From 1ea5bb8649dd2697805eb2f4fc5705f54b44b63e Mon Sep 17 00:00:00 2001
From: EngyNasr <EngyNasr@users.noreply.github.com>
Date: Sun, 12 Jan 2025 23:15:06 +0000
Subject: [PATCH] Update tools

---
 tools.md | 1682 ++++++++++++++++++++++++++++--------------------------
 1 file changed, 888 insertions(+), 794 deletions(-)

diff --git a/tools.md b/tools.md
index 658ffed7..9c142c00 100644
--- a/tools.md
+++ b/tools.md
@@ -2,19 +2,13 @@
 layout: default
 ---
 
-# European Galaxy tools (3554 and counting)
+# European Galaxy tools (3646 and counting)
 <hr/>
 <h3>Get Data</h3>
-<a href="https://usegalaxy.eu/root?tool_id=sdmpredictors_list_layers" title="from environmental predictors for species distribution modeling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SdmPredictors List Layers</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=aquainfra_importer" title="downloads content via the AquaINFRA interaction platform"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AquaINFRA Importer</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=fastq_dump" title="format from NCBI SRA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Download and Extract Reads in FASTQ</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sam_dump" title="format from NCBI SRA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Download and Extract Reads in BAM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=obis_data" title="retrieve data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OBIS occurences</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=argo_getdata" title="for global ocean in situ observing system"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Argo data access</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mavedb_importer" title="import MAVE data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaveDB</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=iedb_api" title="MHC Binding prediction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IEDB</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dbbuilder" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Protein Database Downloader</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=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>
@@ -31,11 +25,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=uniprot" title="ID mapping and retrieval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UniProt</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=get_sequences" title="using REST API"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get sequences by Ensembl ID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=get_genetree" title="using REST API"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get gene tree by Ensembl ID</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=query_impc" title="query tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IMPC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=iabiodiv_smartbiodiv_med_environ" title="From Copernicus and etopo given geolocalized and timestamped observations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Adds environment variables</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=datasets_download_gene" title="download gene sequences and metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI Datasets Gene</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=datasets_download_genome" title="download genome sequence, annotation and metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI Datasets Genomes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=retrieve_bold" title="Functions to search in Bold and download the available sequences of each subtaxa (get_fasta)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Retrieve bold</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=get_feature_info" title="using REST API"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get features by Ensembl ID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=enasearch_search_data" title="given a query"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Search ENA data</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=enasearch_retrieve_data" title="(other than taxon and project)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Retrieve ENA data</button></a>
@@ -48,7 +37,20 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=pyega3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EGA Download Client</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=upload1" title="from your computer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Upload File</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ds_seek_test" title="Trying to get open files out of SEEK"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SEEK test</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=pysradb_search" title="sequence metadata from SRA/ENA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pysradb search</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=datasets_download_gene" title="download gene sequences and metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI Datasets Gene</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastq_dump" title="format from NCBI SRA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Download and Extract Reads in FASTQ</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=query_impc" title="query tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IMPC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mavedb_importer" title="import MAVE data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaveDB</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=argo_getdata" title="for global ocean in situ observing system"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Argo data access</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=obis_data" title="retrieve data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OBIS occurences</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=iabiodiv_smartbiodiv_med_environ" title="From Copernicus and etopo given geolocalized and timestamped observations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Adds environment variables</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=aquainfra_importer" title="downloads content via the AquaINFRA interaction platform"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AquaINFRA Importer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sdmpredictors_list_layers" title="from environmental predictors for species distribution modeling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SdmPredictors List Layers</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=retrieve_bold" title="Functions to search in Bold and download the available sequences of each subtaxa (get_fasta)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Retrieve bold</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=copernicusmarine" title="retrieve marine data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Marine Data Store</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastq_dl" title="Download FASTQ files from ENA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fastq-dl</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>
@@ -83,13 +85,10 @@ layout: default
 <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=pick_value" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pick parameter value</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=__CROSS_PRODUCT_FLAT__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flat Cross Product</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=__CROSS_PRODUCT_NESTED__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nested Cross Product</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=__HARMONIZELISTS__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Harmonize two collections</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=unzip" title="Unzip a file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unzip</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=collection_element_identifiers" title="of a list collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract element identifiers</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=collection_column_join" title="on multiple datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Column join</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pick_value" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pick parameter value</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__UNZIP_COLLECTION__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unzip collection</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__ZIP_COLLECTION__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Zip collections</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__FILTER_FAILED_DATASETS__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter failed datasets</button></a>
@@ -99,6 +98,9 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=__RELABEL_FROM_FILE__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Relabel identifiers</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__FILTER_FROM_FILE__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter collection</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__SORTLIST__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort collection</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=__HARMONIZELISTS__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Harmonize two collections</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=__CROSS_PRODUCT_FLAT__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flat Cross Product</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=__CROSS_PRODUCT_NESTED__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nested Cross Product</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__TAG_FROM_FILE__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tag elements</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__APPLY_RULES__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Apply rules</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__BUILD_LIST__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build list</button></a>
@@ -111,26 +113,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=param_value_from_file" title="from dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Parse parameter value</button></a>
 <hr/><h2>General Text Tools</h2>
 <h3>Text Manipulation</h3>
-<a href="https://usegalaxy.eu/root?tool_id=tp_awk_tool" title="with awk"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Text reformatting</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_cat" title="tail-to-head (cat)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate datasets</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_cut_tool" title="columns from a table (cut)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Advanced Cut</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_easyjoin_tool" title="two files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_find_and_replace" title="parts of text"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_grep_tool" title="(grep)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Search in textfiles</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_head_tool" title="lines from a dataset (head)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select first</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_multijoin_tool" title="(combine multiple files)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Multi-Join</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=nl" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Number lines</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_text_file_with_recurring_lines" title="with recurring lines"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create text file</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_replace_in_column" title="in a specific column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace Text</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_replace_in_line" title="in entire line"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace Text</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_sed_tool" title="with sed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Text transformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_sort_header_tool" title="data in ascending or descending order"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_sort_rows" title="according to their columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort a row</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_uniq_tool" title="assuming sorted input file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unique lines</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_tac" title="reverse a file (reverse cat)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tac</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_tail_tool" title="lines from a dataset (tail)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select last</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_unfold_column_tool" title="columns from a table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unfold</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_sorted_uniq" title="occurrences of each record"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unique</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=histogram_rpy" title="of a numeric column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Histogram</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Add_a_column1" title="on rows"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=diff" title="analyzes two files and generates an unidiff text file with information about the differences and an optional Html report"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">diff</button></a>
@@ -143,17 +125,36 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=regexColumn1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Column Regex Find And Replace</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=regex1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Regex Find And Replace</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=join_files_on_column_fuzzy" title="on column allowing a small difference"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join two files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=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_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=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_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_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=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=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=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_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_cut_tool" title="columns from a table (cut)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Advanced Cut</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_easyjoin_tool" title="two files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_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_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_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_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>
@@ -165,7 +166,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=bg_uniq" title="occurrences of each record"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unique</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=addValue" title="to an existing dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add column</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tp_split_on_column" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split by group</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cat_multi_datasets" title="tail-to-head by specifying how"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate multiple datasets</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cat_multi_datasets" title="tail-to-head while specifying how"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate multiple datasets</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=addValue" title="to an existing dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add column</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cat1" title="tail-to-head"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate datasets</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Cut1" title="columns from a table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cut</button></a>
@@ -180,12 +181,14 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=trimmer" title="leading or trailing characters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trim</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=wc_gnu" title="of a dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Line/Word/Character count</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=secure_hash_message_digest" title="on a dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Secure Hash / Message Digest</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=nl" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Number lines</button></a>
 <h3>Convert Formats</h3>
-<a href="https://usegalaxy.eu/root?tool_id=bbgtobigwig" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BAM BED GFF coverage bigWigs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ucsc_wigtobigwig" title="bedGraph or Wig to bigWig converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">wigtobigwig</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=10x_bamtofastq" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert a 10X BAM file to FASTQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=glimmer_glimmer_to_gff" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Glimmer to GFF</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=agat" title="GTF/GFF analysis toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AGAT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ucsc_wigtobigwig" title="bedGraph or Wig to bigWig converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">wigtobigwig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bbgtobigwig" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BAM BED GFF coverage bigWigs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=uniprot" title="ID mapping and retrieval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UniProt</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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>
@@ -194,14 +197,14 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=Sff_extractor" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SFF converter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bed_to_bigBed" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BED-to-bigBed</button></a>
 <h3>Filter and Sort</h3>
-<a href="https://usegalaxy.eu/root?tool_id=seq_filter_by_id" title="from a tabular file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter sequences by ID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=filter_by_fasta_ids" title="on the headers and/or the sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter FASTA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bg_column_arrange_by_header" title="by header name"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Column arrange</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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=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=bigwig_outlier_bed" title="Writes high and low bigwig runs as features in a bed file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bigwig extremes to bed features</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=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=find_in_reference" title="filter peptides that are present in proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">find in reference</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gffcompare" title="compare assembled transcripts to a reference annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GffCompare</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bigwig_outlier_bed" title="Writes high and low bigwig runs as features in a bed file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bigwig outliers to bed features</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>
@@ -211,8 +214,8 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=gff_filter_by_feature_count" title="using simple expressions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter GFF data by feature count</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gtf_filter_by_attribute_values_list" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter GTF data by attribute values_list</button></a>
 <h3>Join, Subtract and Group</h3>
-<a href="https://usegalaxy.eu/root?tool_id=datamash_transpose" title="rows/columns in a tabular file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Transpose</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=collection_column_join" title="on multiple datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Column join</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=datamash_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_reverse" title="columns in a tabular file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Reverse</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=datamash_ops" title="(operations on tabular data)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Datamash</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=datamash_ops" title="(operations on tabular data)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Datamash</button></a>
@@ -222,53 +225,43 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=Grouping1" title="data by a column and perform aggregate operation on other columns."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Group</button></a>
 <hr/><h2>Genomic File Manipulation</h2>
 <h3>Convert Formats</h3>
-<a href="https://usegalaxy.eu/root?tool_id=maftoaxt" title="Convert file from MAF to axt format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mafToAxt</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tooldistillator_summarize" title="Aggregate several JSON reports from ToolDistillator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ToolDistillator Summarize</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tooldistillator" title="Extract information from output files of specific tools and expose it as JSON files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ToolDistillator</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=graphicsmagick_image_montage" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Image Montage</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_compare" title="with GraphicsMagick"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare two images</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gffread" title="Filters and/or converts GFF3/GTF2 records"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gffread</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_convert" title="with GraphicsMagick"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert image format</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=idpquery" title="Creates text reports from idpDB files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idpQuery</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=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=fasta2tab" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTA-to-Tabular</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tabular_to_fastq" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tabular to FASTQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gfa_to_fa" title="Convert Graphical Fragment Assembly files to FASTA format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFA to FASTA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=thermo_raw_file_converter" title="RAW file converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Thermo</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=msconvert" title="Convert and/or filter mass spectrometry files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">msconvert</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Interval2Maf1" title="given a set of genomic intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract MAF blocks</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=crossmap_wig" title="Convert genome coordinates or annotation files between genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CrossMap Wig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=idconvert" title="Convert mass spectrometry identification files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idconvert</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=msconvert_subset" title="against list of scan numbers or indices."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">msconvert Subset Peak List</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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=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=GeneBed_Maf_Fasta2" title="given a set of coding exon intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stitch Gene blocks</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=crossmap_bam" title="Convert genome coordinates or annotation files between genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CrossMap BAM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mz_to_sqlite" title="Extract mzIdentML and associated proteomics datasets into a SQLite DB"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mz to sqlite</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bed_to_protein_map" title="genomic location of proteins for MVP"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bed to protein map</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gffcompare_to_bed" title="for StringTie results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert gffCompare annotated GTF to BED</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=map_peptides_to_bed" title="for viewing in a genome browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map peptides to a bed file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=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="with GraphicsMagick"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert image format</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=galaxy_intermine_exchange" title="Dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create InterMine Interchange</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_bam_to_cram" title="convert BAM alignments to CRAM format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">samtools BAM to CRAM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bam2fastx" title="PacBio BAM to Fastx"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PacBio bam2fastx</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hictk" title="convert cool to juicebox hic"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hictk</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biom_add_metadata" title="to a BIOM table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add metadata</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biom_normalize_table" title="a BIOM table"><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=biom_subset_table" title="a BIOM table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Subset</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biom_summarize_table" title="in a BIOM table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Summarize sample or observation data</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biom_from_uc" title="from a vsearch/uclust/usearch BIOM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a BIOM table</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=idconvert" title="Convert mass spectrometry identification files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idconvert</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=msconvert_subset" title="against list of scan numbers or indices."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">msconvert Subset Peak List</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=idconvert" title="Convert mass spectrometry identification files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idconvert</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gtftobed12" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GTF to BED12</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ucsc-twobittofa" title="Convert all or part of .2bit file to FASTA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">twoBitToFa</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=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=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=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=ab1_fastq_converter" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ab1 to FASTQ converter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=compress_file" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compress file(s)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=xmlstarlet" title="convert a metadata XML file in one standard to another"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xmlstarlet</button></a>
