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_remove_key" title="Remove metadata entry for all spectra in a library"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms remove key</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_split" title="split a large library into subsets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms split library</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dimet_differential_multigroup_analysis" title="Differential analysis of 3 or more chosen groups of tracer metabolomics data (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet differential multigroup analysis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dimet_isotopologues_plot" title="Figures of isotopologues proportions by metabolite, as stacked barplots (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet isotopologues plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=riassigner" title="compute retention indices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RIAssigner</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=use_theoretical_mz_annotations" title="Overwrite experimentally measured mz values for peaks with theoretical values from peak comments."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">use theoretical m/z values</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=riassigner_from_comment" title="Assign different retention indices from unstructured comment metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RIAssigner init from comment</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=abims_xcms_refine" title="Remove or merge chromatographic peaks based on specific criteria."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xcms refineChromPeaks (refine)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=isoplot" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Isoplot: Generate plots from isocor output</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_generate_feature_table" title="generate feature table from noise-removed HRMS profile data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - generate feature table</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_recover_weaker_signals" title="recover weaker signals from raw data using an aligned feature table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - recover weaker signals</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_correct_time" title="correct retention time across samples for peak alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - correct time</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_compute_clusters" title="compute clusters of mz and rt across samples and assign cluster IDs to individual features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - compute clusters</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_remove_noise" title="filter noise and detect peaks in high resolution mass spectrometry (HRMS) profile data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - remove noise</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_merge_known_table" title="join knowledge from aligned features and known table."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - merge known table</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_compute_template" title="compute retention time correction template feature table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - compute template</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_align_features" title="align peaks across samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - align features</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rmassbank" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RMassBank</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biotransformer" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BioTransformer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=msmetaenhancer" title="annotate MS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSMetaEnhancer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ramclustr" title="A feature clustering algorithm for non-targeted mass spectrometric metabolomics data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RAMClustR</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ramclustr_define_experiment" title="Definition of experimental design used for record keeping and writing spectra data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RAMClustR define experiment</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_xmsannotator_advanced" title="annotate peak intensity table including scores and confidence levels"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-xMSannotator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_similarity" title="calculate the similarity score and matched peaks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms similarity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=waveica" title="removal of batch effects for untargeted metabolomics data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WaveICA</button></a>
 <h3>ChemicalToolBox</h3>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_get_builtin_file" title="from built-in datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS copy file</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gromacs_extract_topology" title="from a GROMACS topology file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extracting Topology Information</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=alphafold" title="Alphafold v2.0: AI-guided 3D structure prediction of proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">alphafold</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tleap" title="interactively build and run tLEaP files to set up systems with AmberTools"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build tLEaP</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rdconf" title="using RDKit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RDConf: Low-energy ligand conformer search</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=traj_selections_and_merge" title="- select specific molecules and merge multiple trajectories."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trajectory select and merge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=docking" title="tool to perform protein-ligand docking with Autodock Vina"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VINA Docking</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_energy" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract energy components with GROMACS</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ctb_rdkit_descriptors" title="calculated with RDKit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Descriptors</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=acpype_Amber2Gromacs" title="using acpype"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Amber topology and coordinate files to GROMACS format</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_solvate" title="to structure and topology files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS solvation and adding ions</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_sim" title="for system equilibration or data collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS simulation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_em" title="of the system prior to equilibration and production MD"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS energy minimization</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qcxms_neutral_run" title="required as first step to prepare for the production runs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCxMS neutral run</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xtb_molecular_optimization" title="Semiempirical quantum mechanical molecular optimization method"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xtb molecular optimization</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ambertools_acpype" title="using acpype"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate MD topologies for small molecules</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chembl" title="for compounds which are similar to a SMILES string"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Search ChEMBL database</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ambertools_antechamber" title="- Amber's molecular input file processor"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AnteChamber</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=parmconv" title="to AMBER prmtop in preparation for MMGBSA/MMPBSA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Parameters</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ambertools_acpype" title="using acpype"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate MD topologies for small molecules</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_makendx" title="using make_ndx"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create GROMACS index files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_restraints" title="using genrestr"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create GROMACS position restraints files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_trj" title="using trjconv and trjcat"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Modify/convert GROMACS trajectories</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_merge_topology_files" title="and GRO files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge GROMACS topologies</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ambertools_parmchk2" title="- Amber's parameter checker"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ParmChk2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ambertools_antechamber" title="- Amber's molecular input file processor"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AnteChamber</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mmpbsa_mmgbsa" title="tool for estimating ligand binding affinities"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MMPBSA/MMGBSA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dpocket" title="to calculate descriptors for protein pockets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dpocket</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=OpenPepXL" title="Tool for protein-protein cross-linking identification using labeled linkers."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenPepXL</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fpocket" title="- find potential binding sites in protein structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fpocket</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ctb_alignit" title="and optimization (Align-it)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pharmacophore alignment</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ctb_alignit_create_db" title="generation (Align-it)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pharmacophore</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=prepare_box" title="for an AutoDock Vina job from a ligand or pocket input file (confounding box)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate the box parameters using RDKit</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=md_converter" title="- interconvert between MD trajectory file formats."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MDTraj file converter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biomd_neqgamma" title="for calculating friction and free energy profiles from TMD ensembles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dcTMD friction correction</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_md" title="for data collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS production simulation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sucos_docking_scoring" title="- compare shape and feature overlap of docked ligand poses to a reference molecule"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Score docked poses using SuCOS</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chembl" title="for compounds which are similar to a SMILES string"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Search ChEMBL database</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chembl_structure_pipeline" title="for curation and standardizing of molecular structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChEMBL structure pipeline</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_solvate" title="to structure and topology files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS solvation and adding ions</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gmx_editconf" title="using editconf"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS structure configuration</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_makendx" title="using make_ndx"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create GROMACS index files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_restraints" title="using genrestr"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create GROMACS position restraints files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_energy" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract energy components with GROMACS</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_trj" title="using trjconv and trjcat"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Modify/convert and concatate GROMACS trajectories</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_sim" title="for system equilibration or data collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS simulation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_em" title="of the system prior to equilibration and production MD"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS energy minimization</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gmx_setup" title="of topology and GRO structure file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS initial setup</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=OpenPepXL" title="Tool for protein-protein cross-linking identification using labeled linkers."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenPepXL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_subsearch" title="of fingerprint data sets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Substructure Search</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=biomd_rmsd_clustering" title="from MD RMSD matrix data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hierarchical clustering</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=biomd_extract_clusters" title="from linkage matrix data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract clusters of MD trajectories</button></a>
@@ -2293,11 +2627,8 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_addh" title="at a certain pH value"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add hydrogen atoms</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_remIons" title="from a library of compounds"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove counterions and fragments</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=chembl_structure_pipeline" title="for curation and standardizing of molecular structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChEMBL structure pipeline</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=md_slicer" title="using the MDTraj package"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slice MD trajectories</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ctb_silicos_qed" title="quantitative estimation (QED) with RDKit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Drug-likeness</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gromacs_modify_topology" title="to a GROMACS topology file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Adding New Topology Information</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biomd_neqgamma" title="for calculating friction and free energy profiles from TMD ensembles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dcTMD friction correction</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_remove_protonation_state" title="of every atom"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove protonation state</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_rg" title="of a molecular structure"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS Radius of Gyration</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mdanalysis_ramachandran_protein" title="- Ramachandran plot for proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Ramachandran Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mdanalysis_endtoend" title="- End-to-End distance timeseries and histogram for the given selections"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">End-to-End Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mdanalysis_cosine_analysis" title="- measure the cosine content of the PCA projection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cosine Content</button></a>
@@ -2314,10 +2645,13 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=prepare_receptor" title="Tool to prepare receptor for docking with Autodock Vina"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prepare receptor</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=enumerate_charges" title="calculated with Dimorphite DL and RDKit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Enumerate changes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sdf_to_tab" title="into a tabular file using RDKit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract values from an SD-file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fpocket" title="- find potential binding sites in protein structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fpocket</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctb_mordred_descriptors" title="with Mordred"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate molecular descriptors</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctb_pubchem_download_as_smiles" title="as canonical SMILES"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PubChem Download</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctb_pubchem_download_assays" title="as table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PubChem Assay Downloader</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=docking" title="tool to perform protein-ligand docking with Autodock Vina"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VINA Docking</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=prepare_ligand" title="for docking with Autodock Vina"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prepare ligand</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=prepare_box" title="for an AutoDock Vina job from a ligand or pocket input file (confounding box)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate the box parameters using RDKit</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_remDuplicates" title="from a library of compounds"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove duplicated molecules</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_filter" title="a set of molecules from a file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_compound_convert" title="- interconvert between various chemistry and molecular modeling data files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compound conversion</button></a>
@@ -2326,6 +2660,9 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_obgrep" title="- an advanced molecular search program using SMARTS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compound search</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_remSmall" title="from a library of compounds"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove small molecules</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=prepare_ligands_for_docking" title="Tool to prepare ligands for docking with tools like Autodock Vina"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prepare ligands for docking</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ctb_rdkit_descriptors" title="calculated with RDKit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Descriptors</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ctb_silicos_qed" title="quantitative estimation (QED) with RDKit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Drug-likeness</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sucos_docking_scoring" title="- compare shape and feature overlap of docked ligand poses to a reference molecule"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Score docked poses using SuCOS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sucos_clustering" title="based on the overlap of 3D features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster ligands using SuCOS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sucos_max_score" title="- determine maximum SuCOS score of ligands against clustered fragment hits"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Max SuCOS score</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_structure_distance_finder" title="- determine the minimum distances between a molecule and a set of 3D points"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Determine distance to defined points</button></a>
@@ -2349,6 +2686,10 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=ctb_im_screen" title="a compound against a library using RDKit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Screen</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctb_im_xcos" title="scoring"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">XCos</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=featurestein" title="feature overlay scoring"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">'FeatureStein' fragment overlay scoring</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_merge_topology_files" title="and GRO files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge GROMACS topologies</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rem_complex" title="Remove molecular coordination complexes from a list of structure representations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove coordination complexes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qcxms_production_run" title="Production run to obtain a QCxMS simulated mass spectrum"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCxMS production run</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qcxms_getres" title="Get result of the Production run to obtain a QCxMS simulated mass spectrum"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCxMS get results</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openduck_chunk" title="for dynamic undocking"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenDUck chunk</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openduck_run_smd" title="steered molecular dynamics runs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run OpenDUck</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=xchem_transfs_scoring" title="using deep learning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">XChem TransFS pose scoring</button></a>
