From 2339a231ca09eb4d213c1d51bfb5f0a7d82a41cf Mon Sep 17 00:00:00 2001
From: annefou <annefou@users.noreply.github.com>
Date: Sun, 28 Aug 2022 23:02:49 +0000
Subject: [PATCH] Update tools

---
 tools.md | 1877 +++++++++++++++++++++++++++++-------------------------
 1 file changed, 994 insertions(+), 883 deletions(-)

diff --git a/tools.md b/tools.md
index 1a53d8ace..78b01556e 100644
--- a/tools.md
+++ b/tools.md
@@ -2,18 +2,43 @@
 layout: default
 ---
 
-# European Galaxy tools (2801 and counting)
+# European Galaxy tools (2910 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=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=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=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=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=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>
+<a href="https://usegalaxy.eu/root?tool_id=microbial_import1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get Microbial Data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biomart" title="Ensembl server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BioMart</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biomart_test" title="Test server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BioMart</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cbi_rice_mart" title="rice mart"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CBI Rice Mart</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gramenemart" title="Central server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GrameneMart</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=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=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=modENCODEfly" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">modENCODE fly</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=intermine" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InterMine</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=flymine" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flymine</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=modmine" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">modENCODE modMine</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mousemine" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MouseMine</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ratmine" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Ratmine</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=yeastmine" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">YeastMine</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=metabolicmine" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metabolicMine</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=modENCODEworm" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">modENCODE worm</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=wormbase" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WormBase</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=zebrafishmine" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ZebrafishMine</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eupathdb" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EuPathDB</button></a>
+<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=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=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=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_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=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, 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=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>
@@ -35,42 +60,18 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=ebi_search_rest_results" title="to obtain search results on resources and services hosted at the EBI"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EBI Search</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dorina_search" title="DoRiNA data source"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DoRiNA Search</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ebi_metagenomics_run_downloader" title="from EBI Metagenomics database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Download run data</button></a>
-<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=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=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>
-<a href="https://usegalaxy.eu/root?tool_id=microbial_import1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get Microbial Data</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biomart" title="Ensembl server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BioMart</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biomart_test" title="Test server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BioMart</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cbi_rice_mart" title="rice mart"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CBI Rice Mart</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gramenemart" title="Central server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GrameneMart</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=modENCODEfly" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">modENCODE fly</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=intermine" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InterMine</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=flymine" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flymine</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=modmine" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">modENCODE modMine</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mousemine" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MouseMine</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ratmine" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Ratmine</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=yeastmine" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">YeastMine</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=metabolicmine" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metabolicMine</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=modENCODEworm" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">modENCODE worm</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=wormbase" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WormBase</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=zebrafishmine" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ZebrafishMine</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=eupathdb" title="server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EuPathDB</button></a>
-<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=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=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=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=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>
 <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=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=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=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>
@@ -88,57 +89,72 @@ layout: default
 <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>
 <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=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>
+<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>
 <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=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=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_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=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>
+<a href="https://usegalaxy.eu/root?tool_id=Convert characters1" title="delimiters to TAB"><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=createInterval" title="as a new dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create single interval</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=ChangeCase" title="of selected columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Change Case</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Paste1" title="two files side by side"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Paste</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Remove beginning1" title="of a file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove beginning</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=random_lines1" title="from a file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select random lines</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Show beginning1" title="lines from a dataset"><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=Show tail1" title="lines from a dataset"><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=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>
+<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=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=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=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=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=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=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=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=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=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=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=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=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=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=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=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=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=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_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_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_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_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_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_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_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_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_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_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_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_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_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=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_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=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>
@@ -146,80 +162,88 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=gops_intersect_1" title="the intervals of two 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=flanking_features_1" title="for every interval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fetch closest non-overlapping feature</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=get_flanks1" title="returns flanking region/s for every gene"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get flanks</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=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=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>
-<a href="https://usegalaxy.eu/root?tool_id=Convert characters1" title="delimiters to TAB"><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=createInterval" title="as a new dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create single interval</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ChangeCase" title="of selected columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Change Case</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Paste1" title="two files side by side"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Paste</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Remove beginning1" title="of a file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove beginning</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=random_lines1" title="from a file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select random lines</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Show beginning1" title="lines from a dataset"><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=Show tail1" title="lines from a dataset"><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=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=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=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=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=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>
 <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=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=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=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>
-<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>
+<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=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=Extract_features1" title="from GFF data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract features</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gff_filter_by_attribute" 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 attribute</button></a>
 <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>
+<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=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>
 <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=join1" title="side by side on a specified field"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join two Datasets</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=comp1" title="to find common or distinct rows"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare two Datasets</button></a>
+<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>