@@ -278,6 +271,22 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff.gff2gb" title="convert gff3 to GenBank"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF3 to GenBank</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt2.gff3.splitGff" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split GFF3+Fasta into separate parts</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.customGbkToGff" title="CPT made Biobython-based solution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">(CPT) Genbank to GFF3: </button></a>
+<a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_compare" title="with GraphicsMagick"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare two images</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hictk" title="convert cool to juicebox hic"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hictk</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bam2fastx" title="PacBio BAM to Fastx"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PacBio bam2fastx</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biom_add_metadata" title="to a BIOM table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add metadata</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biom_normalize_table" title="a BIOM table"><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=biom_subset_table" title="a BIOM table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Subset</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biom_summarize_table" title="in a BIOM table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Summarize sample or observation data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biom_from_uc" title="from a vsearch/uclust/usearch BIOM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a BIOM table</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tooldistillator" title="Extract information from output files of specific tools and expose it as JSON files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ToolDistillator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tooldistillator_summarize" title="Aggregate several JSON reports from ToolDistillator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ToolDistillator Summarize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=maftoaxt" title="Convert file from MAF to axt format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mafToAxt</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ucsc_axtchain" title="Chain together axt alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">axtChain</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ucsc_nettoaxt" title="Convert net (and chain) to axt format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">netToAxt</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ucsc_netfilter" title="Filter out parts of net"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">netFilter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ucsc_chainnet" title="make alignment nets out of alignment chains"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chainNet</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ucsc_wigtobigwig" title="bedGraph or Wig to bigWig converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">wigtobigwig</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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>
@@ -293,36 +302,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=bed_to_bigBed" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BED-to-bigBed</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=liftOver1" title="between assemblies and genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert genome coordinates</button></a>
 <h3>FASTA/FASTQ</h3>
-<a href="https://usegalaxy.eu/root?tool_id=rasusa" title="Randomly subsample reads to a specified coverage"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rasusa</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqkit_sort" title="FASTA or FASTQ files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit sort</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=falco" title="An alternative, more performant implementation of FastQC for high throughput sequence quality control"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Falco</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=art_454" title="simulates pyrosequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ART 454</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=art_illumina" title="simulates sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ART Illumina</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=art_solid" title="simulates SOLiD data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ART SOLiD</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ncbi_fcs_gx" title="detects contamination from foreign organisms in genome sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI FCS GX</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastp" title="fast all-in-one preprocessing for FASTQ files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fastp</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=trimmomatic" title="flexible read trimming tool for Illumina NGS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trimmomatic</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqprep" title="Merge and Trim Adapter Sequences from Paired-End Illumina Reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merging paired-end Illumina reads (SeqPrep)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bbtools_bbduk" title="decontamination using kmers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: BBduk</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_comp" title="get the nucleotide composition of FASTA/Q"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_comp</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_cutN" title="cut sequence at long N"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_cutN</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_dropse" title="drop unpaired from interleaved Paired End FASTA/Q"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_dropse</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_fqchk" title="fastq QC (base/quality summary)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_fqchk</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_hety" title="regional heterozygosity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_hety</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_listhet" title="extract the position of each het"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_listhet</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_mergefa" title="merge two FASTA/Q files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_mergefa</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_mergepe" title="interleave two unpaired FASTA/Q files for a paired-end file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_mergepe</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_mutfa" title="point mutate FASTA at specified positions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_mutfa</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_randbase" title="choose a random base from hets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_randbase</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_sample" title="random subsample of fasta or fastq sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_sample</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_seq" title="common transformation of FASTA/Q"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_seq</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_subseq" title="extract subsequences from FASTA/Q files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_subseq</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_telo" title="find telomeres"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_telo</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_trimfq" title="trim FASTQ using the Phred algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_trimfq</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seq_filter_by_mapping" title="from SAM/BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter sequences by mapping</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=prinseq" title="to process quality of sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PRINSEQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trim_reads" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select high quality segments</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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>
@@ -351,8 +330,10 @@ 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=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=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>
@@ -363,18 +344,28 @@ layout: default
 <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=bbtools_tadpole" title="Kmer-based assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: Tadpole</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bbtools_bbmerge" title="Merge overlapping mates of a read pair"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: BBMerge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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=seqkit_locate" title="subsequences/motifs, mismatch allowed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit locate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqkit_translate" title="nucleotid to protein sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit translate</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>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_hety" title="regional heterozygosity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_hety</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_cutN" title="cut sequence at long N"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_cutN</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_mergefa" title="Merge two FASTA/Q files into a FASTA file output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_mergefa</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_trimfq" title="trim FASTQ using the Phred algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_trimfq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_fqchk" title="fastq QC (base/quality summary)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_fqchk</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_randbase" title="choose a random base from hets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_randbase</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_subseq" title="extract subsequences from FASTA/Q files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_subseq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_dropse" title="drop unpaired from interleaved Paired End FASTA/Q"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_dropse</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_mergepe" title="interleave two unpaired FASTA/Q files for a paired-end file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_mergepe</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_seq" title="common transformation of FASTA/Q"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_seq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_listhet" title="extract the position of each het"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_listhet</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mqc" title="quality control of ribosome profiling mapping results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mQC</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fasta-stats" title="display summary statistics for a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fasta Statistics</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=filtlong" title="Filtering long reads by quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">filtlong</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_clipper" title="adapter sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clip</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=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>
@@ -392,19 +383,38 @@ layout: default
 <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=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=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=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=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=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=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=rcorrector" title="a kmer-based error correction method for RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA-seq Rcorrector</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=iuc_pear" title="Paired-End read merger"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pear</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=seqcomplexity" title="total and per read"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate sequence complexity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqkit_stats" title="of FASTA/Q files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit statistics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqkit_fx2tab" title="convert FASTA/Q to tabular"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit fx2tab</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=adapter_removal" title="from HTS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AdapterRemoval: remove adapter sequences</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqkit_locate" title="subsequences/motifs, mismatch allowed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit locate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fasta_regex_finder" title="Search in fasta for regexp match"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fasta regular expression finder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bbtools_bbmerge" title="Merge overlapping mates of a read pair"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: BBMerge</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.fasta.remove_desc" title="from fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove Description</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.fasta.remove_desc" title="from fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove Description</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_telo" title="find telomeres"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_telo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bbtools_tadpole" title="Kmer-based assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: Tadpole</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqprep" title="Merge and Trim Adapter Sequences from Paired-End Illumina Reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merging paired-end Illumina reads (SeqPrep)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rasusa" title="Randomly subsample reads to a specified coverage"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rasusa</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ncbi_fcs_gx" title="detects contamination from foreign organisms in genome sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI FCS GX</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=art_454" title="simulates pyrosequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ART 454</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=art_illumina" title="simulates sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ART Illumina</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=art_solid" title="simulates SOLiD data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ART SOLiD</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=falco" title="An alternative, more performant implementation of FastQC for high throughput sequence quality control"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Falco</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqkit_translate" title="nucleotid to protein sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit translate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqkit_sort" title="FASTA or FASTQ files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit sort</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fasta_clipping_histogram" title="chart"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Length Distribution</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fasta_clipping_histogram" title="chart"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Length Distribution</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>
@@ -413,12 +423,6 @@ layout: default
 <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=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=sambamba_flagstat" title="Retrieving flag statistics from BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sambamba flagstat</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tasmanian_mismatch" title="Quantify, visualize and summarize mismatches in deep sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Analysis of artifacts with Tasmanian</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mosdepth" title="- fast and flexible depth coverage calculation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mosdepth</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bamtools" title="datasets in various ways"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Operate on and transform BAM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_ampliconclip" title="clip primer bases from bam files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools ampliconclip</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pileup_interval" title="condenses pileup format into ranges of bases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pileup-to-Interval</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pileup_parser" title="on coverage and SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter pileup</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sam2interval" title="to interval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SAM</button></a>
@@ -431,6 +435,8 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=samtools_view" title="- reformat, filter, or subsample SAM, BAM or CRAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools view</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_reheader" title="copy SAM/BAM header between datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools reheader</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qualimap_bamqc" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QualiMap BamQC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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" title="datasets in various ways"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Operate on and transform BAM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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_markdup" title="marks duplicate alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools markdup</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_merge" title="merge multiple sorted alignment files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools merge</button></a>
@@ -447,21 +453,23 @@ layout: default
 <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=bamFilter" title="datasets on a variety of attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter BAM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_calmd" title="recalculate MD/NM tags"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools calmd</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bamtools_split_mapped" title="into a mapped and an unmapped dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by reads mapping status</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_phase" title="call and phase heterozygous SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools phase</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bamhash" title="Hash BAM and FASTQ files to verify data integrity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BamHash</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bamtools_split_paired" title="reads datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM into paired- and single-end</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bamtools_split_ref" title="into a dataset list collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by reference</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bamtools_split_mapped" title="into a mapped and an unmapped dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by reads mapping status</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bamtools_split_tag" title="into a dataset list collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by read tag value</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bamtools_split_tag" title="into a dataset list collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by read tag value</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sambamba_markdup" title="Finds and marks duplicate reads in BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sambamba markdup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sambamba_merge" title="Merge several BAM files into one"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sambamba merge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sambamba_sort" title="Tool to sort BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sambamba sort</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_phase" title="call and phase heterozygous SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools phase</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bamhash" title="Hash BAM and FASTQ files to verify data integrity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BamHash</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=varscan_mpileup" title="mutation caller for targeted, exome, and whole-genome resequencing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan mpileup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=varscan_somatic" title="somatic mutation caller for cancer genomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan Somatic</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=varscan_somatic" title="somatic mutation caller for cancer genomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan Somatic</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bamutil_diff" title="two coordinate sorted SAM/BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BamUtil diff</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=revertR2orientationInBam" title="Revert the mapped orientation of R2 mates in a bam."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">revertR2orientationInBam</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bamtools_split" title="BAM datasets on variety of attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mosdepth" title="- fast and flexible depth coverage calculation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mosdepth</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tasmanian_mismatch" title="Quantify, visualize and summarize mismatches in deep sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Analysis of artifacts with Tasmanian</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sambamba_flagstat" title="Retrieving flag statistics from BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sambamba flagstat</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sambamba_markdup" title="Finds and marks duplicate reads in BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sambamba markdup</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sambamba_merge" title="Merge several BAM files into one"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sambamba merge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sambamba_sort" title="Tool to sort BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sambamba sort</button></a>
 <h3>BED</h3>
 <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_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>
@@ -534,26 +542,12 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=vcfdistance" title="Calculate distance to the nearest variant"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFdistance:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcftools_isec" title="multiple VCF datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Intersect</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcftools_merge" title="multiple VCF datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcf2tsv" title="Convert VCF data into TAB-delimited format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFtoTab-delimited:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcf2tsv" title="Convert VCF data into TAB-delimited format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFtoTab-delimited:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfgeno2haplo" title="Convert genotype-based phased alleles into haplotype alleles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFgenotype-to-haplotype:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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=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=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_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="germline small variant caller for long-reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clair3</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=nanopolish_polya" title="- Estimate the length of the poly-A tail on direct RNA reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nanopolish polyA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=medaka_variant" title="decodes variant calls from medaka consensus output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">medaka variant tool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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=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>
@@ -567,13 +561,13 @@ layout: default
 <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=m6anet" title="to detect m6A RNA modifications from nanopore data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">m6anet</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=porechop" title="adapter trimmer for Oxford Nanopore reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Porechop</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=poretools_times" title="and channel information from a set of FAST5 files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract time</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=poretools_nucdist" title="distribution in nanopore sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Show nucleotide</button></a>
@@ -589,18 +583,20 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=poretools_winner" title="from a set of FAST5 files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get longest read</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=poretools_events" title="from a set of sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract nanopore events</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pycoqc" title="quality control for Nanopore sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pycoqc</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=clair3" title="germline small variant caller for long-reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clair3</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=m6anet" title="to detect m6A RNA modifications from nanopore data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">m6anet</button></a>
 <hr/><h2>Common Genomics Tools</h2>
 <h3>Operate on Genomic Intervals</h3>