@@ -2356,15 +2697,18 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=ctb_chemfp_nxn_clustering" title="of molecular fingerprints"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NxN clustering</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctb_chemfp_butina_clustering" title="of molecular fingerprints"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Taylor-Butina clustering</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctb_sdf2fps" title="- extract fingerprints from sdf file metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SDF to Fingerprint</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=md_converter" title="- interconvert between MD trajectory file formats."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MDTraj file converter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fastpca" title="- dimensionality reduction of MD simulations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fastpca</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rdconf" title="using RDKit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RDConf: Low-energy ligand conformer search</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=traj_selections_and_merge" title="- select specific molecules and merge multiple trajectories."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trajectory select and merge</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=alchemical_analysis" title="Analysis of alchemical free energy calculations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Alchemical Analysis</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=goseq" title="tests for overrepresented gene categories"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">goseq</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vmd_hbonds" title="between two segments of a trajectory"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hydrogen Bond Analysis using VMD</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bio3d_pca_visualize" title="- generate trajectories of principal components of atomic motion"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PCA visualization</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bio3d_rmsf" title="using Bio3D"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RMSF Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bio3d_pca" title="- principal component analysis using Bio3D"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PCA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bio3d_rmsd" title="using Bio3D"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RMSD Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bio3d_dccm" title="- Dynamical Cross-Correlation Maps using Bio3D (DCCM)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DCCM analysis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=md_slicer" title="using the MDTraj package"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slice MD trajectories</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=packmol" title="- initial configurations for molecular dynamics simulations by packing optimization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PACKMOL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=padel" title="calculator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PaDEL descriptor</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctb_online_data_fetch" title="fetching"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Online data</button></a>
@@ -2384,10 +2728,24 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=ctb_pubchem_download_assays" title="as canonical SMILES"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PubChem Assay Downloader</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bgchem_fragment_merger" title="fragmented molecules"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merging</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctb_openmg" title="Exhaustive generation of chemical structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Open Molecule Generator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chembl_structure_pipeline" title="for curation and standardizing of molecular structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChEMBL structure pipeline</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_md" title="for data collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS production simulation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ctb_alignit" title="and optimization (Align-it)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pharmacophore alignment</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ctb_alignit_create_db" title="generation (Align-it)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pharmacophore</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dpocket" title="to calculate descriptors for protein pockets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dpocket</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_rg" title="of a molecular structure"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS Radius of Gyration</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=acpype_Amber2Gromacs" title="using acpype"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Amber topology and coordinate files to GROMACS format</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tleap" title="interactively build and run tLEaP files to set up systems with AmberTools"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build tLEaP</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=alphafold" title="- AI-guided 3D structural prediction of proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Alphafold 2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gromacs_modify_topology" title="to a GROMACS topology file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Adding New Topology Information</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gromacs_extract_topology" title="from a GROMACS topology file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extracting Topology Information</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_get_builtin_file" title="from built-in datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS copy file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pdbfixer" title="to automatically fix a PDB file before performing molecular dynamics simulation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PDBFixer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_check" title="to provide information about GROMACS input files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS check</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_rmsd" title="of molecular structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS RMSD calculation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_rmsf" title="of molecular structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS RMSF calculation</button></a>
 <hr/><h2>Statistics and Visualisation</h2>
 <h3>Statistics</h3>
-<a href="https://usegalaxy.eu/root?tool_id=rgcca" title="performs multiblock data analysis of several sets of variables (blocks) observed on the same group of individuals."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RGCCA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scipy_sparse" title="for manipulating 2-D Scipy sparse numeric data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sparse Matrix Functions</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=maximal_information_based_nonparametric_exploration" title="- Maximal Information-based Nonparametric Exploration"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MINE</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=plot_for_lda_output1" title="on 'Perform LDA' output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Draw ROC plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lda_analy1" title="Linear Discriminant Analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform LDA</button></a>
@@ -2397,106 +2755,105 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=BestSubsetsRegression1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform Best-subsets Regression</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pca1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Principal Component Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=kpca1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kernel Principal Component Analysis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scipy_sparse" title="for manipulating 2-D Scipy sparse numeric data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sparse Matrix Functions</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=kcca1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kernel Canonical Correlation Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cca1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Canonical Correlation Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=t_test_two_samples" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">T Test for Two Samples</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=create_tool_recommendation_model" title="using deep learning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a model to recommend tools</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dwt_var1" title="using Discrete Wavelet Transfoms"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Wavelet variance</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=graphembed" title="Compute and plot a 2D embedding of a data matrix given supervised class information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GraphEmbed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_landmark_registration" title="Landmark Registration"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Landmark Registration</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=plotly_regression_performance_plots" title="of tabular data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Plot actual vs predicted curves and residual plots</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=plotly_ml_performance_plots" title="of tabular data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Plot confusion matrix, precision, recall and ROC and AUC curves</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pandas_rolling_window" title="over a dataframe (e.g. for data smoothing)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Rolling window</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nn_classifier" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nearest Neighbors Classification</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=svm_classifier" title="for classification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Support vector machines (SVMs)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=abims_anova" title="N-way anova. With ou Without interactions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Anova</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Multivariate" title="PCA, PLS and OPLS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Multivariate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Univariate" title="Univariate statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Univariate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=iwtomics_plotwithscale" title="on Test Scale"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IWTomics Plot with Threshold</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=iwtomics_testandplot" title="and Plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IWTomics Test</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=iwtomics_loadandplot" title="Smooth and Plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IWTomics Load</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=seq_composition" title="Count bases or amino-acids"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sequence composition</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biosigner" title="Molecular signature discovery from omics data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Biosigner</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Transformation" title="Transforms the dataMatrix intensity values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Transformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Heatmap" title="Heatmap of the dataMatrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Heatmap</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bg_statistical_hypothesis_testing" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Statistical hypothesis testing</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rgcca" title="performs multiblock data analysis of several sets of variables (blocks) observed on the same group of individuals."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RGCCA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bg_statistical_hypothesis_testing" title="computes several descriptive statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Statistical hypothesis testing</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Summary_Statistics1" title="for any numerical column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Summary Statistics</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Count1" title="occurrences of each record"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Count</button></a>
 <h3>Machine Learning</h3>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_to_categorical" title="Converts a class vector (integers) to binary class matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">To categorical</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biomodels_biomd0000001066" title="to predict efficacy of immune checkpoint blockade across multiple cancer patient cohorts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Random Forest model</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biomodels_biomd0000001076" title="proteins involved in cancer immunotherapy using molecular descriptors and Multi Layer Perceptron (MLP) neural network"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prediction of Breast Cancer (BC)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mcl" title="Markov Cluster Algorithm for graphs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MCL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sklearn_train_test_split" title="into training and test subsets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split Dataset</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sklearn_train_test_eval" title="fit a model using part of dataset and evaluate using the rest"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Train, Test and Evaluation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sklearn_pca" title="with scikit-learn"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Principal component analysis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sklearn_fitted_model_eval" title="using a new batch of labeled data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Evaluate a Fitted Model</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=model_prediction" title="predicts on new data using a preffited model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Model Prediction</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ml_visualization_ex" title="includes several types of plotting for machine learning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Machine Learning Visualization Extension</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_lightgbm" title="- train and apply LightGBM models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LightGBM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_train_test_split" title="into training and test subsets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split Dataset</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_model_fit" title="or other models using a labeled dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fit a Pipeline, Ensemble</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sklearn_numeric_clustering" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Numeric Clustering</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_stacking_ensemble_models" title="builds stacking, voting ensemble models with numerous base options"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacking Ensembles</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=keras_train_and_eval" title="conduct deep training and evaluation either implicitly or explicitly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Deep learning training and evaluation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sklearn_svm_classifier" title="for classification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Support vector machines (SVMs)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sklearn_sample_generator" title="random samples with controlled size and complexity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_estimator_attributes" title="get important attributes from an estimator or scikit object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Estimator attributes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=model_prediction" title="predicts on new data using a preffited model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Model Prediction</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_train_test_eval" title="fit a model using part of dataset and evaluate using the rest"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Train, Test and Evaluation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_model_validation" title="includes cross_validate, cross_val_predict, learning_curve, and more"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Model Validation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_discriminant_classifier" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Discriminant Analysis</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_regression_metrics" title="for regression performance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate metrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_feature_selection" title="module, including univariate filter selection methods and recursive feature elimination algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Feature Selection</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_numeric_clustering" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Numeric Clustering</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_nn_classifier" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nearest Neighbors Classification</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_build_pipeline" title="an all-in-one platform to build pipeline, single estimator, preprocessor and custom wrappers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pipeline Builder</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_searchcv" title="performs hyperparameter optimization using various SearchCVs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hyperparameter Search</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_sample_generator" title="random samples with controlled size and complexity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_svm_classifier" title="for classification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Support vector machines (SVMs)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sklearn_build_pipeline" title="an all-in-one platform to build pipeline, single estimator, preprocessor and custom wrappers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pipeline Builder</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_pairwise_metrics" title="or compute affinity or kernel for sets of samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Evaluate pairwise distances</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sklearn_nn_classifier" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nearest Neighbors Classification</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_ensemble" title="for classification and regression"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Ensemble methods</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sklearn_feature_selection" title="module, including univariate filter selection methods and recursive feature elimination algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Feature Selection</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_data_preprocess" title="raw feature vectors into standardized datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Preprocess</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_clf_metrics" title="for classification performance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate metrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sklearn_regression_metrics" title="for regression performance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate metrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sklearn_discriminant_classifier" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Discriminant Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_generalized_linear" title="for classification and regression"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generalized linear models</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_fitted_model_eval" title="using a new batch of labeled data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Evaluate a Fitted Model</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_pca" title="with scikit-learn"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Principal component analysis</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=keras_train_and_eval" title="conduct deep training and evaluation either implicitly or explicitly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Deep learning training and evaluation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sklearn_model_validation" title="includes cross_validate, cross_val_predict, learning_curve, and more"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Model Validation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sklearn_model_fit" title="or other models using a labeled dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fit a Pipeline, Ensemble</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=keras_batch_models" title="with online data generator for Genomic/Protein sequences and images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build Deep learning Batch Training Models</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=keras_model_builder" title="with an optimizer, loss function and fit parameters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create deep learning model</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=keras_model_config" title="using Keras"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a deep learning model architecture</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scipy_sparse" title="for manipulating 2-D Scipy sparse numeric data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sparse Matrix Functions</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=create_tool_recommendation_model" title="using deep learning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a model to recommend tools</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sklearn_label_encoder" title="Encode target labels with value between 0 and n_classes-1"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Label encoder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sklearn_to_categorical" title="Converts a class vector (integers) to binary class matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">To categorical</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=colorize_labels" title="with NetworkX"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Colorize label map</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=virhunter" title="Deep learning method to identify viruses in sequencing datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virhunter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=decontaminator" title="Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">decontaminator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deepmicro" title="Representation learning and classification framework"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeepMicro</button></a>