 <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=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=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=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=join1" title="side by side on a specified field"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join two Datasets</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=comp1" title="to find common or distinct rows"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare two Datasets</button></a>
-<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=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=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=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>
+<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=lav_to_bed1" title="Converts a LAV formatted file to BED format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LAV 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=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>
+<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=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=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=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=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=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=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=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=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>
@@ -227,41 +251,15 @@ layout: default
 <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=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>
-<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=lav_to_bed1" title="Converts a LAV formatted file to BED format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LAV 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=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>
+<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=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>
 <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=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=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>
@@ -289,15 +287,33 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=cshl_fastq_quality_filter" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter by quality</button></a>
 <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=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=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=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>
+<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=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=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=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=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=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=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=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=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=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>
@@ -313,9 +329,13 @@ layout: default
 <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=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>
@@ -327,40 +347,27 @@ 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=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>
+<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>
 <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_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_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_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_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=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=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=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=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_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>
@@ -368,75 +375,90 @@ layout: default
 <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=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=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_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_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_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_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_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_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=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_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_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_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_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=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=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=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=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=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>
 <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=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=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>
 <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_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=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=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=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=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=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>
@@ -453,7 +475,9 @@ 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=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_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=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>
@@ -468,34 +492,46 @@ layout: default
 <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=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=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=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=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=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=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=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=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=clair3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clair3</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=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=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=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=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_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=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_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=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=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>
@@ -509,23 +545,21 @@ 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=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pycoqc</button></a>
 <hr/><h2>Common Genomics Tools</h2>
 <h3>Operate on Genomic Intervals</h3>
 <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=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=aggregate_scores_in_intervals2" title="Appends the average, min, max of datapoints per interval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Aggregate datapoints</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>
 <a href="https://usegalaxy.eu/root?tool_id=gops_concat_1" title="two BED files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gops_join_1" title="the intervals of two datasets side-by-side"><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=translate_bed_sequences" title="3 frame translation of BED augmented with a sequence column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Translate BED Sequences</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=filter_bed_on_splice_junctions" title="that are not in a reference bed file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter BED on splice junctions</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=aggregate_scores_in_intervals2" title="Appends the average, min, max of datapoints per interval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Aggregate datapoints</button></a>
 <h3>Fetch Sequences / Alignments</h3>
-<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=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>
@@ -539,98 +573,76 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=maf_by_block_number1" title="given a set of block numbers and a MAF file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract MAF by block number</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MAF_Reverse_Complement_1" title="a MAF file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Reverse Complement</button></a>
 <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>
+<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>
 <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=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=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=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=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=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=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=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_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_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=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=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=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=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=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=hamronize_summarize" title="harmorization 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=goslimmer" title="converts a set of annotation from GO to a given GOSlim version"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GOSlimmer</button></a>
 <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>
 <a href="https://usegalaxy.eu/root?tool_id=jcvi_gff_stats" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Genome annotation statistics</button></a>
@@ -657,7 +669,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=smf_utils_filter-by-energy" title="Split entries over two files based on the estimated energy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">filter-by-energy</button></a>
 <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=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>
@@ -670,35 +681,61 @@ layout: default
 <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=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_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_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=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_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=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=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=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=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=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_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=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=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=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=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>
 <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=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=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=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=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=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=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_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=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>
@@ -706,61 +743,59 @@ layout: default
 <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=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=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=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=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=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=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=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=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=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=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=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=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=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=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=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=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=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=""><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=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=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 +803,105 @@ 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=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=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=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=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=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=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>
 <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=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=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=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=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>
+<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=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=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=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=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=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>