-<a href="https://usegalaxy.eu/root?tool_id=gops_basecoverage_1" title="of all intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Base Coverage</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gops_complement_1" title="intervals of a dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Complement</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gops_cluster_1" title="the intervals of a dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gops_subtract_1" title="the intervals of two datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Subtract</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Annotation_Profiler_0" title="for a set of genomic intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Profile Annotations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tbl2gff3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Table to GFF3</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=translate_bed" title="cDNA in 3frames or CDS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Translate BED transcripts</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gops_basecoverage_1" title="of all intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Base Coverage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gops_complement_1" title="intervals of a dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Complement</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=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_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>
@@ -623,54 +619,28 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=MAF_filter" title="by specified attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter MAF</button></a>
 <hr/><h2>Genomics Analysis</h2>
 <h3>Annotation</h3>
-<a href="https://usegalaxy.eu/root?tool_id=sanntis_marine" title="in genomic and metagenomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sanntis biosynthetic gene clusters</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=microsatbed" title="Short Tandem Repeats to bed features from fasta"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">STR to bed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=genenotebook_build" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build a GeneNoteBook</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chewbbaca_extractcgmlst" title="Determine the set of loci that constitute the core genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chewBBACA ExtractCgMLST</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=helixer" title="gene calling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Helixer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=legsta" title="Legionella pneumophila sequence based typing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">legsta</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=krocus" title="Multi-locus sequence typing (MLST) from uncorrected long reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">krocus</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=omark" title="proteome quality assessment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OMArk</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_jackhmmer" title="iteratively search a protein sequence against a protein database (PSIBLAST-like)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">jackhmmer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmemit" title="sample sequence(s) from a profile HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmemit</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmalign" title="align sequences to a profile HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmalign</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=multigsea" title="GSEA-based pathway enrichment analysis for multi-omics data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">multiGSEA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tsebra" title="tanscript selector for BRAKER"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TSEBRA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=annotatemyids" title="annotate a generic set of identifiers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">annotateMyIDs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.fasta.seq_trans" title="Translate fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fasta Translate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=braker3" title="genome annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BRAKER3</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=aegean_locuspocus" title="calculate locus coordinates for the given gene annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn LocusPocus</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bakta" title="Rapid and standardized annotation of bacterial genomes, MAGs and plasmids"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bakta</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=agat" title="GTF/GFF analysis toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AGAT</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=compleasm" title="completeness of genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">compleasm</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mitos2" title="de-novo annotation of metazoan mitochondrial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MITOS2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=isescan" title="Insertion Sequence Elements detection in prokaryotic genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ISEScan</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=funannotate_compare" title="annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Funannotate compare</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=windowmasker_mkcounts" title="Construct WindowMasker unit counts table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WindowMasker mkcounts</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=windowmasker_ustat" title="Mask sequences using a WindowMasker unit counts table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WindowMasker ustat</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_nhmmer" title="search a DNA model or alignment against a DNA database (BLASTN-like)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">nhmmer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deepsig" title="signal peptides predictor"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeepSig</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=funannotate_sort" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort assembly</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=funannotate_clean" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Funannotate assembly clean</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=repeatexplorer_clustering" title="repeat discovery and characterization using graph-based sequence clustering"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RepeatExplorer (clustering)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=funannotate_predict" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Funannotate predict annotation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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=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=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=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=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=busco" title="Assess genome assembly and annotation completeness"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Busco</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=optitype" title="HLA genotyping predictions from NGS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OptiType</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=prokka" title="Prokaryotic genome annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prokka</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=roary" title="the pangenome pipeline - Quickly generate a core gene alignment from gff3 files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Roary</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tb_profiler_profile" title="Infer strain types and drug resistance markers from sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TB-Profiler Profile</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_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=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=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=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=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=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=sistr_cmd" title="Salmonella In Silico Typing Resource command-line 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>
@@ -679,6 +649,7 @@ layout: default
 <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=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>
@@ -686,9 +657,7 @@ layout: default
 <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>
@@ -705,7 +674,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=Add_a_column1" title="an expression on every row"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=socru" title="Calculate the order and orientation of complete bacterial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">socru</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=goseq" title="tests for overrepresented gene categories"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">goseq</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=red" title="repeat masking"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Red</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snap_training" title="ab-initio gene predictor"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Train SNAP</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=maker_map_ids" title="on a Maker annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map annotation ids</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fgsea" title="- fast preranked gene set enrichment analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fgsea</button></a>
@@ -743,64 +711,61 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=orthofinder_onlygroups" title="finds orthogroups in a set of proteomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OrthoFinder</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=miranda" title="finds potential target sites for miRNAs in genomic sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">miRanda</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dotknot" title="pseudoknot prediction in a given RNA sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DotKnot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=repeatmodeler" title="Model repetitive DNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RepeatModeler</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hmmer_alimask" title="append modelmask line to a multiple sequence alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">alimask</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=amrfinderplus" title="NCBI Antimicrobial Resistance Gene Finder"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AMRFinderPlus</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=funannotate_annotate" title="annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Funannotate functional</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_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=cpat" title="coding potential assessment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CPAT</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tapscan_classify" title="Detect Transcription Associated Proteins (TAPs)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TAPScan Classify</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=aegean_canongff3" title="pre-process GFF3 files, removing all features not directly related to protein-coding genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn CanonGFF3</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=aegean_parseval" title="compare two sets of gene annotations for the same sequence."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn ParsEval</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.intersect_and_adjacent" title="Outputs nearby top-level GFF features from two GFF3 files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Intersect and Adjacent</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=integron_finder" title="is a program that detects integrons in DNA sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Integron Finder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_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=hamronize_summarize" title="Concatenate and summarize AMR detection reports"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hamronize summarize:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hamronize_tool" title="Antimicrobial Resistance Analysis Reports into a common data structure"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hAMRonize</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mirmachine" title="A tool to detect miRNA homologs in genome sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MirMachine</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=abritamr" title="AMR gene detection with AMRFinderPlus"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">abriTAMR</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=miniprot" title="align a protein sequence against a genome with affine gap penalty, splicing and frameshift"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Miniprot align</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=miniprot_index" title="build a genome index for miniprot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Miniprot index</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chewbbaca_allelecall" title="Determine the allelic profiles of a set of genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChewBBACA AlleleCall</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chewbbaca_allelecallevaluator" title="Build an interactive report for allele calling results evaluation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chewBBACA AlleleCallEvaluator</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chewbbaca_createschema" title="Create a gene-by-gene schema"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chewBBACA CreateSchema</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chewbbaca_downloadschema" title="Download a schema from Chewie-NS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chewBBACA DownloadSchema</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chewbbaca_joinprofiles" title="Join allele calling results from different runs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chewBBACA JoinProfiles</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chewbbaca_nsstats" title="Retrieve basic information about the species and schemas in Chewie-NS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chewBBACA NSStats</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chewbbaca_prepexternalschema" title="Adapt an external schema to be used with chewBBACA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chewBBACA PrepExternalSchema</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=prodigal" title="A tool for gene prediction in microbial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prodigal Gene Predictor</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=aegean_gaeval" title="compute coverage and integrity scores for gene models using transcript alignments."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn GAEVAL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bg_find_subsequences" title="providing regions in BED format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nucleotide subsequence search</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rbc_gotohscan" title="Find subsequences in db"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GotohScan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sanntis_marine" title="in genomic and metagenomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sanntis biosynthetic gene clusters</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=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="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=hamronize_summarize" title="Concatenate and summarize AMR detection reports"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hamronize summarize:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=list_spaln_tables" title="Given a query species, list the spaln settings tables that exist, from closest related species to most different"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">List spaln parameter tables</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gecco" title="is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GECCO</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interproscan" title="functional annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InterProScan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=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=isescan" title="Insertion Sequence Elements detection in prokaryotic genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ISEScan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=miniprot" title="align a protein sequence against a genome with affine gap penalty, splicing and frameshift"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Miniprot align</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=netboxr" title="enables automated discovery of biological process modules by network analysis."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">netboxr</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=plasmidfinder" title="Plasmid identification in bacteria."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PlasmidFinder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=miniprot_index" title="build a genome index for miniprot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Miniprot index</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=red" title="repeat masking"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Red</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=integron_finder" title="is a program that detects integrons in DNA sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Integron Finder</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edta" title="Whole-genome de-novo TE annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">edta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bakta" title="Rapid and standardized annotation of bacterial genomes, MAGs and plasmids"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bakta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cpat" title="coding potential assessment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CPAT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gffcompare" title="compare assembled transcripts to a reference annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GffCompare</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pfamscan" title="search a FASTA sequence against a library of Pfam HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PfamScan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=groot" title="align reads to references and weight variation graphs and generate report"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Groot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pharokka" title="Rapid standardised annotation tool for bacteriophage genomes and metagenomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pharokka</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=homer_findMotifs" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">findMotifs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=braker" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Braker genome annotation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=multigsea" title="GSEA-based pathway enrichment analysis for multi-omics data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">multiGSEA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=get_orfs_or_cdss" title="e.g. to get peptides from ESTs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get open reading frames (ORFs) or coding sequences (CDSs)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.cdsParents" title="is one step of fixing a gene model--adding parent gene features to CDSs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF3 Add Gene to CDS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.fixsixpack" title="Properly formats naive ORF caller output for Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF3 Add Gene to CDS for Sixpack</button></a>
@@ -810,6 +775,9 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.remove_annots" title="that's unused in our GFF tools"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove Annotation Feature</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.prepForApollo" title="by ensuring that CDS features have a wrapping exon feature"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prep GFF3 Input for Apollo</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt2.util.glimmer3_to_gff3" title="convert formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Glimmer3 to GFF3</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=agat" title="GTF/GFF analysis toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AGAT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=braker3" title="genome annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BRAKER3</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=helixer" title="gene calling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Helixer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt2.phage.intron_detection" title="based on nearby protein blast results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interrupted gene detection tool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.export_seq" title="Export corresponding sequence in genome from GFF3"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF3 Feature Sequence Export</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.fasta.lipory" title="in protein sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Identify Lipoboxes</button></a>
@@ -819,48 +787,67 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt2.phage.annotation_table" title="from gff3 formatted datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Annotation Table</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gff3.rebase" title="against parent features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Rebase GFF3 features</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.require_sd" title="ensures CDSs have an SD"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gff3 Filter: Require SD</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=amrfinderplus" title="NCBI Antimicrobial Resistance Gene Finder"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AMRFinderPlus</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=repeatexplorer_clustering" title="repeat discovery and characterization using graph-based sequence clustering"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RepeatExplorer (clustering)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deepsig" title="signal peptides predictor"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeepSig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=genenotebook_build" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build a GeneNoteBook</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tsebra" title="tanscript selector for BRAKER"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TSEBRA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=windowmasker_mkcounts" title="Construct WindowMasker unit counts table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WindowMasker mkcounts</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=windowmasker_ustat" title="Mask sequences using a WindowMasker unit counts table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WindowMasker ustat</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tapscan_classify" title="Detect Transcription Associated Proteins (TAPs)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TAPScan Classify</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=aegean_canongff3" title="pre-process GFF3 files, removing all features not directly related to protein-coding genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn CanonGFF3</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=aegean_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_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_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=edu.tamu.cpt.fasta.seq_trans" title="Translate fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fasta Translate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=omark" title="proteome quality assessment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OMArk</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=krocus" title="Multi-locus sequence typing (MLST) from uncorrected long reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">krocus</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mirmachine" title="A tool to detect miRNA homologs in genome sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MirMachine</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=prodigal" title="A tool for gene prediction in microbial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prodigal Gene Predictor</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=compleasm" title="completeness of genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">compleasm</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=abritamr" title="AMR gene detection with AMRFinderPlus"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">abriTAMR</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chewbbaca_allelecall" title="Determine the allelic profiles of a set of genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChewBBACA AlleleCall</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chewbbaca_allelecallevaluator" title="Build an interactive report for allele calling results evaluation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chewBBACA AlleleCallEvaluator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chewbbaca_createschema" title="Create a gene-by-gene schema"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chewBBACA CreateSchema</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chewbbaca_downloadschema" title="Download a schema from Chewie-NS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chewBBACA DownloadSchema</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chewbbaca_extractcgmlst" title="Determine the set of loci that constitute the core genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chewBBACA ExtractCgMLST</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chewbbaca_joinprofiles" title="Join allele calling results from different runs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chewBBACA JoinProfiles</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chewbbaca_nsstats" title="Retrieve basic information about the species and schemas in Chewie-NS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chewBBACA NSStats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chewbbaca_prepexternalschema" title="Adapt an external schema to be used with chewBBACA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chewBBACA PrepExternalSchema</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=microsatbed" title="Short Tandem Repeats to bed features from fasta"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">STR to bed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.blast.protein_grouping" title="Based on a BLASTp result"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Protein Blast Grouping</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt2.phage.relatedProphages" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Related Prophages tool</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.intersect_and_adjacent" title="Outputs nearby top-level GFF features from two GFF3 files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Intersect and Adjacent</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=argnorm" title="a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">argNorm</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=evidencemodeler" title="combines ab intio gene predictions, protein and transcript alignments into gene structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EVidenceModeler</button></a>
 <h3>Multiple Alignments</h3>