 <h3>Graph/Display Data</h3>
-<a href="https://usegalaxy.eu/root?tool_id=pygenomeTracks" title="plot genomic data tracks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pyGenomeTracks</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ggplot2_heatmap" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Heatmap w ggplot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ggplot2_violin" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Violin plot w ggplot2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ggplot2_point" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scatterplot with ggplot2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ggplot2_histogram" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Histogram with ggplot2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=circos_aln_to_links" title="reformats alignment files to prepare for Circos"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Alignments to links</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=circos_binlinks" title="reduce links to a density plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Link Density Track</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=circos_bundlelinks" title="reduce numbers of links in datasets before plotting"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Bundle Links</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=circos" title="visualizes data in a circular layout"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=circos_gc_skew" title="calculates skew over genomic sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GC Skew</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=circos_resample" title="reduce numbers of points in a dataset before plotting"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Resample 1/2D data</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=circos_wiggle_to_scatter" title="reformats bigWig files to prepare for Circos 2d scatter/line/histogram plots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: bigWig to Scatter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=circos_wiggle_to_stacked" title="reformats for use in Circos stacked histogram plots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Stack bigWigs as Histogram</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=circos_tableviewer" title="easily creates circos plots from tabular data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Table viewer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=circos_interval_to_text" title="reformats interval files to prepare for Circos text labels"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Interval to Circos Text Labels</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=circos_interval_to_tile" title="reformats interval files to prepare for Circos tile plots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Interval to Tiles</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ggplot2_heatmap2" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">heatmap2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pretext_snapshot" title="image generator for Pretext contact maps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pretext Snapshot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bandage_info" title="determine statistics of de novo assembly graphs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bandage Info</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=intervene_pairwise" title="and heatmap for genomic intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairwise intersection</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=intervene_upset" title="of intersection of genomic regions or list sets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UpSet diagram</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=volcanoplot" title="create a volcano plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Volcano Plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=jbrowse_to_standalone" title="upgrades the bare data directory to a full JBrowse instance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JBrowse - Data Directory to Standalone</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=jbrowse" title="genome browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JBrowse</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pe_histogram" title="of insert size frequency"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Paired-end histogram</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=build_ucsc_custom_track_1" title="for UCSC genome browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build custom track</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scatterplot_rpy" title="of two numeric columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scatterplot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ggplot2_pca" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PCA plot w ggplot2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=histogram_rpy" title="of a numeric column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Histogram</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gmaj_1" title="Multiple Alignment Viewer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GMAJ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=XY_Plot_1" title="for multiple series and graph types"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Plotting tool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=jvarkit_wgscoverageplotter" title="Plot read coverage across a genomic contig"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BAM Coverage Plotter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bandage_image" title="visualize de novo assembly graphs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bandage Image</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=jbrowse_to_standalone" title="upgrades the bare data directory to a full JBrowse instance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JBrowse - Data Directory to Standalone</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=jbrowse" title="genome browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JBrowse</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pygenomeTracks" title="plot genomic data tracks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pyGenomeTracks</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circos_interval_to_tile" title="reformats interval files to prepare for Circos tile plots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Interval to Tiles</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circos_resample" title="reduce numbers of points in a dataset before plotting"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Resample 1/2D data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circos_binlinks" title="reduce links to a density plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Link Density Track</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circos_wiggle_to_scatter" title="reformats bigWig files to prepare for Circos 2d scatter/line/histogram plots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: bigWig to Scatter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circos_interval_to_text" title="reformats interval files to prepare for Circos text labels"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Interval to Circos Text Labels</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circos_aln_to_links" title="reformats alignment files to prepare for Circos"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Alignments to links</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circos_tableviewer" title="easily creates circos plots from tabular data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Table viewer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circos_gc_skew" title="calculates skew over genomic sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GC Skew</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circos_wiggle_to_stacked" title="reformats for use in Circos stacked histogram plots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Stack bigWigs as Histogram</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circos_bundlelinks" title="reduce numbers of links in datasets before plotting"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Bundle Links</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ggplot2_heatmap" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Heatmap w ggplot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ggplot2_violin" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Violin plot w ggplot2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ggplot2_point" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scatterplot with ggplot2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ggplot2_histogram" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Histogram with ggplot2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=plotly_ml_performance_plots" title="of tabular data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Plot confusion matrix, precision, recall and ROC and AUC curves</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=newick_display" title="visualize a phylogenetic tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Newick Display</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=taxonomy_krona_chart" title="from taxonomic profile"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krona pie chart</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bandage_info" title="determine statistics of de novo assembly graphs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bandage Info</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bandage_image" title="visualize de novo assembly graphs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bandage Image</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=intervene_upset" title="of intersection of genomic regions or list sets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UpSet diagram</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=intervene_pairwise" title="and heatmap for genomic intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairwise intersection</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pathview" title="for pathway based data integration and visualization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pathview</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=export2graphlan" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Export to GraPhlAn</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=venn_list" title="from lists"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Venn Diagram</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ggplot2_heatmap2" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">heatmap2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=volcanoplot" title="create a volcano plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Volcano Plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=plotly_regression_performance_plots" title="of tabular data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Plot actual vs predicted curves and residual plots</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=plotly_parallel_coordinates_plot" title="of tabular data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Parallel Coordinates Plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ggplot2_pca" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PCA plot w ggplot2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=four_color_plot" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fasta nucleotide color plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=graphlan" title="to produce graphical output of an input tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GraPhlAn</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=graphlan_annotate" title="for GraPhlAn"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generation, personalization and annotation of tree</button></a>
@@ -2505,36 +2862,59 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=fasta_nucleotide_color_plot" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fasta nucleotide color plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mummerplot_wrapper" title="Combine mummer/nucmer/promer with mummerplot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MUMmer dotplot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=karyotype_Plot_1" title="for multiple series"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Karyotype Plotting tool</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pe_histogram" title="of insert size frequency"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Paired-end histogram</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circos" title="visualizes data in a circular layout"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=barchart_gnuplot" title="for multiple columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bar chart</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pathifier" title=": Quantify deregulation of pathways in cancer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pathifier</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qual_stats_boxplot" title="of quality statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Boxplot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=laj_1" title="Pairwise Alignment Viewer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LAJ</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gene_iobio_display_generation_iframe" title="analyses VCFs for single and trio analysis to find causative variants using gene.iobio's public server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gene.iobio visualisation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.genome_viz.linear_genome_plot" title="Linear Genome Plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Linear Genome Plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcf_to_maf_customtrack1" title="for display at UCSC"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCF to MAF Custom Track</button></a>
+<h3>Muon Spectroscopy</h3>
+<a href="https://usegalaxy.eu/root?tool_id=cif2cell" title="convert .cif file to .cell"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cif2cell</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=muspinsim_config" title="define simulation parameters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MuSpinSim Configure</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=muspinsim" title="perform spin dynamics calculations for muon science experiments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MuSpinSim Simulate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=muspinsim_plot" title="plot values generated from MuSpinSim"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MuSpinSim Plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pm_asephonons" title="calculate phonons using ASE and DFTB+"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyMuonSuite Phonons</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pm_symmetry" title="generate Wyckoff points symmetry report"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyMuonSuite Symmetry</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pm_yaml_config" title="define AIRSS parameters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyMuonSuite AIRSS Configure</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pm_muairss_write" title="generate muonated structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyMuonSuite AIRSS Generate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pm_uep_opt" title="run UEP optimisation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyMuonSuite AIRSS UEP Optimise</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pm_dftb_opt" title="run DFTB+ optimisation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyMuonSuite AIRSS DFTB+ Optimise</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pm_muairss_read" title="run clustering for optimised structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyMuonSuite AIRSS Cluster</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=muspinsim_combine" title="combine datafiles generated from MuSpinSim"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MuSpinSim Combine</button></a>
 <hr/><h2>Miscellaneous Tools</h2>
 <h3>Evolution</h3>
-<a href="https://usegalaxy.eu/root?tool_id=codeml" title="Detects positive selection (paml package)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">codeML</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mutate_snp_codon_1" title="with SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Mutate Codons</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=iqtree" title="Phylogenomic / evolutionary tree construction from multiple sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IQ-TREE</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tn93_cluster" title="sequences that lie within a specific distance of each other"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TN93 Cluster</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tn93" title="compute distances between aligned sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TN93</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=codeml" title="Detects positive selection (paml package)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">codeML</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=structure" title="using multi-locus genotype data to investigate population structure"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Structure</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rapidnj" title="rapidly with RapidNJ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join neighbors</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tn93" title="compute distances between aligned sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TN93</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tn93_filter" title="- remove sequences from a reference that are within a given distance of of a cluster"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TN93 Filter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mutate_snp_codon_1" title="with SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Mutate Codons</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tn93_cluster" title="sequences that lie within a specific distance of each other"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TN93 Cluster</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tn93_readreduce" title="into clusters with TN-93"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge matching reads</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=structure" title="using multi-locus genotype data to investigate population structure"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Structure</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hgv_codingSnps" title="amino-acid changes caused by a set of SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">aaChanges</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hgv_add_scores" title="interspecies conservation scores"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">phyloP</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=revoluzer_crex" title="reconstruct pairwise gene order rearrangement"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CREx</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=revoluzer_distmat" title="for gene orders"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute distance matrix</button></a>
 <h3>Motif Tools</h3>
-<a href="https://usegalaxy.eu/root?tool_id=meme_chip" title="- motif discovery, enrichment analysis and clustering on large nucleotide datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEME-ChIP</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rgweblogo3" title="generator for fasta (eg Clustal alignments)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sequence Logo</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=meme_psp_gen" title="- perform discriminative motif discovery"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEME psp-gen</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=meme_fimo" title="- Scan a set of sequences for motifs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FIMO</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=meme_meme" title="- Multiple EM for Motif Elicitation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEME</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=meme_dreme" title="- Discriminative Regular Expression Motif Elicitation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DREME</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=meme_chip" title="- motif discovery, enrichment analysis and clustering on large nucleotide datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEME-ChIP</button></a>
 <h3>Test Tools</h3>