+<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=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=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=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>
 <h3>Variant Calling</h3>
-<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=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_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=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=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=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=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_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=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_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_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=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=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=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=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=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=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=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=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=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=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=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=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=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=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=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=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=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=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>
@@ -897,18 +924,21 @@ 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=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=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=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=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=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=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>
@@ -925,6 +955,7 @@ layout: default
 <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=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=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>
@@ -933,86 +964,101 @@ layout: default
 <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_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_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=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=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=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=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>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>
+<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=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=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=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=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=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=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=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=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=ribotaper_create_annotation" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ribotaper part 1: creation of annotation files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ribotaper_create_metaplots" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ribotaper part 2: metagene analysis for P-sites definition</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ribotaper_ribosome_profiling" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ribotaper part 3: ribosome profiling</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=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=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=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=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=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=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=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=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=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>
@@ -1030,16 +1076,15 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=deg_annotate" title="Append annotation from GTF to differential expression tool outputs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Annotate DESeq2/DEXSeq output tables</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=locarna_multiple" title="Multiple Alignment and Folding of RNAs (mlocarna)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LocARNA Multiple Aligner</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cmv" title="CMV is a tool for visualization of RNA family models, also known as covariance models (CM)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cmv</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ribotaper_create_metaplots" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ribotaper part 2: metagene analysis for P-sites definition</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ribotaper_ribosome_profiling" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ribotaper part 3: ribosome profiling</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ribotaper_create_annotation" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ribotaper part 1: creation of annotation files</button></a>
 <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>
@@ -1099,6 +1144,12 @@ 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>
@@ -1122,10 +1173,11 @@ 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>
 <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=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=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>
@@ -1145,8 +1197,6 @@ layout: default
 <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>
 <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=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>
@@ -1166,6 +1216,8 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=minfi_qc" title="provides a simple quality control matrix and plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Minfi QC</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=minfi_analysis" title="Determines differentially methylated regions and positions from Infinium Methylation Assays"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Infinium Human Methylation BeadChip</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metilene" title="calling differentially methylated regions from bisulfite sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metilene</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=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=hicup_truncater" title="terminates sequence reads at specified Hi-C ligation junctions."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hicup Truncater</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicup_hicup" title="controls the other programs in the HiCUP pipeline."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hicup Pipeline</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicup_filter" title="classifies read pairs, identifying valid Hi-C di-tags"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hicup Filter</button></a>
@@ -1174,31 +1226,24 @@ layout: default
 <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>
 <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=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=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=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_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=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=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=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=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=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>
@@ -1207,8 +1252,7 @@ layout: default
 <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 +1262,14 @@ 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=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=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=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>
 <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>
@@ -1237,97 +1289,98 @@ 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=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=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_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_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_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=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_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=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_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=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=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_manipulate_eset" title="Manipulate ExpressionSet objects by a variety of attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Manipulate 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=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=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’ 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=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_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_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=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=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_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=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_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=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_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=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_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=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>
 <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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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=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>
 <a href="https://usegalaxy.eu/root?tool_id=rgEstLibComp" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Estimate Library Complexity</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=PicardInsertSize" title="for PAIRED data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Insertion size metrics</button></a>
 <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>
+<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>
 <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>
 <h3>Gemini</h3>
@@ -1344,127 +1397,125 @@ layout: default
 <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_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_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_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>
 <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>
-<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: pepwindow73" title="Displays protein hydropathy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pepwindow</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: pepwindowall74" title="Displays protein hydropathy of a set of sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pepwindowall</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: degapseq20" title="Removes gap characters from sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">degapseq</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: infoseq46" title="Displays some simple information about sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">infoseq</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: splitter92" title="Split a sequence into (overlapping) smaller sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">splitter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: skipseq91" title="Reads and writes sequences, skipping first few"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">skipseq</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: needle56" title="Needleman-Wunsch global alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">needle</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: patmatdb67" title="Search a protein sequence with a motif"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">patmatdb</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: marscan49" title="Finds MAR/SAR sites in nucleic sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">marscan</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: water107" title="Smith-Waterman local alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">water</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: getorf42" title="Finds and extracts open reading frames (ORFs)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">getorf</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: msbar55" title="Mutate sequence beyond all recognition"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">msbar</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: oddcomp64" title="Find protein sequence regions with a biased composition"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">oddcomp</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: fuzztran39" title="Protein pattern search after translation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fuzztran</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: tcode97" title="Fickett TESTCODE statistic to identify protein-coding DNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tcode</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: helixturnhelix43" title="Report nucleic acid binding