-<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=mashmap" title="Fast local alignment boundaries"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mashmap</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=maf_stats1" title="Alignment coverage information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAF Coverage Stats</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=format_cd_hit_output" title="to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Format cd-hit outputs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=clustalw" title="multiple sequence alignment program for DNA or proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ClustalW</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sina" title="reference based multiple sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SINA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gecko" title="Ungapped genome comparison"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gecko</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hammock_1.0" title="Clusters short peptide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hammock - cluster peptides</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=chromeister" title="ultra-fast pairwise genome comparisons"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Chromeister</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=mummer_mummer" title="Align two or more sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Mummer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mummer_mummerplot" title="Generate 2-D dotplot of aligned sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Mummerplot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mummer_delta_filter" title="Filters alignment (delta) file from nucmer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delta-Filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mummer_nucmer" title="Align two or more sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nucmer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mummer_dnadiff" title="Evaluate similarities/differences between two sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DNAdiff</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mummer_show_coords" title="Parse delta file and report coordinates and other information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Show-Coords</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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=kc-align" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kc-Align</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pipelign" title="alignment with pipelign"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Automated multiple sequence</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=selectsequencesfrommsa" title="Tool to select representative sequences from a multiple sequence alignment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select Sequences</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=msaboot" title="Output PHYLIP file with bootstrapped multiple sequence alignment data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSABOOT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hammock_1.0" title="Clusters short peptide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hammock - cluster peptides</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=format_cd_hit_output" title="to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Format cd-hit outputs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=muscle" title="multiple aligner"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MUSCLE</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=compalignp" title="Fractional identities between alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compalignp</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=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=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=mashmap" title="Fast local alignment boundaries"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mashmap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=trimal" title="for automated alignment trimming"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">trimAl</button></a>
 <h3>Assembly</h3>
+<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=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=make_ear" title="A tool to compile assembly reports and statistics from assembly pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ERGA Assembly Reporting Tool (EAR)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=wtdbg" title="Fast de novo sequence assembler for long noisy reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WTDBG2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=refseq_masher_contains" title="Find NCBI RefSeq Genomes contained in your sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RefSeq Masher Contains</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=refseq_masher_matches" title="Find closest matching NCBI RefSeq Genomes to your sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RefSeq Masher Matches</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pairtools_dedup" title="Find and remove PCR/optical duplicates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairtools dedup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pairtools_sort" title="Sort a 4dn pairs/pairsam file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairtools sort</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pairtools_split" title="Split a pairsam file into pairs and SAM/BAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairtools split</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pairtools_parse" title="Find ligation pairs in alignments and create pairs."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairtools parse</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastk_fastk" title="A k-mer counter for high-quality assembly datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastK</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=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=cactus_cactus" title="whole-genome multiple sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cactus</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=merquryplot" title="evaluate the assembly quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merqury histogram plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hapog" title="genome polishing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hapo-G</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pretext_map" title="converts SAM or BAM files into genome contact maps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PretextMap</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trycycler_cluster" title="cluster the contigs of your input assemblies into per-replicon groups"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trycycler cluster</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trycycler_consensus" title="generate a consensus contig sequence for each cluster"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trycycler consensus</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trycycler_partition" title="assign the reads to the clusters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trycycler partition</button></a>
@@ -883,7 +870,6 @@ layout: default
 <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=racon" title="Consensus module for raw de novo DNA assembly of long uncorrected reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Racon</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=minia" title="Short-read assembler based on a de Bruijn graph"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Minia</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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=quast" title="Genome assembly Quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Quast</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=miniasm" title="Ultrafast de novo assembly for long noisy reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">miniasm</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=abyss-pe" title="de novo sequence assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ABySS</button></a>
@@ -893,10 +879,14 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=spades" title="genome assembler for genomes of regular and single-cell projects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SPAdes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=velvetoptimiser" title="Automatically optimize Velvet assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VelvetOptimiser</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pilon" title="An automated genome assembly improvement and variant detection tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pilon</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=wtdbg" title="Fast de novo sequence assembler for long noisy reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WTDBG2</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=disco" title="to assemble metagenomics data using an overlap-layout-consensus (OLC) approach"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DISCO</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rnaspades" title="de novo transcriptome assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rnaSPAdes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=meryl" title="a genomic k-mer counter and sequence utility"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Meryl</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mira_assembler" title="Takes Sanger, Roche, Illumina, and Ion Torrent data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Assemble with MIRA v3.4</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=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=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>
 <a href="https://usegalaxy.eu/root?tool_id=sopra_wpc" title="for Illumina libraries"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SOPRA with prebuilt contigs</button></a>
@@ -905,6 +895,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=minced" title="(minced)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">detect CRISPR sequences</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=merqury" title="evaluate the assembly quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merqury</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=genomescope" title="reference-free genome profiling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GenomeScope</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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>
@@ -917,6 +908,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=spades_metaviralspades" title="extract and assembly viral genomes from metagenomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaviralSPAdes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=spades_metaplasmidspades" title="extract and assembly plasmids from metagenomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaplasmidSPAdes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=spades_coronaspades" title="SARS-CoV-2 de novo genome assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">coronaSPAdes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=links" title="- scaffold genome assemblies with long reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LINKS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gfastats" title="the swiss army knife for genome assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gfastats</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=yahs" title="yet another HI-C scaffolding tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">YAHS</button></a>
@@ -924,70 +916,74 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=velveth" title="Prepare a dataset for the Velvet velvetg Assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">velveth</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cap3" title="Sequence Assembly tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cap3</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=smudgeplot" title="inference of ploidy and heterozygosity structure using whole genome sequencing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Smudgeplot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cactus_export" title="whole-genome multiple sequence alignment to other formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cactus: export</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pretext_graph" title="Embed bedgraph formatted data inside a Pretext contact map."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pretextgraph</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pairtools_stats" title="Calculates pairs statistics for input pairs and pairsam files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairtools Stats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hapog" title="genome polishing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hapo-G</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=get_organelle_from_reads" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get organelle from reads</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=reago" title="to assemble rRNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Reago</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=blobtoolkit" title="Genome Assembly QC"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BlobToolKit</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=minipolish" title="polishing miniasm assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">minipolish</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cactus_cactus" title="whole-genome multiple sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cactus</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cactus_export" title="whole-genome multiple sequence alignment to other formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cactus: export</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=instagraal" title="Large genome reassembly based on Hi-C data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">instaGRAAL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=necat" title="Error correction and de-novo assembly for ONT Nanopore reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">necat</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=biscot" title="Bionano scaffolding correction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BiSCoT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hifiasm_meta" title="for metagenome assembly using Hifi reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hifiasm_meta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=blobtoolkit" title="Genome Assembly QC"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BlobToolKit</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nextdenovo" title="string graph-based de novo assembler for long reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NextDenovo</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=get_annotated_regions_from_gb" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get annotated regions from genbank files (getorganelle)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=aligned_to_consensus" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Consensus sequence from aligned FASTA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=verkko" title="hybrid genome assembly pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">verkko</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=velvetg" title="Velvet sequence assembler for very short reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">velvetg</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rna_quast" title="A quality assessment tool for De Novo transcriptome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rnaQUAST</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=velveth" title="Prepare a dataset for the Velvet velvetg Assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">velveth</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastk_fastk" title="A k-mer counter for high-quality assembly datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastK</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pairtools_dedup" title="Find and remove PCR/optical duplicates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairtools dedup</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pairtools_parse" title="Find ligation pairs in alignments and create pairs."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairtools parse</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pairtools_split" title="Split a pairsam file into pairs and SAM/BAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairtools split</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pairtools_sort" title="Sort a 4dn pairs/pairsam file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairtools sort</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pairtools_stats" title="Calculates pairs statistics for input pairs and pairsam files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairtools Stats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastk_logex" title="Performs binary operations on the generated Ktab files from FASTK suite"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastK Logex</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastk_histex" title="Reads and displays a kmer histogram produced by FastK"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastK Histex</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=merquryplot" title="evaluate the assembly quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merqury histogram plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pretext_graph" title="Embed bedgraph formatted data inside a Pretext contact map."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pretextgraph</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=reago" title="to assemble rRNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Reago</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=refseq_masher_contains" title="Find NCBI RefSeq Genomes contained in your sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RefSeq Masher Contains</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=refseq_masher_matches" title="Find closest matching NCBI RefSeq Genomes to your sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RefSeq Masher Matches</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=make_ear" title="A tool to compile assembly reports and statistics from assembly pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ERGA Assembly Reporting Tool (EAR)</button></a>
 <h3>Mapping</h3>
-<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=pbmm2" title="map PacBio reads to a reference genome."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pbmm2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rna_starsolo" title="mapping, demultiplexing and gene quantification for single cell RNA-seq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA STARSolo</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bbtools_bbmap" title="short-read aligner"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: BBMap</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=megablast_xml_parser" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Parse blast XML output</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=megablast_wrapper" title="compare short reads against htgs, nt, and wgs databases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Megablast</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bwameth" title="Fast and accurate aligner of BS-Seq reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bwameth</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lastz_paired_reads_wrapper" title="map short paired reads against reference sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Lastz paired reads</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lastz_wrapper_2" title=": align long sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LASTZ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bowtie_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with Bowtie for Illumina</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=minimap2" title="A fast pairwise aligner for genomic and spliced nucleotide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with minimap2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hisat2" title="A fast and sensitive alignment program"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HISAT2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rna_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=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_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=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=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=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=tophat2" title="Gapped-read mapper for RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TopHat</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bowtie_color_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with Bowtie for SOLiD</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=winnowmap" title="a mapping tool optimized for repetitive sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Winnowmap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=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=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=pbmm2" title="map PacBio reads to a reference genome."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pbmm2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=PerM" title="for SOLiD and Illumina"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with PerM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=srma_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Re-align with SRMA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mosaik_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with Mosaik</button></a>
 <h3>Variant Calling</h3>
-<a href="https://usegalaxy.eu/root?tool_id=beacon2_datasets" title="Query the datasets collection in the beacon database groupings of variants or individuals who belong to the same repository"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Datasets</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hgvsparser" title="parsing and building variant descriptor strings compliant with the HGVS standard"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hgvsParseR</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_reference" title="Compile a copy-number reference from the given files or directory containing normal samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Reference</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_diagram" title="Draw copy number on chromosomes as a diagram"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Diagram</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_coverage" title="Calculate coverage in the given regions from BAM read depths"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Coverage</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnv_vcf2json" title="Converts 1000hg structural variants VCF file to JSON"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNV VCF2JSON</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vcfanno" title="VCF annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">vcfanno</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bbtools_callvariants" title="in aligned Bam files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: call variants</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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=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=cnvkit_heatmap" title="Plot copy number for multiple samples as a heatmap"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Heatmap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_batch" title="Run the CNVkit pipeline on one or more BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Batch</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fatovcf" title="Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">faToVcf</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=strelka_germline" title="small variant caller for germline variation in small cohorts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Strelka Germline</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sansa_annotate" title="structural variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sansa annotate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=strelka_somatic" title="small variant caller for somatic variation in tumor/normal sample pairs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Strelka Somatic</button></a>
@@ -998,19 +994,20 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=bcftools_consensus" title="Create consensus sequence by applying VCF variants to a reference fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools consensus</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=delly_classify" title="somatic or germline copy-number variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly classify</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=delly_cnv" title="discover and genotype copy-number variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly cnv</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=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=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=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=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=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>
@@ -1063,6 +1060,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=snp_sites" title="from a multi-FASTA alignment file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Finds SNP sites</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=exomedepth" title="Calls copy number variants (CNVs) from targeted sequence data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ExomeDepth</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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=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=varscan_somatic" title="Call germline/somatic and LOH variants from tumor-normal sample pairs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan somatic</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=basil" title="Breakpoint detection, including large insertions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">basil</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_int" title="Filter variants using intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Intervals</button></a>