 <a href="https://usegalaxy.eu/root?tool_id=chipeakanno_annopeaks" title="annotate peaks by annoGR object in the given range"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChIPpeakAnno annoPeaks</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=clusterprofiler_bitr" title="converting ID types"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster Profiler Bitr</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=clusterprofiler_go" title="run GO Analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster Profiler GO</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hifive" title="manipulate, analyze, and plot HiC and 5C chromatin interaction data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hifive</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_zeppelin_notebook" title="Zeppelin Notebook"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">zeppelin</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=concatenate_icenet_data" title="for concatenating yearly sea ice concentration netcdf files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate Icenet Data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=icenet_forecast" title="for forecasting sea ice concentration with IceNet"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Icenet Forecast</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=preprocess_icenet_data" title="for regridding and normalizing icenet data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Preprocess Icenet Data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=create_API_requests_for_icenet_data" title="for creating request text files for downloading Icenet Data with the Copernicus Climate Data Store Tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">create API requests for Icenet Data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=visualize_icenet_forecast" title="for visualizing and analyzing the Icenet forecast"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Visualize Icenet Forecast</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pyiron_meta" title="meta tools"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyIron</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcgr" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Personal Cancer Genome Reporter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tombo_resquiggle" title="Raw Signal (electric current nanopore measurements) Genomic Alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tombo Re-squiggle</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tombo_text_output" title="browser text output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tombo create</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tombo_detect_modifications" title="detecting shifts in raw current signal level, indicative of non-canonical bases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tombo detect modifications</button></a>
@@ -2543,19 +2923,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=proteomics_search_peptide_prophet_1" title="Calculate Peptide Prophet statistics on search results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Peptide Prophet</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=proteomics_search_protein_prophet_1" title="Calculate Protein Prophet statistics on search results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Protein Prophet</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=proteomics_search_interprophet_1" title="Combine Peptide Prophet results from multiple search engines"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InterProphet</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_discriminant_classifier" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Discriminant Analysis</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=eden_sequence_converter" title="sequences to graphs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=eden_vectorizer" title="real vector graphs to sparse vectors"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Transform</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=nn_classifier" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nearest Neighbors Classification</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_numeric_clustering" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Numeric Clustering</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=svm_classifier" title="for classification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Support vector machines (SVMs)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scipy_sparse" title="for manipulating 2-D Scipy sparse numeric data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sparse Matrix Functions</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_data_preprocess" title="raw feature vectors into standardized datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Preprocess</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_pairwise_metrics" title="or compute affinity or kernel for sets of samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Evaluate pairwise distances</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_sample_generator" title="random samples with controlled size and complexity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_ensemble" title="for classification and regression"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Ensemble methods</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_clf_metrics" title="for classification performance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate metrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=eden_protease_prediction" title="based on cleavage sites"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Protease prediction</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bwtool-lift" title="Project data base-by-base into a new assembly using a liftOver chain file from UCSC"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bwtool-lift</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bg_protein_properties" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate protein properties</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=biopython_base_distribution" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Base Count</button></a>
@@ -2567,12 +2934,13 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=translate_nucleotides" title="to amino acids"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Translate nucleotides</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rnalfoldz" title="calculates locally stable secondary structures of RNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNALfoldz</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=re_he_maldi_image_registration" title="Registration of MALDI and HE Image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HE/ MALDI Image Registration</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=netcdf2zarr" title="Rewrite a netCDF to Zarr"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF to Zarr</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=jbrowse2" title="genome browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JBrowse2</button></a>
 <h3>GIS Data Handling</h3>
-<a href="https://usegalaxy.eu/root?tool_id=xarray_mapplot" title="Visualize netCDF variables on a geographical map"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray map plotting</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=xarray_coords_info" title="Get values for each coordinate of a Netcdf file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Coordinate Info</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=otb_mean_shift_smoothing" title="smooths an image using the MeanShift algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OTB.MeanShiftSmoothing</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interpolation_run_idw_interpolation" title="based on Inverse Distance Weighting (IDW)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run interpolation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=xarray_metadata_info" title="summarize content of a Netcdf file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Metadata Info</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=xarray_select" title="extracts variable values with custom conditions on dimensions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Selection</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=xarray_netcdf2netcdf" title="manipulate xarray from netCDF and save back to netCDF"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray operations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gdal_ogrinfo" title="lists information about an OGR supported data source"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OGR Informations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gdal_ogr2ogr" title="converts simple features data between file formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OGR2ogr</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gdal_gdalwarp" title="image reprojection and warping utility"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL Warp</button></a>
@@ -2581,12 +2949,24 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=gdal_gdalinfo" title="lists information about a raster dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL Informations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gdal_gdalbuildvrt" title="builds a VRT from a list of datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL Build VRT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gdal_gdaladdo" title="builds or rebuilds overview images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL addo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=otb_band_math" title="outputs a monoband image as a result of a mathematical operation on several multi-band images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OTB.BandMath</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xarray_netcdf2netcdf" title="manipulate xarray from netCDF and save back to netCDF"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray operations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xarray_mapplot" title="Visualize netCDF variables on a geographical map"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray map plotting</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xarray_coords_info" title="Get values for each coordinate of a Netcdf file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Coordinate Info</button></a>
 <h3>Animal Detection on Acoustic Recordings</h3>
 <a href="https://usegalaxy.eu/root?tool_id=spocc_occ" title="from GBIF, ALA, iNAT and others"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get species occurrences data</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vigiechiro_bilanenrichipf" title="from Animal Detection on Acoustic Recordings"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Advanced restitution: 'Point fixe' protocol</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vigiechiro_bilanenrichirp" title="from Animal Detection on Acoustic Recordings"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Advanced restitution: 'Routier'or 'Pedestre' protocols</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vigiechiro_idcorrect_2ndlayer" title="clean data from animal detection on acoustic recordings"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tadarida data cleaner</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vigiechiro_idvalid" title="Integrate identifications from animal detection on acoustic recordings"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tadarida identifications validation</button></a>
+<h3>Compute indicators for satellite remote sensing</h3>
+<a href="https://usegalaxy.eu/root?tool_id=srs_pca" title="from remote sensing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute a PCA raster</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=srs_diversity_maps" title="from remote sensing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map diversity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=srs_preprocess_s2" title="read, crop, resample and write it as a raster stack"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Preprocess sentinel 2 data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=srs_spectral_indices" title="as NDVI from remote sensing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute spectral indices</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=srs_process_data" title="with remote sensing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare diversity indicators</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=srs_global_indices" title="from remote sensing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute biodiversity indices</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=srs_metadata" title="metadata documents"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Validate ISO 19139</button></a>
 <h3>Regional Variation</h3>
 <a href="https://usegalaxy.eu/root?tool_id=indels_3way" title="from 3-way alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fetch Indels</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=draw_stacked_barplots" title="for different categories and different criteria"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Draw Stacked Bar Plots</button></a>
@@ -2636,124 +3016,138 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=gd_new_oscar" title=": Look up KEGG pathways for given Ensembl transcripts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get Pathways</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gd_cluster_kegg" title=": Group gene categories connected by shared genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster KEGG</button></a>
 <h3>Climate Analysis</h3>
-<a href="https://usegalaxy.eu/root?tool_id=cdo_info" title="Climate Data Information Operators to get information on Climate and NWP model data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CDO get info</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cdo_operations" title="Climate Data Manipulation Operators operations for standard processing of climate and NWP model output."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CDO Operations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=eodie" title="converts simple features data between file formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EODIE</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cads" title="for retrieving data from the Atmosphere Monitoring Service"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Atmosphere Data Store</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cesm" title="Community Earth System Model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CESM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=c3s" title="for retrieveing climate data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Climate Data Store</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=c3s" title="for retrieving climate data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Climate Data Store</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctsm_fates" title="Functionally Assembled Terrestrial Ecosystem Simulator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CTSM/FATES-EMERALD</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cds_essential_variability" title="for assessing climate variability"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Essential Climate Variables</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=climate_stripes" title="from timeseries"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">climate stripes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=psy_maps" title="gridded (lat/lon) netCDF data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">map plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cds_essential_variability" title="for assessing climate variability"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Essential Climate Variables</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mean_per_zone" title="over each area"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">zonal statistics</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=shyft_longitudes" title="from netCDF data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">shift longitudes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cesm" title="Community Earth System Model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CESM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cads" title="for retrieving data from the Atmosphere Monitoring Service"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Atmosphere Data Store</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eodie" title="converts simple features data between file formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EODIE</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cdo_operations" title="Climate Data Manipulation Operators operations for standard processing of climate and NWP model output."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CDO Operations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cdo_info" title="Climate Data Information Operators to get information on Climate and NWP model data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CDO get info</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=timeseries_extraction" title="Extract and plot time series"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF timeseries Extractor</button></a>
 <h3>Apollo</h3>
+<a href="https://usegalaxy.eu/root?tool_id=create_account" title="with Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Register Account</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=list_organism" title="in Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">List Organisms</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=iframe" title="opens an IFrame to Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Annotate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fetch_jbrowse" title="for an organism, from Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Retrieve JBrowse</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=feat_from_gff3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF3 to Apollo Annotations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=export" title="from Apollo into Galaxy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Retrieve Data</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=iframe" title="opens an IFrame to Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Annotate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=create_or_update" title="will create the organism if it doesn't exist, and update otherwise"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create or Update Organism</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=delete_organism" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delete an Apollo record</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=create_account" title="with Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Register Account</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=list_organism" title="in Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">List Organisms</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=delete_features" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delete all annotations from an Apollo record</button></a>
 <h3>Imaging</h3>
-<a href="https://usegalaxy.eu/root?tool_id=ip_localthreshold" title="applies a local threshold algorithm to an image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Local Threshold</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_threshold" title="applies a standard thresholding algorithm to an image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Auto Threshold</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_projective_transformation_points" title="of ROIs defined by pixel (point) coordinates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Projective Transformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_projective_transformation" title="of 2D images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Projective Transformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=idr_download_by_ids" title="- download images from any OMERO instance using image IDs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDR/OMERO Download</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_spot_detection_2d" title="in a 2D image (sequence)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Spot Detection</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_points_association_nn" title="in consecutive frames (slices) using the nearest neighbor algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Association of points</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_curve_fitting" title="to data points using (1st- or 2nd-degree) polynomial function"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Curve Fitting</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_cellprofiler" title="run a CellProfiler pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CellProfiler</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_common" title="load images and metadata into CellProfiler (Images, Metadata, NamesAndTypes, Groups)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Starting Modules</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_color_to_gray" title="converts color and channel-stacked images to grayscale"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ColorToGray</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_tile" title="tiles images together to form large montage images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tile</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_image_registration" title="based on intensity information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Image Registration</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_track_objects" title="tracking objects throughout sequential frames of a series of images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TrackObjects</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_overlay_outlines" title="places outlines of objects over a desired image."