motifs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">helixturnhelix</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: iep45" title="Calculates the isoelectric point of a protein"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">iep</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: merger54" title="Merge two overlapping nucleic acid sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">merger</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: equicktandem31" title="Finds tandem repeats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">equicktandem</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: newcpgseek58" title="Reports CpG rich region"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">newcpgseek</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: extractseq35" title="Extract regions from a sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">extractseq</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: maskfeat50" title="Mask off features of a sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">maskfeat</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: newcpgreport57" title="Report CpG rich areas"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">newcpgreport</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: codcmp12" title="Codon usage table comparison"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">codcmp</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: supermatcher95" title="Match large sequences against one or more other sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">supermatcher</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: 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: 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: equicktandem31" title="Finds tandem repeats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">equicktandem</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: cutseq18" title="Removes a specified section from a sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cutseq</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: tranalign100" title="Align nucleic coding regions given the aligned proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tranalign</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: cai_custom6" title="CAI codon adaptation index using custom codon usage file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cai custom</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: newcpgreport57" title="Report CpG rich areas"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">newcpgreport</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: noreturn60" title="Removes carriage return from ASCII files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">noreturn</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: 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: octanol63" title="Displays protein hydropathy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">octanol</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: sigcleave88" title="Reports protein signal cleavage sites"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sigcleave</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: 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: union105" title="Reads sequence fragments and builds one sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">union</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: preg78" title="Regular expression search of a protein sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">preg</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: 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: 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: 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: 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: 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: msbar55" title="Mutate sequence beyond all recognition"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">msbar</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=EMBOSS: getorf42" title="Finds and extracts open reading frames (ORFs)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">getorf</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=EMBOSS: pepstats71" title="Protein statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pepstats</button></a>
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+<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=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=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=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>
@@ -1480,49 +1531,51 @@ 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=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=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=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_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=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=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>
 <h3>HiCExplorer</h3>
+<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_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_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_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_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_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_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_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_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_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_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_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_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=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_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_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_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_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_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_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_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>
@@ -1539,22 +1592,27 @@ layout: default
 <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_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>
+<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_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>
 <h3>RAD-seq</h3>
+<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=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=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_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_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_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_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=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=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=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_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_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=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>
@@ -1601,81 +1659,68 @@ 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=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=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=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=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=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=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=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=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=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=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_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_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" 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=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=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_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_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_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_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_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_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" 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_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=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=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=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=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=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=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=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=coverm_contig" title=""><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="read coverage and relative abundance calculator focused on metagenomics applications"><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=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=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_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=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=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=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_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=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" 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=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=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=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=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=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=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=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=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=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=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=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=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>
@@ -1685,6 +1730,12 @@ layout: default
 <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=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>
@@ -1693,12 +1744,25 @@ layout: default
 <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=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=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=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-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=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>
@@ -1714,11 +1778,37 @@ layout: default
 <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=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=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=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=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=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=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=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=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=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=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>
 <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 +1980,7 @@ 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>
@@ -1897,79 +1988,47 @@ 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>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=cooc_tabmut" title="export cooccurrence mutations as a table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cojac: tabmut</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cooc_pubmut" title="render a JSON or YAML file to a pretty table"><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_mutbamscan" title="scan 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=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=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_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_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=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=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=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>
 <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=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=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=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_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>
-<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=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=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=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=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=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=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=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=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=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=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>
-<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=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_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=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=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=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=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>
@@ -1980,6 +2039,9 @@ layout: default
 <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=MSGFPlusAdapter" title="MS/MS database search using MS-GF+."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSGFPlusAdapter</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_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>