@@ -1083,38 +1081,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_dbnsfp_generic" title="Add Annotations from dbNSFP and similar annotation DBs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift dbNSFP</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpEff_download" title="download a pre-built database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff download:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpEff" title="annotate variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff eff:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=beacon2_csv2xlsx" title="v2 CSV Models to XLSX"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 CSV2XLSX</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=beacon2_pxf2bff" title="converts Phenopacket PXF (JSON) to BFF (JSON)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 PXF2BFF</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=beacon2_vcf2bff" title="converting annotated VCF files to Beacon v2 format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 VCF2BFF</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=manta" title="Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Manta</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnv_phenopacket" title="Builds Phenopacket schema for the structural variants metadata from the 1000hg project"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNV Phenopacket</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_antitarget" title="lists the chromosomal coordinates for targeted resequencing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Antitarget</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_autobin" title="Estimates read counts or depths in a BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Autobin</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_batch" title="Run the CNVkit pipeline on one or more BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Batch</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_breaks" title="List the targeted genes with segmentaion breakpoint"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Breaks</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_call" title="Call copy number variants from segmented log2 ratios"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Call</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_fix" title="Adjust raw coverage data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Fix</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_genemetrics" title="Identify targeted genes with copy number gain or loss"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit genemetrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_heatmap" title="Plot copy number for multiple samples as a heatmap"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Heatmap</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_access" title="Calculate the sequence-accessible coordinates in chromosomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Access</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_scatter" title="Plot bin-level log2 coverages and segmentation calls together"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Scatter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_segment" title="Infer copy number segments from the given coverage table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Segment</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_segmetrics" title="calculate summary statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Segmetrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_sex" title="Guess samples’ chromosomal sex from the relative coverage of chromosomes X and Y"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Sex</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_target" title="Prepare a BED file of baited regions for use with CNVkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Target</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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=smgu_frameshift_deletions_checks" title="reports on frameshifting indels in consensus sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Frameshift Deletions Checks</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=beacon2_biosamples" title="Query the biosamples collection in the beacon database for samples taken from individuals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Biosamples</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=beacon2_bracket" title="Specifies a sequence ranges for both the start and end positions of a genomic variation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Bracket</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=beacon2_cnv" title="Retrieve the copy number varients from genomicVariations collection from the beacon database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 CNV</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=beacon2_cohorts" title="Query the Cohorts collection in the beacon database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Cohorts</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=beacon2_gene" title="Queries the beacon database and retrieve the genomic variants matching gene symbol"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Gene</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=beacon2_analyses" title="َQuery the analyses collection in the beacon database for bioinformatic procedures to identify variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Analyses</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=beacon2_import" title="Import JSON formatted datasets to beacon database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Import</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=beacon2_individuals" title="Query the individuals collection in the beacon database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Individuals</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=beacon2_range" title="Retrieve the genomic variants from the beacon database by specifying start and end positions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Range</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=beacon2_runs" title="Query the runs collection in the beacon database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Runs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=beacon2_sequence" title="َQuery for the existence of a specified sequence at a given genomic position"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Sequence</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=varscan_copynumber" title="Determine relative tumor copy number from tumor-normal pileups"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan copynumber</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=varscan" title="for variant detection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=varscan_mpileup" title="for variant detection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan mpileup</button></a>
@@ -1140,15 +1106,52 @@ layout: default
 <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=king" title="Kinship-based INference for GWAS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">KING</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=artic_guppyplex" title="Filter Nanopore reads by read length and (optionally) quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ARTIC guppyplex</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pharmcat" title="Pharmacogenomics Clinical Annotation Tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pharmCAT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=ensembl_vep" title="with VEP"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Predict variant effects</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=breseq" title="find mutations in haploid microbial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">breseq</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcf2maf" title="with vcf2maf"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert VCF to MAF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_access" title="Calculate the sequence-accessible coordinates in chromosomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Access</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_antitarget" title="lists the chromosomal coordinates for targeted resequencing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Antitarget</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_autobin" title="Estimates read counts or depths in a BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Autobin</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_call" title="Call copy number variants from segmented log2 ratios"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Call</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_coverage" title="Calculate coverage in the given regions from BAM read depths"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Coverage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_diagram" title="Draw copy number on chromosomes as a diagram"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Diagram</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_fix" title="Adjust raw coverage data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Fix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_genemetrics" title="Identify targeted genes with copy number gain or loss"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit genemetrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_breaks" title="List the targeted genes with segmentaion breakpoint"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Breaks</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_reference" title="Compile a copy-number reference from the given files or directory containing normal samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Reference</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_scatter" title="Plot bin-level log2 coverages and segmentation calls together"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Scatter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_segment" title="Infer copy number segments from the given coverage table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Segment</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_segmetrics" title="calculate summary statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Segmetrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_sex" title="Guess samples’ chromosomal sex from the relative coverage of chromosomes X and Y"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Sex</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_target" title="Prepare a BED file of baited regions for use with CNVkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Target</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bcftools_plugin_setgt" title="plugin Sets genotypes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools setGT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bcftools_plugin_setgt" title="plugin Sets genotypes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools setGT</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fatovcf" title="Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">faToVcf</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=smgu_frameshift_deletions_checks" title="reports on frameshifting indels in consensus sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Frameshift Deletions Checks</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beacon2_csv2xlsx" title="v2 CSV Models to XLSX"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 CSV2XLSX</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beacon2_pxf2bff" title="converts Phenopacket PXF (JSON) to BFF (JSON)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 PXF2BFF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beacon2_vcf2bff" title="converting annotated VCF files to Beacon v2 format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 VCF2BFF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=manta" title="Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Manta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnv_phenopacket" title="Builds Phenopacket schema for the structural variants metadata from the 1000hg project"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNV Phenopacket</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnv_vcf2json" title="Converts 1000hg structural variants VCF file to JSON"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNV VCF2JSON</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hgvsparser" title="parsing and building variant descriptor strings compliant with the HGVS standard"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hgvsParseR</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beacon2_analyses" title="َQuery the analyses collection in the beacon database for bioinformatic procedures to identify variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Analyses</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beacon2_biosamples" title="Query the biosamples collection in the beacon database for samples taken from individuals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Biosamples</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beacon2_bracket" title="Specifies a sequence ranges for both the start and end positions of a genomic variation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Bracket</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beacon2_cnv" title="Retrieve the copy number varients from genomicVariations collection from the beacon database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 CNV</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beacon2_cohorts" title="Query the Cohorts collection in the beacon database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Cohorts</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beacon2_datasets" title="Query the datasets collection in the beacon database groupings of variants or individuals who belong to the same repository"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Datasets</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beacon2_gene" title="Queries the beacon database and retrieve the genomic variants matching gene symbol"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Gene</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beacon2_import" title="Import JSON formatted datasets to beacon database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Import</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beacon2_individuals" title="Query the individuals collection in the beacon database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Individuals</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beacon2_range" title="Retrieve the genomic variants from the beacon database by specifying start and end positions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Range</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beacon2_runs" title="Query the runs collection in the beacon database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Runs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beacon2_sequence" title="َQuery for the existence of a specified sequence at a given genomic position"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Sequence</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>
 <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=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>
@@ -1161,14 +1164,6 @@ 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=infer_rnaformer" title="Predict the secondary structure of an RNA with RNAformer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAformer</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=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=cmsearch_deoverlap" title="removes lower scoring overlaps from cmsearch results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CMsearch deoverlap</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rbpbench" title="- Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RBPBench</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ribowaltz_plot" title="visual inspection of ribosome profiling data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">riboWaltz-plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=arriba" title="detect gene fusions from STAR aligned RNA-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Arriba</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=filter_combined_via_tracking" title="using tracking file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter Combined Transcripts</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=express" title="Quantify the abundances of a set of target sequences from sampled subsequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eXpress</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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>
@@ -1195,8 +1190,12 @@ layout: default
 <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=salmon" title="Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Salmon quant</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=deseq2" title="Determines differentially expressed features from count tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DESeq2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=stringtie" title="transcript assembly and quantification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">StringTie</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=stringtie_merge" title="transcripts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">StringTie merge</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trinity_align_and_estimate_abundance" title="on a de novo assembly of RNA-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align reads and estimate abundance</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trinity" title="de novo assembly of RNA-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trinity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sRNAPipe" title="In-depth study of small RNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sRNAPipe</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=graphprot_predict_profile" title="- Train models and predict RBP binding profiles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GraphProt</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=heinz_visualization" title="the optimal scoring subnetwork"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Visualize</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=slamdunk" title="- streamlining SLAM-seq analysis with ultra-high sensitivity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slamdunk</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=alleyoop" title="- post-processing and QC of Slamdunk analyses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Alleyoop</button></a>
@@ -1254,46 +1253,41 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=trinity_samples_qccheck" title="for transcript quantification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNASeq samples quality check</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=describe_samples" title="and replicates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Describe samples</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trinity_define_clusters_by_cutting_tree" title="after differential expression analysis using a Trinity assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Partition genes into expression clusters</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=arriba_draw_fusions" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Arriba Draw Fusions</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=arriba_get_filters" title="to history"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Arriba Get Filters</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_FPKM_count" title="calculates raw read count, FPM, and FPKM for each gene"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FPKM Count</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_RNA_fragment_size" title="calculates the fragment size for each gene/transcript"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA fragment size</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_RPKM_saturation" title="calculates raw count and RPKM values for transcript at exon, intron, and mRNA level"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RPKM Saturation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_bam2wig" title="converts all types of RNA-seq data from BAM to Wiggle"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BAM to Wiggle</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_bam_stat" title="reads mapping statistics for a provided BAM or SAM file."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BAM/SAM Mapping Stats</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_clipping_profile" title="estimates clipping profile of RNA-seq reads from BAM or SAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clipping Profile</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_deletion_profile" title="calculates the distributions of deleted nucleotides across reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Deletion Profile</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rseqc_geneBody_coverage" title="read coverage over gene body"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gene Body Coverage (BAM)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_geneBody_coverage2" title="read coverage over gene body"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gene Body Coverage (Bigwig)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_infer_experiment" title="speculates how RNA-seq were configured"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Infer Experiment</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_inner_distance" title="calculate the inner distance (or insert size) between two paired RNA reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Inner Distance</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_insertion_profile" title="calculates the distribution of inserted nucleotides across reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Insertion Profile</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_junction_annotation" title="compares detected splice junctions to reference gene model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Junction Annotation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_junction_saturation" title="detects splice junctions from each subset and compares them to reference gene model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Junction Saturation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_mismatch_profile" title="calculates the distribution of mismatches across reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Mismatch Profile</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_read_GC" title="determines GC% and read count"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Read GC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_read_NVC" title="to check the nucleotide composition bias"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Read NVC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_read_distribution" title="calculates how mapped reads were distributed over genome feature"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Read Distribution</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_read_duplication" title="determines reads duplication rate with sequence-based and mapping-based strategies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Read Duplication</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_read_hexamer" title="calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hexamer frequency</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_read_quality" title="determines Phred quality score"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Read Quality</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rseqc_tin" title="evaluates RNA integrity at a transcript level"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Transcript Integrity Number</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ribowaltz_process" title="calculation of optimal P-site offsets and diagnostic analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">riboWaltz</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=brew3r_r" title="Extend GTF"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BREW3R.r</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=heinz_bum" title="with p-values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fit a BUM model</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=heinz" title="using Heinz"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Identify optimal scoring subnetwork</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=heinz_scoring" title="for each node"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate a Heinz score</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sshmm" title="- RNA sequence-structure motif finder"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ssHMM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pizzly" title="- fast fusion detection using kallisto"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pizzly</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rcas" title="- RNA Centric Annotation System"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RCAS</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=graphprot_predict_profile" title="- Predict RBP binding profiles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GraphProt predict profile</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_geneBody_coverage2" title="read coverage over gene body"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gene Body Coverage (Bigwig)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_RPKM_saturation" title="calculates raw count and RPKM values for transcript at exon, intron, and mRNA level"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RPKM Saturation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_infer_experiment" title="speculates how RNA-seq were configured"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Infer Experiment</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_RNA_fragment_size" title="calculates the fragment size for each gene/transcript"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA fragment size</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_tin" title="evaluates RNA integrity at a transcript level"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Transcript Integrity Number</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_junction_saturation" title="detects splice junctions from each subset and compares them to reference gene model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Junction Saturation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_FPKM_count" title="calculates raw read count, FPM, and FPKM for each gene"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FPKM Count</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_read_distribution" title="calculates how mapped reads were distributed over genome feature"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Read Distribution</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rbc_rnacode" title="Analyze the protein coding potential in MSA."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAcode</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_junction_annotation" title="compares detected splice junctions to reference gene model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Junction Annotation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_inner_distance" title="calculate the inner distance (or insert size) between two paired RNA reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Inner Distance</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rnaz" title="predicting structurally conserved and thermodynamically stable RNA secondary structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAz</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=RNAshapes" title="RNA Secondary structure prediction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAshapes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=viennarna_rnafold" title="Calculate minimum free energy secondary structures and partition function of RNAs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAfold</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=idr" title="compare ranked list of identifications"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDR</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=viennarna_rnacofold" title="Calculate secondary structures of two RNAs with dimerization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAcofold</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=viennarna_rnaalifold" title="Calculate minimum free energy secondary structures and partition function on a multiple alignment file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAalifold</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_deletion_profile" title="calculates the distributions of deleted nucleotides across reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Deletion Profile</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_read_NVC" title="to check the nucleotide composition bias"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Read NVC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_bam_stat" title="reads mapping statistics for a provided BAM or SAM file."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BAM/SAM Mapping Stats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_read_duplication" title="determines reads duplication rate with sequence-based and mapping-based strategies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Read Duplication</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_read_GC" title="determines GC% and read count"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Read GC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_insertion_profile" title="calculates the distribution of inserted nucleotides across reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Insertion Profile</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_bam2wig" title="converts all types of RNA-seq data from BAM to Wiggle"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BAM to Wiggle</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_clipping_profile" title="estimates clipping profile of RNA-seq reads from BAM or SAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clipping Profile</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_read_quality" title="determines Phred quality score"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Read Quality</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_read_hexamer" title="calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hexamer frequency</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rseqc_mismatch_profile" title="calculates the distribution of mismatches across reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Mismatch Profile</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=sailfish" title="transcript quantification from RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sailfish</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cuffquant" title="Precompute gene expression levels"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cuffquant</button></a>