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OverlayOutlines</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_convert_objects_to_image" title="convert the identified objects into an image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ConvertObjectsToImage</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_display_data_on_image" title="produce an image with data on top of identified objects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DisplayDataOnImage</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_enhance_or_suppress_features" title="to improve subsequent identification of objects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EnhanceOrSuppressFeatures</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_export_to_spreadsheet" title="export measurements into one or more files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ExportToSpreadsheet</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_gray_to_color" title="take grayscale images and produces a color image from them"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GrayToColor</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_identify_primary_objects" title="identify biological objects of interest"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IdentifyPrimaryObjects</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_mask_image" title="hide portions of an image based on previously identified objects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaskImage</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_measure_granularity" title="output spectra of size measurements of the textures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MeasureGranularity</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_measure_image_area_occupied" title="measure the area in an image occupied by objects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MeasureImageAreaOccupied</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_measure_image_intensity" title="measure several intensity features across an entire image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MeasureImageIntensity</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_measure_image_quality" title="measure features that indicate image quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MeasureImageQuality</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_measure_object_intensity" title="measure several intensity features for identified objects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MeasureObjectIntensity</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_measure_object_size_shape" title="measure area and shape features of identified objects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MeasureObjectSizeShape</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_measure_texture" title="quantify the roughness and smoothness of the textures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MeasureTexture</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_relate_objects" title="assign relationships parent-children between objects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RelateObjects</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_save_images" title="or movie files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SaveImages</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_image_math" title="perform simple mathematical operations on images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ImageMath</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_landmark_registration_ls" title="using least squares"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Landmark Registration</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spyboat" title="wavelet analyzes image stacks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpyBOAT</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_binary_to_edm" title="(Euclidean Distance Map)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to EDM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_skeletonize3d" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Skeletonize</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_find_edges" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Find edges</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_shadows" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add shadow effect</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_enhance_contrast" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Enhance contrast</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_find_maxima" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Find maxima</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_watershed_binary" title="of binary image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Watershed segmentation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_raw_transform" title="with bUnwarpJ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Apply raw transformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_math" title="with a mathematical expression"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Operate on pixels</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_elastic_transform" title="with bUnwarpJ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Apply elastic transformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_viz_overlay_moving_and_fixed_image" title="moving and fixed image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Overlay</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_wsi_extract_top_view" title="from whole-slice image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract top view</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gstf_preparation" title="converts data for the workflow"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GeneSeqToFamily preparation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_convert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Image Converter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_landmark_registration" title="Landmark Registration"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Landmark Registration</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_adapt_transform" title="to a new image size with bUnwarpJ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Adapt an elastic transformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_adjust_threshold_binary" title="of binary image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Adjust threshold</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compose_elastic" title="into a raw transformation with bUnwarpJ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compose two elastic transformations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_sharpen" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sharpen</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_make_binary" title="(black and white)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert to binary</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_convert_to_raw" title="with bUnwarpJ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert elastic transformation to raw</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compare_raw" title="by warping index with bUnwarpJ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare two raw deformations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compare_elastic" title="by warping index with bUnwarpJ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare opposite elastic deformations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_analyze_skeleton" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Analyze skeleton</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_smooth" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Smooth</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_align" title="with bUnwarpJ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align two images</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compose_raw" title="into another raw transformation with bUnwarpJ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compose two raw transformations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_noise" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add or remove noise</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_create_image" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create new image</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_analyze_particles_binary" title="of binary image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Analyze particles</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_points_to_binaryimage" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert point coordinates to binary image</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=label_to_binary" title="with NumPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert label map to binary image</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=orientationpy" title="with OrientationPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute image orientation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gate_finder" title="with Vitessce"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform gating</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cellpose" title="with Cellpose"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run generalist cell and nucleus segmentation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bia_download" title="Download images from Bioimage Archive"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FTP Link for Bioimage Archive</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_binary_to_labelimage" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to label map</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_curve_fitting" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform curve fitting</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_image_registration" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform affine image registration (intensity-based)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_landmark_registration" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform affine image registration (landmark-based)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_segmetrics" title="with SegMetrics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute image segmentation and object detection performance measures</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_color_deconvolution" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform color decomposition</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_overlay_images" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Overlay images</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spyboat" title="with SpyBOAT"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform wavelet transformation on 3D-image stack</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rfove" title="with RFOVE"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform segmentation using region-based fitting of overlapping ellipses</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=idr_download_by_ids" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Download IDR/OMERO</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_visceral_evaluatesegmentation" title="with EvaluateSegmentation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Evaluate segmentation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_2d_feature_extraction" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract 2D features</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_scale_image" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scale image</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_binary_to_edm" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to EDM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_cellprofiler" title="with CellProfiler 3"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run CellProfiler pipeline</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_common" title="Load images and metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Starting Modules</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_color_to_gray" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ColorToGray</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_tile" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tile</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_track_objects" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TrackObjects</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_overlay_outlines" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OverlayOutlines</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_convert_objects_to_image" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ConvertObjectsToImage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_display_data_on_image" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DisplayDataOnImage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_enhance_or_suppress_features" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EnhanceOrSuppressFeatures</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_export_to_spreadsheet" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ExportToSpreadsheet</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_gray_to_color" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GrayToColor</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_identify_primary_objects" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IdentifyPrimaryObjects</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_mask_image" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaskImage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_measure_granularity" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MeasureGranularity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_measure_image_area_occupied" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MeasureImageAreaOccupied</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_measure_image_intensity" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MeasureImageIntensity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_measure_image_quality" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MeasureImageQuality</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_measure_object_intensity" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MeasureObjectIntensity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_measure_object_size_shape" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MeasureObjectSizeShape</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_measure_texture" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MeasureTexture</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_relate_objects" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RelateObjects</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_save_images" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SaveImages</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_image_math" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ImageMath</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_projective_transformation_points" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Performs projective transformation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_skeletonize3d" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Skeletonize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_find_edges" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Find edges</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_shadows" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add shadow effect</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_enhance_contrast" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Enhance contrast</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_find_maxima" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Find maxima</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_watershed_binary" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform segmentation using watershed transformation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_raw_transform" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Apply raw transformation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_math" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Operate on pixels</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_elastic_transform" title="with ImageJ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Apply elastic transformation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_cellprofiler4" title="with CellProfiler 4"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run CellProfiler pipeline</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compare_elastic_raw" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare elastic and raw deformation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compose_raw_elastic" title="into a raw transformation with bUnwarpJ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compose a raw and an elastic transformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compare_elastic_raw" title="by warping index with bUnwarpJ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare elastic and raw deformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_imageinfo" title="Show Image Info"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Image Info</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_detection_viz" title="Detection Visualization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Detection Visualization</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_histogram_equalization" title="automatic histogram equalization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Histogram equalization</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_convertimage" title="Convert image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert image</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_colocalization" title="of two segmentation maps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Colocalization</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_2d_feature_extraction" title="Feature Extraction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">2D Feature Extraction</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_permutate_axis" title="along an axis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Permutate image</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_labelimage_to_points" title="Converts label image to points"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Label to Points</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_points_to_label" title="Points to Label Image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Points to Label</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_concat_channels" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate images</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_scale_image" title="Scales image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scale Image</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_merge_neighbours_in_label" title="Merge Neighbours in Label Image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge Neighbours in Label</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_binary_to_labelimage" title="Converts Binary to Label Image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Binary 2 Label</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_2d_filter_segmentation_by_features" title="Filter segmentation by rules"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter segmentation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_analyze_particles_binary" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Analyze particles</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_create_image" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create new image</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_noise" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add or remove noise</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compose_raw" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compose two raw transformations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_align" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align two images</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_smooth" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Smooth image</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_analyze_skeleton" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Analyze skeleton</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compare_elastic" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare opposite elastic deformations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compare_raw" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare two raw deformations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_convert_to_raw" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert elastic transformation to raw</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_make_binary" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert to binary</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_sharpen" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sharpen</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compose_elastic" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compose two elastic transformations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_adjust_threshold_binary" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Adjust threshold</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_adapt_transform" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Adapt an elastic transformation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_filter_standard" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter 2D image</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_mahotas_features" title="with Mahotas"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute image features</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_threshold" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Threshold image</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_convertimage" title="with Bioformats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert image format</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_histogram_equalization" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform histogram equalization</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_superdsm" title="with SuperDSM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform segmentation using deformable shape models</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_anisotropic_diffusion" title="with MedPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Apply anisotropic diffusion</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_projective_transformation" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Performs projective transformation with/without labels</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_spot_detection_2d" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform 2D spot detection</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_points_association_nn" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform linking in time series (nearest neighbors)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagecoordinates_flipaxis" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Switch axis coordinates</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_2d_filter_segmentation_by_features" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter label map by rules</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_imageinfo" title="with Bioformats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Show image info</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_binaryimage_to_points" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to points (center of masses)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_merge_neighbours_in_label" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge neighbors in label map</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_slice_image" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slice image</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_split_labelmap" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split label map using morphological operators</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_concat_channels" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate images or channels</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_points_to_label" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert point coordinates to label map</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_labelimage_to_points" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert label map to points (center of masses)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_permutate_axis" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Permutate image