From 5ef5536581de52274def9dc4113e048228c451d3 Mon Sep 17 00:00:00 2001
From: annefou <annefou@users.noreply.github.com>
Date: Sun, 13 Mar 2022 23:03:48 +0000
Subject: [PATCH] Update tools

---
 tools.md | 34 ++++++++++++++++++++--------------
 1 file changed, 20 insertions(+), 14 deletions(-)

diff --git a/tools.md b/tools.md
index 1a53d8ace..29fb0cb5c 100644
--- a/tools.md
+++ b/tools.md
@@ -2,7 +2,7 @@
 layout: default
 ---
 
-# European Galaxy tools (2801 and counting)
+# European Galaxy tools (2807 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>
@@ -63,9 +63,9 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=hbvar" title="Human Hemoglobin Variants and Thalassemias"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HbVar</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=omicsdi" title="Sync dataset's files from OmicsDI"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OmicsDI</button></a>
 <h3>Send Data</h3>
+<a href="https://usegalaxy.eu/root?tool_id=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=directory_uri" title="to different data storages"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Export datasets</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ena_upload" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ENA Upload tool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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>
@@ -259,9 +259,9 @@ layout: default
 <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=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=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>
@@ -474,13 +474,13 @@ layout: default
 <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=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=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=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>
@@ -603,6 +603,7 @@ layout: default
 <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=legsta" title="Legionella pneumophila sequence based typing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">legsta</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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>
@@ -707,14 +708,16 @@ layout: default
 <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>
 <h3>Assembly</h3>
-<a href="https://usegalaxy.eu/root?tool_id=spades_biosyntheticspades" title="biosynthetic gene cluster assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">biosyntheticSPAdes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=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=links" title="- scaffold genome assemblies with long reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LINKS</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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_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=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>
@@ -805,13 +808,13 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=srma_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Re-align with SRMA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mosaik_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with Mosaik</button></a>
 <h3>Variant Calling</h3>
+<a href="https://usegalaxy.eu/root?tool_id=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=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>
@@ -945,10 +948,10 @@ layout: default
 <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=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=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>
@@ -1174,9 +1177,9 @@ 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=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=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_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>
@@ -1910,6 +1913,7 @@ layout: default
 <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>
 <hr/><h2>Proteomics, Metabolomics, Chemistry</h2>
 <h3>Proteomics</h3>
+<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=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>
@@ -1965,6 +1969,7 @@ layout: default
 <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=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=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>
@@ -2659,10 +2664,13 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=list_organism" title="in Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">List Organisms</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=delete_features" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delete all annotations from an Apollo record</button></a>
 <h3>Imaging</h3>
+<a href="https://usegalaxy.eu/root?tool_id=ip_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_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_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_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=ip_localthreshold" title="applies a local threshold algorithm to an image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Local Threshold</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_threshold" title="applies a standard thresholding algorithm to an image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Auto Threshold</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_projective_transformation_points" title="of ROIs defined by pixel (point) coordinates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Projective Transformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_projective_transformation" title="of 2D images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Projective Transformation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=idr_download_by_ids" title="- download images from any OMERO instance using image IDs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDR/OMERO Download</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_spot_detection_2d" title="in a 2D image (sequence)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Spot Detection</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_points_association_nn" title="in consecutive frames (slices) using the nearest neighbor algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Association of points</button></a>
@@ -2671,8 +2679,8 @@ layout: default
 <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=ip_landmark_registration" title="estimates the affine transformation matrix"><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=cp_overlay_outlines" title="places outlines of objects over a desired image."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OverlayOutlines</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cp_convert_objects_to_image" title="convert the identified objects into an image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ConvertObjectsToImage</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cp_display_data_on_image" title="produce an image with data on top of identified objects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DisplayDataOnImage</button></a>
@@ -2691,7 +2699,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=cp_relate_objects" title="assign relationships parent-children between objects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RelateObjects</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cp_save_images" title="or movie files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SaveImages</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cp_image_math" title="perform simple mathematical operations on images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ImageMath</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_landmark_registration_ls" title="using least squares"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Landmark Registration</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=spyboat" title="wavelet analyzes image stacks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpyBOAT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=imagej2_binary_to_edm" title="(Euclidean Distance Map)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to EDM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=imagej2_skeletonize3d" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Skeletonize</button></a>
@@ -2707,7 +2714,6 @@ layout: default
 <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>