@@ -1343,9 +1337,15 @@ 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=infer_rnaformer" title="Predict the secondary structure of an RNA with RNAformer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAformer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=genomic_super_signature" title="interpretation of RNAseq experiments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GenomicSuperSignature</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=barrnap" title="Locate ribosomal RNA's in a fasta file. (GFF output)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">barrnap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=arriba_draw_fusions" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Arriba Draw Fusions</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=arriba_get_filters" title="to history"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Arriba Get Filters</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=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=ribowaltz_process" title="calculation of optimal P-site offsets and diagnostic analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">riboWaltz</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ribowaltz_plot" title="visual inspection of ribosome profiling data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">riboWaltz-plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cemitool" title="gene co-expression network analyses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CEMiTool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cherri_train" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Train a CheRRI model using RRIs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mirnature" title="Computational detection of canonical microRNAs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">miRNAture</button></a>
@@ -1353,33 +1353,43 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=isoformswitchanalyzer" title="statistical identification of isoform switching"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IsoformSwitchAnalyzeR</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sleuth" title="differential expression analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sleuth</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trinity_stats" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trinity Stats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cmsearch_deoverlap" title="removes lower scoring overlaps from cmsearch results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CMsearch deoverlap</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=psiclass" title="reference-based transcriptome assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PsiCLASS</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rbpbench" title="- Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RBPBench</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=brew3r_r" title="Extend GTF"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BREW3R.r</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seurat_preprocessing" title="- Normalize, Find Variable Features, Scale and Regress"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Seurat Preprocessing</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seurat_integrate" title="and manipulate layers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Seurat Integrate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seurat_reduce_dimension" title="- PCA, tSNE or UMAP"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Seurat Run Dimensional Reduction</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seurat_create" title="- Prepare data for the pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Seurat Create</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seurat_plot" title="- Plot cells, features and dimensions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Seurat Visualize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seurat_data" title="- Inspect and Manipulate"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Seurat Data Management</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seurat_clustering" title="- Neighbors and Markers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Seurat Find Clusters</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sfold" title="Prediction of  RNA secondary structures through structure ensemble sampling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sfold</button></a>
 <h3>Peak Calling</h3>
+<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=pileometh" title="A tool for processing bisulfite sequencing alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MethylDackel</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=macs2_bdgbroadcall" title="Call broad peaks from bedGraph output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 bdgbroadcall</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=macs2_bdgcmp" title="Deduct noise by comparing two signal tracks in bedGraph"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 bdgcmp</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=macs2_bdgbroadcall" title="Call broad peaks from bedGraph output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 bdgbroadcall</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=macs2_refinepeak" title="Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 refinepeak</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=macs2_bdgdiff" title="Differential peak detection based on paired four bedgraph files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 bdgdiff</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=macs2_bdgpeakcall" title="Call peaks from bedGraph output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 bdgpeakcall</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=macs2_callpeak" title="Call peaks from alignment results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 callpeak</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=macs2_filterdup" title="Remove duplicate reads at the same position"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 filterdup</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=macs2_predictd" title="Predict 'd' or fragment size from alignment results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 predictd</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=macs2_randsample" title="Randomly sample number or percentage of total reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 randsample</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=macs2_refinepeak" title="Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 refinepeak</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=peakcalling_macs" title="Model-based Analysis of ChIP-Seq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=peakcalling_sicer" title="Statistical approach for the Identification of ChIP-Enriched Regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SICER</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=peakcalling_ccat" title="Control-based ChIP-seq Analysis Tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CCAT</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=genrich" title="Detecting sites of genomic enrichment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Genrich</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=peakzilla" title="Identify transcription factor binding sites from ChIP-seq and ChIP-exo experiments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Peakzilla</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=macs2_filterdup" title="Remove duplicate reads at the same position"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 filterdup</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=macs2_callpeak" title="Call peaks from alignment results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MACS2 callpeak</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=peakachu" title="Calls Peaks in CLIP data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PEAKachu</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=zerone" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">zerone</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pureclip" title="- HMM based peak caller designed for eCLIP/iCLIP data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PureCLIP</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=jamm" title="Calls peaks on NGS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JAMM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=piranha" title="peak-caller for CLIP- and RIP-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Piranha</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=htseq_clip" title="- A toolset for the analysis of eCLIP/iCLIP datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">htseq-clip</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dewseq" title="- A sliding window based peak caller for eCLIP/iCLIP data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DEWSeq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=peakzilla" title="Identify transcription factor binding sites from ChIP-seq and ChIP-exo experiments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Peakzilla</button></a>
 <h3>Epigenetics</h3>
-<a href="https://usegalaxy.eu/root?tool_id=hifive" title="manipulate, analyze, and plot HiC and 5C chromatin interaction data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hifive</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcf_filter" title="a VCF file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=seacr" title="for sparse enrichment analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SEACR</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=moabs" title="MOdel based Analysis of Bisulfite Sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MOABS</button></a>
@@ -1395,11 +1405,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=minfi_getbeta" title="obtain Beta value matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Minfi Get Beta</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=minfi_getsnp" title="retrieve the chromosome and the position of each SNP"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Minfi Get SNPs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=minfi_maptogenome" title="mapping Ilumina methylation array data to the genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Minfi Map to Genome</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cooler_makebins" title="Generate fixed-width genomic bins."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cooler_makebins</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cooler_csort_tabix" title="Sort and index a contact list."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cooler csort with tabix</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cooler_cload_tabix" title="Create a cool file from a tabix-indexed contact file and a list of genomic bins."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cooler_cload_tabix</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cooler_balance" title="Copy and balance a cool file."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cooler_balance</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cooler_zoomify" title="Generate a multi-resolution cooler file by coarsening"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cooler zoomify</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=minfi_getM" title="returns the Fisher information corresponding to a model and a design"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Minfi Get M</button></a>
 <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>
@@ -1411,9 +1416,14 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=hicup_deduplicator" title="removes duplicated di-tags (retaining one copy of each) from the data set."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hicup Deduplicator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=epicseg_segment" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EpiCSeg - Chromatin segmentation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicup_mapper" title="aligns paired reads independently to a reference genome and retains reads where both partners align."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hicup Mapper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hifive" title="manipulate, analyze, and plot HiC and 5C chromatin interaction data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hifive</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cooler_makebins" title="Generate fixed-width genomic bins."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cooler_makebins</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cooler_csort_tabix" title="Sort and index a contact list."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cooler csort with tabix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cooler_cload_tabix" title="Create a cool file from a tabix-indexed contact file and a list of genomic bins."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cooler_cload_tabix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cooler_balance" title="Copy and balance a cool file."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cooler_balance</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicup2juicer" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hicup to juicer converter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cooler_zoomify" title="Generate a multi-resolution cooler file by coarsening"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cooler zoomify</button></a>
 <h3>Phylogenetics</h3>
-<a href="https://usegalaxy.eu/root?tool_id=raxml" title="Maximum Likelihood based inference of large phylogenetic trees"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RAxML</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hyphy_prime" title="Property Informed Models of Evolution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-PRIME</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hyphy_busted" title="Branch-site Unrestricted Statistical Test for Episodic Diversification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-BUSTED</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hyphy_bgm" title="- Detecting coevolving sites via Bayesian graphical models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-BGM</button></a>
@@ -1427,14 +1437,11 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=hyphy_fel" title="Fixed Effects Likelihood"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-FEL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=t_coffee" title="multiple sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">T-Coffee</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hyphy_relax" title="Detect relaxed selection in a codon-based    phylogenetic framework"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-RELAX</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=usher_matutils" title="analyze, edit, and manipulate mutation annotated tree files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UShER matUtils</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=usher" title="ultrafast sample placement on existing trees"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UShER</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sarscov2formatter" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sarscov2formatter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=raxml" title="Maximum Likelihood based inference of large phylogenetic trees"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RAxML</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gstf_preparation" title="converts data for the workflow"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GeneSeqToFamily preparation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=phyml" title="Phylogeny software based on the maximum-likelihood method"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PhyML</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sarscov2summary" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sarscov2summary</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pangolin" title="Phylogenetic Assignment of Outbreak Lineages"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pangolin</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hybpiper" title="Analyse targeted sequence capture data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HybPiper</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ete_gene_csv_finder" title="from a genetree using the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gene Copy Number Finder</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hcluster_sg_parser" title="converts hcluster_sg 3-column output into lists of IDs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hcluster_sg parser</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ete_lineage_generator" title="from a list of species/taxids using the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ETE lineage generator</button></a>
@@ -1451,11 +1458,14 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=hcluster_sg" title="Hierarchically clustering on a sparse graph"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hcluster_sg</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=blast_parser" title="Convert 12- or 24-column BLAST output into 3-column hcluster_sg input"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BLAST parser</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nextalign" title="Viral genome sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NextAlign</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=nextclade" title="Viral genome clade assignment, mutation calling, and sequence quality checks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nextclade</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hyphy_conv" title="translate an in-frame codon alignment to proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-Conv</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hyphy_annotate" title="a newick tree with HyPhy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Annotate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hyphy_strike_ambigs" title="in a multiple alignment using HyPhy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace ambiguous codons</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hyphy_cfel" title="Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-CFEL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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>
 <a href="https://usegalaxy.eu/root?tool_id=picrust2_add_descriptions" title="column to a function abundance table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PICRUSt2 Add descriptions</button></a>
@@ -1466,8 +1476,10 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=picrust2_place_seqs" title="into reference tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PICRUSt2 Sequence placement</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=picrust2_shuffle_predictions" title="for a specified number of replicates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PICRUSt2 Generation of shuffled predictions</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.blast.relatedness.nuc" title="based on nucleotide blast results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Related Genomes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.blast.relatedness.prot" title="based on protein blast results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Related Genomes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=xmfa2tbl" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert XMFA to percent identity table</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hybpiper" title="Analyse targeted sequence capture data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HybPiper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pacu_map" title="Map ONT / Illumina reads to a reference genome for PACU"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PACU - mapping</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pacu_snp" title="whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PACU</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>
@@ -1485,32 +1497,22 @@ 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=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=infercnv" title="Infer Copy Number Variation from Single-Cell RNA-Seq Data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InferCNV</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snapatac2_preprocessing" title="and integration"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnapATAC2 Preprocessing</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snapatac2_clustering" title="and dimension reduction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnapATAC2 Clustering</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snapatac2_peaks_and_motif" title="analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnapATAC2 peaks and motif</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snapatac2_plotting" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnapATAC2 Plotting</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_normalize" title="and impute with scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Normalize</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_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=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=sceasy_convert" title="Convert between common single cell formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SCEasy Converter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=baredsc_1d" title="Compute distribution for a single gene"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">baredSC 1d</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=anndata_inspect" title="object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Inspect AnnData</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=anndata_export" title="Interconvert AnnData and Loom formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Export AnnData and loom files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_remove_confounders" title="with scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove confounders</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=baredsc_combine_2d" title="from baredSC"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Combine multiple 2D Models</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=baredsc_combine_1d" title="from baredSC"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Combine multiple 1D Models</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=anndata_import" title="from different format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Import Anndata and loom</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=anndata_manipulate" title="object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Manipulate AnnData</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=modify_loom" title="Add layers, or row/column attributes to a loom file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Manipulate loom object</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=anndata_import" title="from different formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Import Anndata</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=anndata_export" title="matrix and annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Export AnnData</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=modify_loom" title="Manipulate, export and import loom data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Loom operations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dropletutils" title="Utilities for handling droplet-based single-cell RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DropletUtils</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dropletutils_read_10x" title="into SingleCellExperiment object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DropletUtils Read10x</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dropletutils_empty_drops" title="Distinguish between droplets containing cells and ambient RNA in a droplet-based single-cell RNA sequencing experiment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DropletUtils emptyDrops</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=alevin" title="Quantification and analysis of 3-prime tagged-end single-cell sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Alevin</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=music_deconvolution" title="estimate cell type proportions in bulk RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MuSiC Deconvolution</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scanpy_filter" title="mark and subsample"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scanpy_inspect" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy Inspect and manipulate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scanpy_normalize" title="and impute"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy normalize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scanpy_plot" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy 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">Scanpy remove confounders</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="and infer trajectories"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy cluster, embed</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>
@@ -1519,13 +1521,12 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=scater_normalize" title="Compute normalised expression values for SCE"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: normalize SCE</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scater_filter" title="with user-defined parameters or PCA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: filter SCE</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scater_create_qcmetric_ready_sce" title="from single-cell expression matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: calculate QC metrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=baredsc_2d" title="Compute distribution for a pair of genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">baredSC 2d</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=velocyto_cli" title="pre-process data for the analysis of RNA velocity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">velocyto CLI</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=raceid_inspectclusters" title="examines gene expression within clusters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster Inspection using RaceID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=raceid_filtnormconf" title="performs filtering, normalisation, and confounder removal to generate a normalised and filtered count matrix of single-cell RNA data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Initial processing using RaceID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=raceid_clustering" title="performs clustering, outlier detection, dimensional reduction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clustering using RaceID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=raceid_trajectory" title="generates lineage from prior clustering"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Lineage computation using StemID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=raceid_inspecttrajectory" title="inspects branches of a lineage tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Lineage Branch Analysis using StemID</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=music_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_construct_eset" title="Create an ExpressionSet object from tabular and textual data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Construct Expression Set Object</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=music_inspect_eset" title="Inspect an ExpressionSet object by a variety of attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Inspect Expression Set Object</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=music_compare" title="estimate and compare cell type proportions in multiple sets of bulk RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MuSiC Compare</button></a>