axes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_count_objects" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Count objects in label map</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_coordinates_of_roi" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to points (point coordinates)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bf2raw" title="with Bioformats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert to OME-Zarr</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=woundhealing_scratch_assay" title="image analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Wound healing scratch assay</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vitessce_spatial" title="with Vitessce"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run multi-modal single-cell visualization</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=squidpy_spatial" title="with Squidpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Analyze and visualize spatial multi-omics data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rename_tiff_channels" title="with ome-types"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Rename OME-TIFF channels</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cell_intensity_processing" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Process single-cell intensities</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=voronoi_tessellation" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute Voronoi tessellation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=morphological_operations" title="with SciPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Apply a morphological operation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=image_math" title="with NumPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Process images using arithmetic expressions</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_detection_viz" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Visualize detections</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_wsi_extract_top_view" title="with OpenSlide"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract top view from whole-slide image</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_convert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Image Converter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_localthreshold" title="applies a local threshold algorithm to an image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Local Threshold</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_2d_split_binaryimage_by_watershed" title="Split binary image by using watershed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split objects</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_anisotropic_diffusion" title="Edge-preserving, Anisotropic diffusion"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Anisotropic Diffusion</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_color_deconvolution" title="Color deconvolution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Color Deconvolution</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_filter_standard" title="applies a standard filter to an image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter Image</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_points_to_labe" title="Points to Label Image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Points to Label</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagecoordinates_flipaxis" title="Switches the axes of an image and flips the y axis."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Switch axis coordinates</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_coordinates_of_roi" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Coordinates of ROI</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_count_objects" title="in labled images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Count Objects</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_mahotas_features" title="Compute features using mahotas"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Mahotas-features</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_overlay_segmentation" title="Overlay Segmentation Mask"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Overlay Segmentation Mask</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_points_to_binaryimage" title="Converts points to a binary image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Points to Binary Image</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_visceral_evaluatesegmentation" title="Evaluate Segmentation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Visceral</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_binaryimage_to_points" title="Converts Binary Image to Points"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Binary To Points</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_slice_image" title="into smaller patches"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slice Image</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_split_labelmap" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split Labelmap</button></a>
 <h3>Species abundance</h3>
 <a href="https://usegalaxy.eu/root?tool_id=pampa_glmsp" title="Compute a GLM of your choice on population data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute GLM on population data</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pampa_glmcomm" title="Compute a GLM of your choice on community data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute GLM on community data</button></a>
@@ -2774,16 +3168,51 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=regionalgam_gls_adjusted" title="for autocorrelation in the residuals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Linear regression ajusted</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=regionalgam_plot_trend" title="with trend line"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Plot abundance</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=regionalgam_ab_index" title="computation across species, sites and years"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Abundance index</button></a>
+<h3>Compute indicators for turnover boulders fields</h3>
+<a href="https://usegalaxy.eu/root?tool_id=cb_dissim" title="indicator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QECB-Dissimilarity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cb_ivr" title="indicator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IVR</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cb_div" title="indicators"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diversity</button></a>
+<h3>Ecoregionalization</h3>
+<a href="https://usegalaxy.eu/root?tool_id=ecoregion_brt_analysis" title="for species distribution modelling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BRT tool prediction</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ecoregion_taxa_seeker" title="for recover list of taxa"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TaxaSeeker</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ecoregion_eco_map" title="Create map from cluster to visualize ecoregions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EcoMap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ecoregion_cluster_estimate" title="Find an optimal number of cluster with SIH index"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ClusterEstimate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ecoregion_clara_cluster" title="Make cluster from BRT prediction with Clara algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ClaraClust</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ecoregion_GeoNearestNeighbor" title="Merge two data tables by finding the closest points based on latitude and longitude coordinates (WGS84 projection)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GeoNearestNeighbor</button></a>
+<h3>Indicators from geometric mean</h3>
+<a href="https://usegalaxy.eu/root?tool_id=Map_shp" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make a map with a shapefile</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Mean_geom" title="- calcul of the geometric means for the 'bois mort' indicator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Geometric means</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bar_plot" title="for simple discrete data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bar plot</button></a>
+<h3>Astronomy</h3>
+<a href="https://usegalaxy.eu/root?tool_id=astronomical_archives" title="queries astronomical archives through Virtual Observatory protocols"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Astronomical Archives (IVOA)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=astropy_fits2bitmap" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">astropy fits2bitmap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=astropy_fits2csv" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">astropy fits2csv</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=astropy_fitsinfo" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">astropy fitsinfo</button></a>
 <h3>Interactive tools</h3>
-<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_jupyter_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive Jupyter Notebook</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_ml_jupyter_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GPU enabled Interactive Jupyter Notebook for Machine Learning</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_source" title="Sea Observations Utility for Reprocessing, Calibration and Evaluation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive Source Notebooks</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_napari" title="interactive tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run Napari</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_cellprofiler" title="interactive tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run CellProfiler</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_tadviewer" title="interactive table viewer with SQL enginer for filtering"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tadviewer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_qgis" title="interactive geographic information system (GIS)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QGIS</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_qupath" title="interactive Open Software for Bioimage Analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QuPath</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_odv" title="interactive plotting tool for geo-referenced data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ODV</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_ilastik" title="interactive learning and segmentation toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Ilastik</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_metashrimps" title="Metadata Shiny for Retroactive Information Management and Production of data paper Sketches"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metashrimps</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_hdfview" title="Desktop application to display netcdf, hdf4 or hdf5 files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive Hdfview tool</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_scoop3_argo" title="Interactive visual quality control of Argo netCDF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scoop3-Argo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_divand" title="Data-Interpolating Variational Analysis in n dimensions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive DIVAnd Notebooks</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_blobtoolkit" title="genome assembly QC viewer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive BlobToolKit</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_pavian" title="Interactive analysis of metagenomics data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pavian</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_mgnify_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive MGnify Notebook</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_jupyter_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive JupyTool and notebook</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_ml_jupyter_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GPU-enabled Interactive Jupyter Notebook for Machine Learning</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_climate_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive Climate Notebook</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_pangeo_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive Pangeo Notebook</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_pangeo_ml_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive Pangeo Machine Learning Notebook</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_rstudio" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RStudio</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_pyiron" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyIron Interactive Jupyter Notebook</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_higlass" title="an interactive Hi-C data visualizer."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HiGlass</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_openrefine" title="Working with messy data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenRefine</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_guacamole_desktop" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Ubuntu XFCE Desktop</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_panoply" title="interative plotting tool for geo-referenced data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Panoply</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_askomics" title="a visual SPARQL query builder"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AskOmics</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_cellxgene" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive CellXgene Environment</button></a>
@@ -2800,6 +3229,15 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_vrm_editor" title="interative tool for creating Variable Resolution Mesh for NorESM/CESM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VRM Editor</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_simtext_app" title="Interactive shiny app to explore SimText output data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SimText</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_isee" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">iSEE</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_metashark" title="Metadata Shiny Automated Resource and Knowledge"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metashark</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_audiolabeler" title="Nature+Energy Audio Labeller audio data annotation tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NEAL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_genenotebook" title="viewer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GeneNoteBook</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_holoviz" title="High-level tools to simplify visualization in Python"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Holoviz</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook" title="sample notebooks to access and discover data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Data Space Ecosystem</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_qiskit_jupyter_notebook" title="interactive tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Qiskit Jupyter notebook</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_stac" title="for searching, aggregating and downloading data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">STAC catalog</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_ideal" title="Interactive Differential Expression AnaLysis in RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDEAL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_phyloseq" title="Explore microbiome profiles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq</button></a>
 <h3>OBO Ontology manipulation</h3>
 <a href="https://usegalaxy.eu/root?tool_id=onto_tk_get_ancestor_terms" title="Collects the ancestor terms from a given term in the given OBO ontology"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get the ancestor terms of a given OBO term</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=onto_tk_get_relationship_types" title="from the given OBO ontology"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get all the relationship types</button></a>
@@ -2819,7 +3257,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=onto_tk_get_root_terms" title="of a given OBO term"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get the root terms</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=onto_tk_get_relationship_id_vs_relationship_name" title="from the given OBO ontology"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get all the relationship IDs and names</button></a>
 <h3>HCA-Single Cell</h3>
-<a href="https://usegalaxy.eu/root?tool_id=ucsc_cell_browser" title="displays single-cell clusterized data in an interactive web application."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UCSC Cell Browser</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_find_markers" title="to find differentially expressed genes between groups"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy FindMarkers</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_scale_data" title="to make expression variance the same for all genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy ScaleData</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_run_umap" title="visualise cell clusters using UMAP"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy RunUMAP</button></a>
@@ -2834,52 +3271,274 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_compute_graph" title="to derive kNN graph"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy ComputeGraph</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hca_matrix_downloader" title="retrieves expression matrices and metadata from the Human Cell Atlas."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Human Cell Atlas Matrix Downloader</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=_ensembl_gtf2gene_list" title="extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GTF2GeneList</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ucsc_cell_browser" title="displays single-cell clusterized data in an interactive web application."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UCSC Cell Browser</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_parameter_iterator" title="produce an iteration over a defined parameter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy ParameterIterator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_plot_trajectory" title="visualise cell trajectories"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy PlotTrajectory</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scmap_index_cell" title="creates a cell index for a dataset to enable fast approximate nearest neighbour search"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scmap index cells</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=retrieve_scxa" title="Retrieves expression matrixes and metadata from EBI Single Cell Expression Atlas (SCXA)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EBI SCXA Data Retrieval</button></a>
-<h3>SAM/BAM Manipulation</h3>
-<a href="https://usegalaxy.eu/root?tool_id=pileup_parser" title="on coverage and SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter pileup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sam2interval" title="to interval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SAM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sam_merge2" title="merges BAM files together"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge BAM Files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sam_pileup" title="from BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate pileup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_flagstat" title="provides simple stats on BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">flagstat</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_mpileup" title="SNP and indel caller"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MPileup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_rmdup" title="remove PCR duplicates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rmdup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_slice_bam" title="by provided regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slice BAM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pileup_interval" title="condenses pileup format into ranges of bases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pileup-to-Interval</button></a>
-<h3>Metagenomic Analysis</h3>
-<a href="https://usegalaxy.eu/root?tool_id=t2t_report" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Summarize taxonomy</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Draw_phylogram" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Draw phylogeny</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=poisson2test" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Poisson two-sample test</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=lca1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Find lowest diagnostic rank</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Fetch Taxonomic Ranks" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fetch taxonomic representation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=find_diag_hits" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Find diagnostic hits</button></a>
-<h3>GATK Tools</h3>
-<a href="https://usegalaxy.eu/root?tool_id=gatk_count_covariates" title="on BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Count Covariates</button></a>
 <h3>Other Tools</h3>