@@ -2013,73 +2075,81 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=CompNovoCID" title="Performs a de novo peptide identification using the CompNovo engine."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CompNovoCID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=IDMerger" title="Merges several protein/peptide identification files into one file."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDMerger</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MetaboliteSpectralMatcher" title="Perform a spectral library search."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaboliteSpectralMatcher</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=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=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=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=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=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=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=RTEvaluation" title="Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RTEvaluation</button></a>
 <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=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=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=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=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=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=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=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=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=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>
@@ -2102,12 +2172,19 @@ layout: default
 <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=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=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=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=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>
 <a href="https://usegalaxy.eu/root?tool_id=MascotAdapter" title="Annotates MS/MS spectra using Mascot."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MascotAdapter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MetaboliteAdductDecharger" title="Decharges and merges different feature charge variants of the same metabolite."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaboliteAdductDecharger</button></a>
@@ -2127,15 +2204,20 @@ 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=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=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>
@@ -2148,15 +2230,20 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=pyprophet_peptide" title="Peptide error-rate estimation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyProphet peptide</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pyprophet_protein" title="Protein error-rate estimation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyProphet protein</button></a>
 <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=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=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=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=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=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>
 <a href="https://usegalaxy.eu/root?tool_id=percolator" title="accurate peptide identification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Percolator</button></a>
@@ -2178,18 +2265,27 @@ layout: default
 <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_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_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=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=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_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=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>
 <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=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 +2304,7 @@ 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 +2332,11 @@ 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>
@@ -2249,42 +2348,26 @@ 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=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>
 <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=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=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_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=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_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_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_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=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>
@@ -2293,11 +2376,8 @@ 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>
@@ -2305,6 +2385,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=mdanalysis_ramachandran_plot" title="- calculate and plot the distribution of two dihedrals in a trajectory"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Ramachandran Plots</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mdanalysis_distance" title="- time series using MDAnalysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Distance Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mdanalysis_dihedral" title="Time series of dihedrals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Dihedral Analysis</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_change_title" title="to metadata value."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Change title</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mdanalysis_rdf" title="- Radial Distribution Function between two atoms"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RDF Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_spectrophore_search" title="- similarity search based on 1D chemical features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Spectrophores search</button></a>
@@ -2314,10 +2395,13 @@ 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 +2410,9 @@ 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 +2436,7 @@ 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=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>
@@ -2356,7 +2444,10 @@ 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>
@@ -2365,6 +2456,7 @@ layout: default
 <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>
@@ -2384,9 +2476,20 @@ 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=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>
 <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>
@@ -2401,6 +2504,8 @@ layout: default
 <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=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>
 <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>
@@ -2419,84 +2524,86 @@ layout: default
 <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=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=""><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=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=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_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_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_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_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=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_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_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_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_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_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_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_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_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_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_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_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_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_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=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=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>
 <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=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=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=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=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>
+<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=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" 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_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=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=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=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=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=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=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>
@@ -2505,31 +2612,30 @@ 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=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=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=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>
+<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=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>
 <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=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=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_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_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=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_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=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=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_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>
 <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_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_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=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=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>
@@ -2569,10 +2675,10 @@ layout: default
 <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>
 <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_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_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=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=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=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>
@@ -2636,42 +2742,37 @@ 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=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>
 <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=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=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>
 <h3>Apollo</h3>
-<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>
+<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=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=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_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=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=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=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=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>
 <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_landmark_registration" title="estimates the affine transformation matrix or performs piecewise affine transformation"><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=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>
@@ -2690,9 +2791,12 @@ layout: default
 <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=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=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=ip_overlay_images" title="for visualization"><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=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=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=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=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>
@@ -2703,11 +2807,10 @@ layout: default
 <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=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_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>
@@ -2727,9 +2830,10 @@ layout: default
 <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_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_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>
@@ -2748,8 +2852,8 @@ layout: default
 <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_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=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>
@@ -2800,6 +2904,8 @@ 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="Label audio file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Audio Labeler</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 +2925,6 @@ 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>
@@ -2834,10 +2939,42 @@ 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>Other Tools</h3>
+<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_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=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=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>
+<h3>Sanger Sequencing</h3>
+<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_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=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>
+<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=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=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>
 <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>
@@ -2857,29 +2994,3 @@ layout: default
 <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=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=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=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_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>
-<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=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_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>
-<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>