@@ -1536,6 +1537,20 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=episcanpy_build_matrix" title="with EpiScanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build count matrix</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=episcanpy_preprocess" title="with EpiScanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scATAC-seq Preprocessing</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=episcanpy_cluster_embed" title="with EpiScanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster, embed and annotate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=velocyto_cli" title="pre-process data for the analysis of RNA velocity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">velocyto CLI</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=baredsc_1d" title="Compute distribution for a single gene"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">baredSC 1d</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=baredsc_2d" title="Compute distribution for a pair of genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">baredSC 2d</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=baredsc_combine_1d" title="from baredSC"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Combine multiple 1D Models</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=baredsc_combine_2d" title="from baredSC"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Combine multiple 2D Models</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sceasy_convert" title="Convert between common single cell formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SCEasy Converter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snapatac2_plotting" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnapATAC2 Plotting</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snapatac2_clustering" title="and dimension reduction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnapATAC2 Clustering</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snapatac2_preprocessing" title="and integration"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnapATAC2 Preprocessing</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snapatac2_peaks_and_motif" title="analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnapATAC2 peaks and motif</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=infercnv" title="Infer Copy Number Variation from Single-Cell RNA-Seq Data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InferCNV</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cosg" title="Cell marker gene identification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">COSG</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spapros_selection" title="of marker genes with spapros"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Selection</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spapros_evaluation" title="of marker genes with spapros"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Evaluation</button></a>
 <h3>Spatial Omics</h3>
 <a href="https://usegalaxy.eu/root?tool_id=mesmer" title="with Mesmer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform segmentation of multiplexed tissue data</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=basic_illumination" title="ImageJ BaSiC shading correction for use with Ashlar"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BaSiC Illumination</button></a>
@@ -1546,43 +1561,43 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=quantification" title="a module for single-cell data extraction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MCQUANT</button></a>
 <hr/><h2>Genomics Toolkits</h2>
 <h3>Picard</h3>
-<a href="https://usegalaxy.eu/root?tool_id=picard_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_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_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_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_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_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_CollectBaseDistributionByCycle" title="charts the nucleotide distribution per cycle in a SAM or BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectBaseDistributionByCycle</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_CollectGcBiasMetrics" title="charts the GC bias metrics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectGcBiasMetrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_CollectHsMetrics" title="compute metrics about datasets generated through hybrid-selection (e.g. exome)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectHsMetrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_CollectInsertSizeMetrics" title="plots distribution of insert sizes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectInsertSizeMetrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_CollectRnaSeqMetrics" title="collect metrics about the alignment of RNA to various functional classes of loci in the genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectRnaSeqMetrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_artifact_metrics" title="Collect metrics to quantify single-base sequencing artifacts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Picard Collect Sequencing Artifact Metrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_CollectWgsMetrics" title="compute metrics for evaluating of whole genome sequencing experiments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectWgsMetrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_DownsampleSam" title="Downsample a file to retain a subset of the reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Downsample SAM/BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_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_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_FilterSamReads" title="include or exclude aligned and unaligned reads and read lists"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FilterSamReads</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_FixMateInformation" title="ensure that all mate-pair information is in sync between each read and it's mate pair"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FixMateInformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_MarkDuplicates" title="examine aligned records in BAM datasets to locate duplicate molecules"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MarkDuplicates</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_MarkDuplicatesWithMateCigar" title="examine aligned records in BAM datasets to locate duplicate molecules"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MarkDuplicatesWithMateCigar</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_MeanQualityByCycle" title="chart distribution of base qualities"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MeanQualityByCycle</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=picard_MergeBamAlignment" title="merge alignment data with additional info stored in an unmapped BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MergeBamAlignment</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_MergeSamFiles" title="merges multiple SAM/BAM datasets into one"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MergeSamFiles</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_NormalizeFasta" title="normalize fasta datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NormalizeFasta</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_QualityScoreDistribution" title="chart quality score distribution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QualityScoreDistribution</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_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_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_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_RevertOriginalBaseQualitiesAndAddMateCigar" title="revert the original base qualities and add the mate cigar tag"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RevertOriginalBaseQualitiesAndAddMateCigar</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_RevertSam" title="revert SAM/BAM datasets to a previous state"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RevertSam</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_SamToFastq" title="extract reads and qualities from SAM/BAM dataset and convert to fastq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SamToFastq</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_SortSam" title="sort SAM/BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SortSam</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=picard_ValidateSamFile" title="assess validity of SAM/BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ValidateSamFile</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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_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_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=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=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=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=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>
+<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>
 <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_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>
@@ -1734,7 +1749,6 @@ layout: default
 <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=blastxml_to_tabular" title="Convert BLAST XML output to tabular"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BLAST XML to tabular</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=get_species_taxids" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI get species taxids</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_blastdbcmd_info" title="Show BLAST database information from blastdbcmd"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI BLAST+ database info</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_blastdbcmd_wrapper" title="Extract sequence(s) from BLAST database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI BLAST+ blastdbcmd entry(s)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_blastn_wrapper" title="Search nucleotide database with nucleotide query sequence(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI BLAST+ blastn</button></a>
@@ -1752,45 +1766,45 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=bg_diamond_view" title="generate formatted output from DAA files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diamond view</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bg_diamond" title="alignment tool for short sequences against a protein database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diamond</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bg_diamond_makedb" title="Build database from a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diamond makedb</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=magicblast" title="against a whole genome or transcriptome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Magic-BLAST: map large RNA or DNA sequences</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=blast_reciprocal_best_hits" title="from two FASTA files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BLAST Reciprocal Best Hits (RBH)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=blastxml_to_top_descr" title="Make a table from BLAST output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BLAST top hit descriptions</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bbtools_callvariants" title="in aligned Bam files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: call variants</button></a>
+<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=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>
 <h3>HiCExplorer</h3>
 <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_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_hicnormalize" title="normalizes a matrix to norm range or smallest read count"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicNormalize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicsummatrices" title="combine Hi-C matrices of the same size"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicSumMatrices</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_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_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_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_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_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_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_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_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_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_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_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_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_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_hictransform" title="transform a matrix to obs/exp, pearson and covariance matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicTransform</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hictadclassifier" title="TAD detection based on ML models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicTADClassifier</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_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_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_hichyperoptDetectLoops" title="optimizes parameters for hicDetectLoops"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicHyperoptDetectLoops</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicdetectloops" title="searches for enriched regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicDetectLoops</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hiccorrelate" title="compute pairwise correlations between multiple Hi-C contact matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicCorrelate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hiccompartmentspolarization" title="compute pairwise correlations between multiple Hi-C contact matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicCompartmentalization</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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_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_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_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_hicsummatrices" title="combine Hi-C matrices of the same size"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicSumMatrices</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicconvertformat" title="Convert between different file formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicConvertFormat</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_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_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_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_hicfindrestrictionsites" title="identify restriction enzyme sites"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicFindRestSite</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicinfo" title="get information about the content of a Hi-C matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicInfo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_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_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>
@@ -1808,12 +1822,13 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=schicexplorer_schicclustercompartments" title="clusters single-cell Hi-C interaction matrices with A/B compartments dimension reduction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scHicClusterCompartments</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=schicexplorer_schiccluster" title="clusters single-cell Hi-C interaction matrices on the raw data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scHicCluster</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=schicexplorer_schicadjustmatrix" title="clusters single-cell Hi-C interaction matrices on the raw data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scHicAdjustMatrix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_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_chicexportdata" title="exports data of hdf to txt based files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicExportData</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicdifferentialtad" title="searches for differential TADs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicDifferentialTAD</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicinterintratad" title="computes the ratio of inter TAD-scores vs. intra TADs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicInterIntraTAD</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicmergedomains" title="Merges TAD domains"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicMergeDomains</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hictadclassifier" title="TAD detection based on ML models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicTADClassifier</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hictraintadclassifier" title="train a TAD detection ML model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicTrainTADClassifier</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicplottads" title="plot Hi-C contact matrices heatmaps alongside other data tracks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPlotTADs</button></a>
 <h3>RAD-seq</h3>
 <a href="https://usegalaxy.eu/root?tool_id=BayeScan" title="Detecting natural selection from population-based genetic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BayeScan</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=stacks_assembleperead" title="run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks: assemble read pairs by locus</button></a>
@@ -1876,41 +1891,16 @@ 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=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=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=cami_amber_add" title="Create gold standard file for CAMI AMBER"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CAMI AMBER add length column</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cami_amber_convert" title="Create binning file(s) for CAMI AMBER"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CAMI AMBER convert to biobox</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=cami_amber" title="Evaluation package for MAGs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CAMI AMBER</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tiara" title="Deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tiara</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=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_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=metawrapmg_binning" title="metagenome binning pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaWRAP</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bigscape" title="Construct sequence similarity networks of BGCs and group them into GCF"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BiG-SCAPE</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=phyloseq_plot_ordination" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq: plot ordination</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_otu_network" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 OTU network plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_frequency" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 frequency plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kraken_taxonomy_report" title="view report of classification for multiple samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken taxonomic report</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=recentrifuge" title="Robust comparative analysis and contamination removal for metagenomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Recentrifuge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=das_tool" title="for genome-resolved metagenomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DAS Tool</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_core" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 core community analysis</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=extract_metaphlan_database" title="from the MetaPhlAn database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract the marker sequences and metadata</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=lotus2" title="fast OTU processing pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LotuS2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=maxbin2" title="clusters metagenomic contigs into bins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaxBin2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=polypolish" title="Short-read polishing of long-read bacterial genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Polypolish</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_alpha_diversity" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 alpha diversity</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=taxonomy_krona_chart" title="from taxonomic profile"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krona pie chart</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kraken-filter" title="filter classification by confidence score"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken-filter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kraken-translate" title="convert taxonomy IDs to names"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken-translate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=semibin_generate_cannot_links" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Contig annotations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kleborate" title="screen genome assemblies of Klebsiella pneumoniae"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kleborate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phyloseq_add_rank_names" title="Add taxonomy rank names to a phyloseq object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add Rank Names to Phyloseq Object</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=decontam" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Decontam</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_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_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_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=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>
@@ -1920,6 +1910,7 @@ layout: default
 <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=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=last_al" title="finds local alignments between query sequences, and reference sequences."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LASTal</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=drep_dereplicate" title="De-replicate a list of genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dRep dereplicate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=drep_compare" title="compare a list of genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dRep compare</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=last_db" title="prepares sequences for subsequent comparison and alignment using lastal."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LASTdb</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=last_split" title="finds 'split alignments' (typically for DNA) or 'spliced alignments' (typically for RNA)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LAST-split</button></a>
@@ -1931,7 +1922,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=sixgill_filter" title="a metapeptide database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sixgill filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sixgill_build" title="a metapeptide database from metagenome fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sixgill build</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sixgill_makefasta" title="from a metapeptide database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sixgill makefasta</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=srst2" title="Short Read Sequence Typing for Bacterial Pathogens"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SRST2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cat_bins" title="annotate with taxonomic classification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CAT bins</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cat_contigs" title="annotate with taxonomic classification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CAT contigs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=khmer_filter_abundance" title="by minimal k-mer abundance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">khmer: Filter reads</button></a>
@@ -1944,9 +1934,11 @@ layout: default
 <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=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=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>
@@ -1965,73 +1957,47 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=bio_hansel" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Salmonella Subtyping</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nonpareil" title="to estimate average coverage and generate Nonpareil curves"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nonpareil</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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=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=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=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=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=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=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_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=metabat2" title="metagenome binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaBAT2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_boxplot" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 boxplot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_export_fasta" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 export fasta</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_heatmap" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 heatmap</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_load" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 load</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_merge_ampvis2" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 merge ampvis2 data sets</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_mergereplicates" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 merge replicates</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_octave" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 octave plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_ordinate" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 ordination plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_rankabundance" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 rank abundance plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_rarecurve" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 rarefaction curve</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_setmetadata" title="types"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 set metadata</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_subset_samples" title="by sample metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 subset samples</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_subset_taxa" title="by taxonomy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 subset data</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_timeseries" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 timeseries plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_venn" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 venn diagram</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqsero2" title="Salmonella serotype prediction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqSero2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=est_abundance" title="to re-estimate abundance at a taxonomic level from kraken output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bracken</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=coverm_contig" title="Calculate read coverage per contig"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CoverM contig</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=coverm_genome" title="Calculate coverage of individual genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CoverM genome</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Fasta_to_Contig2Bin" title="to scaffolds-to-bin table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Converts genome bins in fasta format</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=phyloseq_from_dada2" title="from dada2 sequence and taxonomy tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create phyloseq object</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=phyloseq_from_biom" title="from a BIOM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create phyloseq object</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=virannot_blast2tsv" title="convert XML blast results to tabular file with taxonomic informations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virAnnot Blast2tsv</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=virannot_otu" title="create viral OTUs based on RPS and Blast annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virAnnot OTU</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=virAnnot_rps2tsv" title="Convert xml rpstblast results to tab file with taxonomic informations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virAnnot Rps2tsv</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sirius_csifingerid" title="is used to identify metabolites using single and        tandem mass spectrometry"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SIRIUS-CSI:FingerID</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gtdbtk_classify_wf" title="by placement in GTDB reference tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GTDB-Tk Classify genomes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qiime2__dada2__denoise_ccs" title="Denoise and dereplicate single-end Pacbio CCS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 dada2 denoise-ccs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=taxpasta" title="standardise taxonomic profiles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">taxpasta</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=genomad_end_to_end" title="identify virus and plasmid genomes from nucleotide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">geNomad</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=krakentools_combine_kreports" title="into a combined report file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krakentools: Combine multiple Kraken reports</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mg_toolkit_original_metadata" title="Download original metadata for a study"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Metagenomics toolkit Original Metadata</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mg_toolkit_bulk_download" title="Download result files in bulks for an entire study"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Metagenomics toolkit Bulk Download</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=phyloseq_plot_richness" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq: plot alpha diverstiy measure</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=metabat2_jgi_summarize_bam_contig_depths" title="for MetaBAT2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate contig depths</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=semibin" title="for Semi-supervised Metagenomic Binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=semibin_bin" title="into bins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Group the contigs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=semibin_concatenate_fasta" title="for multi-sample binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Concatenate fasta files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=semibin_generate_sequence_features" title="(kmer and abundance) as training data for semi-supervised deep learning model training"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Generate sequence features</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=semibin_train" title="the semi-supervised deep learning model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Train</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=instrain_profile" title="Creates an inStrain profile (microdiversity analysis) from a mapping file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InStrain Profile</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=instrain_compare" title="Compares multiple inStrain profiles (popANI, coverage_overlap, etc.)