-<a href="https://usegalaxy.eu/root?tool_id=ffindex_dbkit_merge" title="two databases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DBKit Merge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ffindex_dbkit_extract" title="entries"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DBKit Extract</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spring_model" title="complex structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SPRING Model</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spring_minz" title="filter operation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SPRING Min-Z</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spring_cross" title="reference builder"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SPRING Cross</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pubmed_by_queries" title="download a defined number of abstracts or PMIDs from PubMed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PubMed query</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=text_to_wordmatrix" title="by extracting most frequent words"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Text to wordmatrix</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=abstracts_by_pmids" title="by PMID IDs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get PubMed abstracts</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=text_to_wordmatrix" title="by extracting most frequent words"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Text to wordmatrix</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pmids_to_pubtator_matrix" title="binary matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PMIDs to PubTator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pubmed_by_queries" title="download a defined number of abstracts or PMIDs from PubMed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PubMed query</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spring_cross" title="reference builder"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SPRING Cross</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=spring_model_all" title="complex structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SPRING Model-All</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ffindex_dbkit_create" title="database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DBKit Create</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=spring_map" title="with BLAST"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SPRING Map</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spring_minz" title="filter operation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SPRING Min-Z</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spring_model" title="complex structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SPRING Model</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=spring_mcc" title="plot generator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SPRING MCC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ffindex_dbkit_create" title="database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DBKit Create</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ffindex_dbkit_extract" title="entries"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DBKit Extract</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ffindex_dbkit_merge" title="two databases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DBKit Merge</button></a>
 <h3>Biodiversity data exploration</h3>
-<a href="https://usegalaxy.eu/root?tool_id=ecology_stat_presence_abs" title="of a numeric variable"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Statistics on presence-absence</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ecology_link_between_var" title="Shows interaction, correlation, colinearity, produces a PCA and computes VIF for biodiversity abundance data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Variables exploration</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tool_anonymization" title="without loss of the spatial relationships"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Spatial coordinates anonymization</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ecology_beta_diversity" title="Computes a measure of beta diversity, SCBD and representations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Local Contributions to Beta Diversity (LCBD)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ecology_homogeneity_normality" title="Checks the homogeneity of the variance and the normality of the distribution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Homoscedasticity and normality</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ecology_link_between_var" title="Shows interaction, correlation, colinearity, produces a PCA and computes VIF for biodiversity abundance data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Variables exploration</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ecology_presence_abs_abund" title="Community abundance map, presence barplot and rarefaction curves"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Presence-absence and abundance</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tool_anonymization" title="without loss of the spatial relationships"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Spatial coordinates anonymization</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ecology_stat_presence_abs" title="of a numeric variable"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Statistics on presence-absence</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cb_div" title="indicators"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diversity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=obisindicators" title="from OBIS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Ocean biodiversity indicators</button></a>
 <h3>Sanger Sequencing</h3>
-<a href="https://usegalaxy.eu/root?tool_id=tracy_assemble" title="genomic region from tiled, overlapping Sanger Chromatogram trace files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tracy Assemble</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tracy_basecall" title="from Sanger chromatogram tracefile"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tracy Basecall</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tracy_decompose" title="heterozygous mutations (and call variants)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tracy Decompose</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tracy_align" title="chromatogram to a FASTA reference"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tracy Align</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tracy_decompose" title="heterozygous mutations (and call variants)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tracy Decompose</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tracy_assemble" title="genomic region from tiled, overlapping Sanger Chromatogram trace files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tracy Assemble</button></a>
+<h3>Extract Features</h3>
+<a href="https://usegalaxy.eu/root?tool_id=length_and_gc_content" title="from GTF and FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gene length and GC content</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=parse_mito_blast" title="overlap-conscious coverage calculation between scaffold-accession number pairs from blast output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Parse mitochondrial blast</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=orfipy" title="a versatile ORF finder"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ORFipy</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=b2btools_single_sequence" title="from their amino-acid sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">b2bTools: Biophysical predictors for single sequences</button></a>
+<h3>QIIME 2</h3>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__deblur__denoise_16S" title="Deblur sequences using a 16S positive filter."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 deblur denoise-16S</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__first_differences" title="Compute first differences or difference from baseline between sequential states"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal first-differences</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__alignment__mafft" title="De novo multiple sequence alignment with MAFFT"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 alignment mafft</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__alignment__mafft_add" title="Add sequences to multiple sequence alignment with MAFFT."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 alignment mafft-add</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__alignment__mask" title="Positional conservation and gap filtering."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 alignment mask</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__composition__add_pseudocount" title="Add pseudocount to table."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 composition add-pseudocount</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__composition__ancom" title="Apply ANCOM to identify features that differ in abundance."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 composition ancom</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__composition__ancombc" title="Analysis of Composition of Microbiomes with Bias Correction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 composition ancombc</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__composition__tabulate" title="View tabular output from ANCOM-BC."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 composition tabulate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__cutadapt__demux_paired" title="Demultiplex paired-end sequence data with barcodes in-sequence."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 cutadapt demux-paired</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__cutadapt__demux_single" title="Demultiplex single-end sequence data with barcodes in-sequence."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 cutadapt demux-single</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__cutadapt__trim_paired" title="Find and remove adapters in demultiplexed paired-end sequences."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 cutadapt trim-paired</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__cutadapt__trim_single" title="Find and remove adapters in demultiplexed single-end sequences."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 cutadapt trim-single</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__dada2__denoise_ccs" title="Denoise and dereplicate single-end Pacbio CCS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 dada2 denoise-ccs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__dada2__denoise_paired" title="Denoise and dereplicate paired-end sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 dada2 denoise-paired</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__dada2__denoise_pyro" title="Denoise and dereplicate single-end pyrosequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 dada2 denoise-pyro</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__dada2__denoise_single" title="Denoise and dereplicate single-end sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 dada2 denoise-single</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__deblur__denoise_other" title="Deblur sequences using a user-specified positive filter."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 deblur denoise-other</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__deblur__visualize_stats" title="Visualize Deblur stats per sample."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 deblur visualize-stats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__demux__emp_paired" title="Demultiplex paired-end sequence data generated with the EMP protocol."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 demux emp-paired</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__demux__emp_single" title="Demultiplex sequence data generated with the EMP protocol."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 demux emp-single</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__demux__filter_samples" title="Filter samples out of demultiplexed data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 demux filter-samples</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__demux__subsample_paired" title="Subsample paired-end sequences without replacement."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 demux subsample-paired</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__demux__subsample_single" title="Subsample single-end sequences without replacement."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 demux subsample-single</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__demux__summarize" title="Summarize counts per sample."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 demux summarize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__adonis" title="adonis PERMANOVA test for beta group significance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity adonis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__alpha" title="Alpha diversity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity alpha</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__alpha_correlation" title="Alpha diversity correlation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity alpha-correlation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__alpha_group_significance" title="Alpha diversity comparisons"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity alpha-group-significance</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__alpha_phylogenetic" title="Alpha diversity (phylogenetic)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity alpha-phylogenetic</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__alpha_rarefaction" title="Alpha rarefaction curves"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity alpha-rarefaction</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__beta" title="Beta diversity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity beta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__beta_correlation" title="Beta diversity correlation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity beta-correlation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__beta_group_significance" title="Beta diversity group significance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity beta-group-significance</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__beta_phylogenetic" title="Beta diversity (phylogenetic)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity beta-phylogenetic</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__beta_rarefaction" title="Beta diversity rarefaction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity beta-rarefaction</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__bioenv" title="bioenv"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity bioenv</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__core_metrics" title="Core diversity metrics (non-phylogenetic)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity core-metrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__core_metrics_phylogenetic" title="Core diversity metrics (phylogenetic and non-phylogenetic)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity core-metrics-phylogenetic</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__filter_distance_matrix" title="Filter samples from a distance matrix."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity filter-distance-matrix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__mantel" title="Apply the Mantel test to two distance matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity mantel</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__pcoa" title="Principal Coordinate Analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity pcoa</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__pcoa_biplot" title="Principal Coordinate Analysis Biplot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity pcoa-biplot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__procrustes_analysis" title="Procrustes Analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity procrustes-analysis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__tsne" title="t-distributed stochastic neighbor embedding"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity tsne</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__umap" title="Uniform Manifold Approximation and Projection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity umap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity_lib__alpha_passthrough" title="Alpha Passthrough (non-phylogenetic)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity-lib alpha-passthrough</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity_lib__beta_passthrough" title="Beta Passthrough (non-phylogenetic)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity-lib beta-passthrough</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity_lib__beta_phylogenetic_meta_passthrough" title="Beta Phylogenetic Meta Passthrough"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity-lib beta-phylogenetic-meta-passthrough</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity_lib__beta_phylogenetic_passthrough" title="Beta Phylogenetic Passthrough"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity-lib beta-phylogenetic-passthrough</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity_lib__bray_curtis" title="Bray-Curtis Dissimilarity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity-lib bray-curtis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity_lib__faith_pd" title="Faith's Phylogenetic Diversity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity-lib faith-pd</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity_lib__jaccard" title="Jaccard Distance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity-lib jaccard</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity_lib__observed_features" title="Observed Features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity-lib observed-features</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity_lib__pielou_evenness" title="Pielou's Evenness"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity-lib pielou-evenness</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity_lib__shannon_entropy" title="Shannon's Entropy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity-lib shannon-entropy</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity_lib__unweighted_unifrac" title="Unweighted Unifrac"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity-lib unweighted-unifrac</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity_lib__weighted_unifrac" title="Weighted Unifrac"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity-lib weighted-unifrac</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__emperor__biplot" title="Visualize and Interact with Principal Coordinates Analysis Biplot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 emperor biplot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__emperor__plot" title="Visualize and Interact with Principal Coordinates Analysis Plots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 emperor plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__emperor__procrustes_plot" title="Visualize and Interact with a procrustes plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 emperor procrustes-plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__blast" title="BLAST+ local alignment search."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier blast</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__classify_consensus_blast" title="BLAST+ consensus taxonomy classifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier classify-consensus-blast</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__classify_consensus_vsearch" title="VSEARCH-based consensus taxonomy classifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier classify-consensus-vsearch</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__classify_hybrid_vsearch_sklearn" title="ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier classify-hybrid-vsearch-sklearn</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__classify_sklearn" title="Pre-fitted sklearn-based taxonomy classifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier classify-sklearn</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__extract_reads" title="Extract reads from reference sequences."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier extract-reads</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__find_consensus_annotation" title="Find consensus among multiple annotations."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier find-consensus-annotation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__fit_classifier_naive_bayes" title="Train the naive_bayes classifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier fit-classifier-naive-bayes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__fit_classifier_sklearn" title="Train an almost arbitrary scikit-learn classifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier fit-classifier-sklearn</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__vsearch_global" title="VSEARCH global alignment search"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier vsearch-global</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__core_features" title="Identify core features in table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table core-features</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__filter_features" title="Filter features from table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table filter-features</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__filter_features_conditionally" title="Filter features from a table based on abundance and prevalence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table filter-features-conditionally</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__filter_samples" title="Filter samples from table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table filter-samples</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__filter_seqs" title="Filter features from sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table filter-seqs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__group" title="Group samples or features by a metadata column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table group</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__heatmap" title="Generate a heatmap representation of a feature table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table heatmap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__merge" title="Combine multiple tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table merge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__merge_seqs" title="Combine collections of feature sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table merge-seqs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__merge_taxa" title="Combine collections of feature taxonomies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table merge-taxa</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__presence_absence" title="Convert to presence/absence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table presence-absence</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__rarefy" title="Rarefy table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table rarefy</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__relative_frequency" title="Convert to relative frequencies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table relative-frequency</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__rename_ids" title="Renames sample or feature ids in a table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table rename-ids</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__subsample" title="Subsample table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table subsample</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__summarize" title="Summarize table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table summarize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__tabulate_seqs" title="View sequence associated with each feature"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table tabulate-seqs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__transpose" title="Transpose a feature table."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table transpose</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__fragment_insertion__classify_otus_experimental" title="Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 fragment-insertion classify-otus-experimental</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__fragment_insertion__filter_features" title="Filter fragments in tree from table."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 fragment-insertion filter-features</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__fragment_insertion__sepp" title="Insert fragment sequences using SEPP into reference phylogenies."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 fragment-insertion sepp</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__gneiss__assign_ids" title="Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 gneiss assign-ids</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__gneiss__correlation_clustering" title="Hierarchical clustering using feature correlation."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 gneiss correlation-clustering</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__gneiss__dendrogram_heatmap" title="Dendrogram heatmap."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 gneiss dendrogram-heatmap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__gneiss__gradient_clustering" title="Hierarchical clustering using gradient information."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 gneiss gradient-clustering</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__gneiss__ilr_hierarchical" title="Isometric Log-ratio Transform applied to a hierarchical clustering"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 gneiss ilr-hierarchical</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__gneiss__ilr_phylogenetic" title="Isometric Log-ratio Transform applied to a phylogenetic tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 gneiss ilr-phylogenetic</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__gneiss__ilr_phylogenetic_differential" title="Differentially abundant Phylogenetic Log Ratios."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 gneiss ilr-phylogenetic-differential</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__gneiss__ilr_phylogenetic_ordination" title="Ordination through a phylogenetic Isometric Log Ratio transform."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 gneiss ilr-phylogenetic-ordination</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__anova" title="ANOVA test"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal anova</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__feature_volatility" title="Feature volatility analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal feature-volatility</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__first_distances" title="Compute first distances or distance from baseline between sequential states"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal first-distances</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__linear_mixed_effects" title="Linear mixed effects modeling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal linear-mixed-effects</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__maturity_index" title="Microbial maturity index prediction."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal maturity-index</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__nmit" title="Nonparametric microbial interdependence test"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal nmit</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__pairwise_differences" title="Paired difference testing and boxplots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal pairwise-differences</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__pairwise_distances" title="Paired pairwise distance testing and boxplots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal pairwise-distances</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__plot_feature_volatility" title="Plot longitudinal feature volatility and importances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal plot-feature-volatility</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__volatility" title="Generate interactive volatility plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal volatility</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__metadata__distance_matrix" title="Create a distance matrix from a numeric Metadata column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 metadata distance-matrix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__metadata__shuffle_groups" title="Shuffle values in a categorical sample metadata column."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 metadata shuffle-groups</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__metadata__tabulate" title="Interactively explore Metadata in an HTML table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 metadata tabulate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__align_to_tree_mafft_fasttree" title="Build a phylogenetic tree using fasttree and mafft alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny align-to-tree-mafft-fasttree</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__align_to_tree_mafft_iqtree" title="Build a phylogenetic tree using iqtree and mafft alignment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny align-to-tree-mafft-iqtree</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__align_to_tree_mafft_raxml" title="Build a phylogenetic tree using raxml and mafft alignment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny align-to-tree-mafft-raxml</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__fasttree" title="Construct a phylogenetic tree with FastTree."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny fasttree</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__filter_table" title="Remove features from table if they're not present in tree."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny filter-table</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__filter_tree" title="Remove features from tree based on metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny filter-tree</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__iqtree" title="Construct a phylogenetic tree with IQ-TREE."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny iqtree</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__iqtree_ultrafast_bootstrap" title="Construct a phylogenetic tree with IQ-TREE with bootstrap supports."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny iqtree-ultrafast-bootstrap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__midpoint_root" title="Midpoint root an unrooted phylogenetic tree."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny midpoint-root</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__raxml" title="Construct a phylogenetic tree with RAxML."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny raxml</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__raxml_rapid_bootstrap" title="Construct a phylogenetic tree with bootstrap supports using RAxML."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny raxml-rapid-bootstrap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__robinson_foulds" title="Calculate Robinson-Foulds distance between phylogenetic trees."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny robinson-foulds</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__quality_control__bowtie2_build" title="Build bowtie2 index from reference sequences."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 quality-control bowtie2-build</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__quality_control__evaluate_composition" title="Evaluate expected vs. observed taxonomic composition of samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 quality-control evaluate-composition</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__quality_control__evaluate_seqs" title="Compare query (observed) vs. reference (expected) sequences."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 quality-control evaluate-seqs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__quality_control__evaluate_taxonomy" title="Evaluate expected vs. observed taxonomic assignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 quality-control evaluate-taxonomy</button></a>
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+<a href="https://usegalaxy.eu/root?tool_id=qiime2__quality_control__filter_reads" title="Filter demultiplexed sequences by alignment to reference database."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 quality-control filter-reads</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__quality_filter__q_score" title="Quality filter based on sequence quality scores."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 quality-filter q-score</button></a>
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+<a href="https://usegalaxy.eu/root?tool_id=qiime2__sample_classifier__classify_samples_from_dist" title="Run k-nearest-neighbors on a labeled distance matrix."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 sample-classifier classify-samples-from-dist</button></a>
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+<a href="https://usegalaxy.eu/root?tool_id=qiime2__sample_classifier__heatmap" title="Generate heatmap of important features."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 sample-classifier heatmap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__sample_classifier__metatable" title="Convert (and merge) positive numeric metadata (in)to feature table."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 sample-classifier metatable</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__sample_classifier__predict_classification" title="Use trained classifier to predict target values for new samples."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 sample-classifier predict-classification</button></a>
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+<a href="https://usegalaxy.eu/root?tool_id=qiime2__sample_classifier__regress_samples_ncv" title="Nested cross-validated supervised learning regressor."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 sample-classifier regress-samples-ncv</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__sample_classifier__scatterplot" title="Make 2D scatterplot and linear regression of regressor predictions."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 sample-classifier scatterplot</button></a>
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+<a href="https://usegalaxy.eu/root?tool_id=qiime2__sample_classifier__summarize" title="Summarize parameter and feature extraction information for a trained estimator."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 sample-classifier summarize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__taxa__barplot" title="Visualize taxonomy with an interactive bar plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 taxa barplot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__taxa__collapse" title="Collapse features by their taxonomy at the specified level"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 taxa collapse</button></a>
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+<a href="https://usegalaxy.eu/root?tool_id=qiime2__taxa__filter_table" title="Taxonomy-based feature table filter."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 taxa filter-table</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__vsearch__cluster_features_closed_reference" title="Closed-reference clustering of features."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 vsearch cluster-features-closed-reference</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__vsearch__cluster_features_de_novo" title="De novo clustering of features."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 vsearch cluster-features-de-novo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__vsearch__cluster_features_open_reference" title="Open-reference clustering of features."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 vsearch cluster-features-open-reference</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__vsearch__dereplicate_sequences" title="Dereplicate sequences."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 vsearch dereplicate-sequences</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__vsearch__fastq_stats" title="Fastq stats with vsearch."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 vsearch fastq-stats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__vsearch__merge_pairs" title="Merge paired-end reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 vsearch merge-pairs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__vsearch__uchime_denovo" title="De novo chimera filtering with vsearch."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 vsearch uchime-denovo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__vsearch__uchime_ref" title="Reference-based chimera filtering with vsearch."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 vsearch uchime-ref</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2_core__tools__export" title="Export data from a QIIME 2 artifact"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 tools export</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2_core__tools__import" title="Import data into a QIIME 2 artifact"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 tools import</button></a>
+<h3>Metagenomic Analysis</h3>
+<a href="https://usegalaxy.eu/root?tool_id=t2t_report" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Summarize taxonomy</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Draw_phylogram" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Draw phylogeny</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=poisson2test" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Poisson two-sample test</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lca1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Find lowest diagnostic rank</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Fetch Taxonomic Ranks" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fetch taxonomic representation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=find_diag_hits" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Find diagnostic hits</button></a>
+<h3>GATK Tools</h3>
+<a href="https://usegalaxy.eu/root?tool_id=gatk_count_covariates" title="on BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Count Covariates</button></a>
+<h3>Built-in Converters</h3>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bz2_to_uncompressed" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert compressed file to uncompressed.</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_uncompressed_to_gz" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert uncompressed file to compressed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_biom" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Biom datasets</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_mdconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert XTC, DCD, and TRR</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bed_to_fli_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BED to Feature Location Index</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_maf_to_interval_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert MAF to Genomic Intervals</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bedstrict_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Strict BED</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_fai" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to fai file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bam_to_qname_sorted_bam" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM to queryname-sorted BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BED, GFF, or VCF to BigWig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gz_to_uncompressed" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert compressed file to uncompressed.</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_parquet_to_csv" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Parquet to csv</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bgzip_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Interval to BGZIP</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_molecules" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenBabel converter for molecular formats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_ref_to_seq_taxomony" title="converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Ref taxonomy to Seq Taxonomy</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_wiggle_to_interval_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Wiggle to Interval</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Coverage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_sam_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SAM to BigWig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lped2fpedconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert lped to fped</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_tar_to_directory" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert tar to directory</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_tabix_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Interval to tabix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_neostorezip_to_neostore" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert neostore.zip files to neostore</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gff_to_bed_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GFF to BED</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_len_to_linecount" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Len file to Linecount</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gff_to_fli_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GFF to Feature Location Index</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_Gro_to_Pdb_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GRO to PDB</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_tabular" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to Tabular</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_cram_to_bam_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert CRAM to BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bam_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM to BigWig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_2bit" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to 2bit</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fastq_to_fqtoc0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTQ files to seek locations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_mol2_to_mol" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert MOL2 to MOL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bed12_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Strict BED12</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_len" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to len file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert compressed and uncompressed BCF files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pbed2lpedconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert plink pbed to linkage lped</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_wig_to_bigwig" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Wiggle to BigWig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_inchi_to_mol" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert InChI to MOL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_bowtie_base_index" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to Bowtie base space Index</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_cml_to_smiles" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert CML to SMILES</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bedgraph_to_bigwig" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BedGraph to BigWig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_picard_interval_list_to_bed6" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Picard Interval List to BED6</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=csv_to_tabular" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert CSV to tabular</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tabular_to_csv" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert tabular to CSV</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bed_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To BED</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_maf_to_fasta_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert MAF to Fasta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_bowtie_color_index" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to Bowtie color space Index</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_smiles_to_smiles" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SMILES to SMILES</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM to coordinate-sorted BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pbed2ldindepconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert plink pbed to ld reduced format</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tabular_to_dbnsfp" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert tabular to dbnsfp</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gff_to_interval_index_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GFF to Interval Index</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_SMILES_to_MOL" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SMILES to MOL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bed6_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Strict BED6</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_Bam_Bai_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Bam to Bai</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bigwigtowig" title="Convert bigWig to wig"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BigWig to Wiggle</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BGZ VCF to tabix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lped2pbedconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert lped to plink pbed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bed_to_gff_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BED to GFF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_sam_to_unsorted_bam" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SAM to BAM without sorting</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_Pdb_to_Gro_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert PDB to GRO</button></a>