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InStrain Compare</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cami_amber_add" title="Create gold standard file for CAMI AMBER"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CAMI AMBER add length column</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=metabuli_classify" title="metagenomic sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metabuli classify</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cami_amber_convert" title="Create binning file(s) for CAMI AMBER"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CAMI AMBER convert to biobox</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=coverm_contig" title="Calculate read coverage per contig"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CoverM contig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=coverm_genome" title="Calculate coverage of individual genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CoverM genome</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=est_abundance" title="to re-estimate abundance at a taxonomic level from kraken output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bracken</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=maaslin2" title="Microbiome Multivariable Association with Linear Models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaAsLin 2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=malt_run" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MALT analyzer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=megan_sam2rma" title="from a DIAMOND or MALT sam file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAN: Generate a MEGAN rma6 file</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=megan_blast2rma" title="from BLAST output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAN: Generate RMA files</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=megan_blast2lca" title="to produce a taxonomic classification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAN Blast2LCA: apply LCA alignment</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=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=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_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_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=concoct" title="for metagenome binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CONCOCT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=concoct_coverage_table" title="for CONCOCT"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CONCOCT: Generate the input coverage table</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=concoct_cut_up_fasta" title="in non-overlapping or overlapping parts of equal length"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CONCOCT: Cut up contigs</button></a>
@@ -2042,6 +2008,9 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=megan_daa_meganizer" title="for use with MEGAN"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAN: meganize a DIAMOND file</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=megan_read_extractor" title="by classification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAN: Extract reads</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=itsx" title="identifies ITS sequences and extracts the ITS region"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ITSx</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=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=aldex2" title="differential abundance analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ALDEx2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ancombc" title="differential abundance analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ANCOM-BC</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=checkm_taxonomy_wf" title="Analyze all genome bins with the same marker set"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM taxonomy_wf</button></a>
@@ -2054,8 +2023,36 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=checkm_taxon_set" title="Generate taxonomic-specific marker set"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM taxon_set</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=checkm_plot" title="for assessing the quality of genome bins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=checkm_lineage_set" title="Infer lineage-specific marker sets for each bin"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM lineage_set</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=kraken_biom" title="Create BIOM-format tables from kraken output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken-biom</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vapor" title="Classify Influenza samples from short reads sequence data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VAPOR</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kleborate" title="screen genome assemblies of Klebsiella pneumoniae"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kleborate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=polypolish" title="Short-read polishing of long-read bacterial genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Polypolish</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=semibin_generate_cannot_links" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Contig annotations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=semibin" title="for Semi-supervised Metagenomic Binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=semibin_train" title="the semi-supervised deep learning model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Train</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=semibin_generate_sequence_features" title="(kmer and abundance) as training data for semi-supervised deep learning model training"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Generate sequence features</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=semibin_bin" title="into bins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Group the contigs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=semibin_concatenate_fasta" title="for multi-sample binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Concatenate fasta files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_alpha_diversity" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 alpha diversity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_boxplot" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 boxplot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_core" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 core community analysis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_export_fasta" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 export fasta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_frequency" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 frequency plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_heatmap" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 heatmap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_load" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 load</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_merge_ampvis2" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 merge ampvis2 data sets</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_mergereplicates" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 merge replicates</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_octave" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 octave plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_ordinate" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 ordination plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_otu_network" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 OTU network plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_rankabundance" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 rank abundance plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_rarecurve" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 rarefaction curve</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_setmetadata" title="types"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 set metadata</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_subset_samples" title="by sample metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 subset samples</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_subset_taxa" title="by taxonomy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 subset data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_timeseries" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 timeseries plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_venn" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 venn diagram</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dram_strainer" title="down to genes of interest"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DRAM strain annotations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dram_distill" title="metagenome-assembled-genomes (MAGs)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DRAM distill</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dram_annotate" title="metagenome-assembled-genomes (MAGs)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DRAM annotate</button></a>
@@ -2065,9 +2062,37 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=krakentools_beta_diversity" title="from Kraken, Krona and Bracken files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krakentools: calculates beta diversity (Bray-Curtis dissimilarity)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=krakentools_alpha_diversity" title="from the Bracken abundance estimation file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krakentools: Calculates alpha diversity</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=krakentools_kreport2mpa" title="to MetaPhlAn-style"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krakentools: Convert kraken report file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=krakentools_combine_kreports" title="into a combined report file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krakentools: Combine multiple Kraken reports</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=krakentools_extract_kraken_reads" title="Extract reads that were classified by the Kraken family at specified taxonomic IDs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krakentools: Extract Kraken Reads By ID</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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_primerCheck" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: primer check</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phyloseq_plot_bar" title="Generate bar charts from a phyloseq object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq: Bar Chart</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phyloseq_from_biom" title="from a BIOM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create phyloseq object</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=combine_metaphlan_humann" title="to relate genus/species abundances and gene families/pathways abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Combine MetaPhlAn and HUMAnN outputs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mapseq" title="sequence read classification designed to assign taxonomy and OTU classifications"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAPseq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqsero2" title="Salmonella serotype prediction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqSero2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bigscape" title="Construct sequence similarity networks of BGCs and group them into GCF"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BiG-SCAPE</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=virannot_blast2tsv" title="convert XML blast results to tabular file with taxonomic informations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virAnnot Blast2tsv</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=virannot_otu" title="create viral OTUs based on RPS and Blast annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virAnnot OTU</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=virAnnot_rps2tsv" title="Convert xml rpstblast results to tab file with taxonomic informations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virAnnot Rps2tsv</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sirius_csifingerid" title="is used to identify metabolites using single and        tandem mass spectrometry"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SIRIUS-CSI:FingerID</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=metawrapmg_binning" title="metagenome binning pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaWRAP</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gtdbtk_classify_wf" title="by placement in GTDB reference tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GTDB-Tk Classify genomes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__dada2__denoise_ccs" title="Denoise and dereplicate single-end Pacbio CCS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 dada2 denoise-ccs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cami_amber" title="Evaluation package for MAGs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CAMI AMBER</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=taxpasta" title="standardise taxonomic profiles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">taxpasta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=genomad_end_to_end" title="identify virus and plasmid genomes from nucleotide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">geNomad</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mg_toolkit_original_metadata" title="Download original metadata for a study"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Metagenomics toolkit Original Metadata</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mg_toolkit_bulk_download" title="Download result files in bulks for an entire study"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Metagenomics toolkit Bulk Download</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=name2taxid" title="Convert taxon names to NCBI Taxids"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Name2taxid</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gtdb_to_taxdump" title="Map taxonomic classifications between the NCBI and GTDB taxonomies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI-GTDB map</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biobox_add_taxid" title="Add taxid output from BAT or GTDB to biobox binning data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Biobox add taxid</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mereg_mOTUs_tables" title="Merge mOTUs aboundance or count 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=motus_profiler" title="performs taxonomic profiling of metagenomics and metatrancriptomics samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mOTUs_profiler</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tiara" title="Deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tiara</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vibrant" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VIBRANT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=virsorter" title="identify DNA and RNA virus"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VirSorter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=profile2cami" title="Convert metagenomic profile table to CAMI format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Profile2CAMI</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>
@@ -2244,105 +2269,59 @@ layout: default
 <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>
 <a href="https://usegalaxy.eu/root?tool_id=obi_clean" title="tags a set of sequences for PCR/sequencing errors identification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">obiclean</button></a>
-<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_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_illumina_pairend" title="Construct consensus reads from Illumina pair-end reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Illuminapairedend</button></a>
-<h3>Data and Metadata Management</h3>
-<a href="https://usegalaxy.eu/root?tool_id=raster_template" title="attributes for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates for raster files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=eal_table_template" title="attributes and categorical variables for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates for data tables</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=eal_templates" title="for core features of a data package for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=makeeml" title="Create EML from EAL templates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make EML</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=eml2eal" title="Create EAL templates from EML metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EML to EAL</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=geo_cov_template" title="for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make geographic coverage template</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=taxo_cov_template" title="for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make taxonomic coverage template</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vector_template" title="attributes for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates for vector files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=entities_template" title="for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make entities templates for raster, vector and other entities files</button></a>
-<h3>Virology</h3>
-<a href="https://usegalaxy.eu/root?tool_id=cooc_mutbamscan" title="scans an alignment file for mutation co-occurrences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cojac: mutbamscan</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=varvamp" title="design primers for highly diverse viruses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">varVAMP</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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=lineagespot" title="identifies SARS-CoV-2 lineages contributing to metagenomic samples from per-sample variant files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">lineagespot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snipit" title="Summarise snps relative to a reference sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snipit</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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=read_it_and_keep" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Read It and Keep</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=freyja_variants" title="and get sequencing depth information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Freyja: Call variants</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=freyja_demix" title="lineage abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Freyja: Demix</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=freyja_boot" title="method"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Freyja: Bootstrapping</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=freyja_aggregate_plot" title="demixed results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Freyja: Aggregate and visualize</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cooc_pubmut" title="pretty-prints cojac mutbamscan co-occurrence results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cojac: pubmut</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cooc_tabmut" title="exports co-occurrence results from mutbamscan as a table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cojac: tabmut</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=virheat" title="from VCFs as a heatmap and map mutations to respective genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VirHEAT: visualize allele frequencies</button></a>
-<hr/><h2>Proteomics, Metabolomics, Chemistry</h2>
-<h3>Proteomics</h3>
-<a href="https://usegalaxy.eu/root?tool_id=qupath_roi_splitter" title="Split ROI coordinates of QuPath TMA annotation by cell type (classification)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QuPath ROI Splitter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=OpenMSInfo" title="Prints configurations details of OpenMS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenMSInfo</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fragpipe" title="Data analysis for mass spectrometry-based proteomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FragPipe -  Academic Research and Education User License (Non-Commercial)</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_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=SageAdapter" title="Annotates MS/MS spectra using Sage"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SageAdapter</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=OpenSwathAnalyzer" title="Picks peaks and finds features in an SWATH-MS or SRM experiment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathAnalyzer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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=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=ClusterMassTraces" title="Creates pseudo spectra"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ClusterMassTraces</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=QualityControl" title="Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QualityControl</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=FeatureFinderMetaboIdent" title="Detects features in MS1 data based on metabolite identifications"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureFinderMetaboIdent</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=GNPSExport" title="Tool to export representative consensus MS/MS scan per consensusElement into a .MGF file format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GNPSExport</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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=CometAdapter" title="Annotates MS/MS spectra using Comet"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CometAdapter</button></a>
-<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=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=FeatureLinkerUnlabeledKD" title="Groups corresponding features from multiple maps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureLinkerUnlabeledKD</button></a>
-<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=IDRTCalibration" title="Can be used to calibrate RTs of peptide hits linearly to standards"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDRTCalibration</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=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=IDSplitter" title="Splits protein/peptide identifications off of annotated data files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDSplitter</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=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=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=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=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=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=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=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=XMLValidator" title="Validates XML files against an XSD schema"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">XMLValidator</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=OpenSwathConfidenceScoring" title="Compute confidence scores for OpenSwath results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathConfidenceScoring</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=PeakPickerIterative" title="Finds mass spectrometric peaks in profile mass spectra"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PeakPickerIterative</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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=RNPxlXICFilter" title="Remove MS2 spectra from treatment based on the fold change between control and treatment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNPxlXICFilter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=MassTraceExtractor" title="Detects mass traces in centroided LC-MS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MassTraceExtractor</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ERPairFinder" title="Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ERPairFinder</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=FileMerger" title="Merges several MS files into one file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FileMerger</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=FeatureFinderMRM" title="Detects two-dimensional features in LC-MS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureFinderMRM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ConsensusID" title="Computes a consensus of peptide identifications of several identification engines"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ConsensusID</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=SpectraFilterMarkerMower" title="Applies thresholdfilter to peak spectra"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpectraFilterMarkerMower</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=BaselineFilter" title="Removes the baseline from profile spectra using a top-hat filter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BaselineFilter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=TextExporter" title="Exports various XML formats to a text file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TextExporter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=proteinortho_summary" title="summaries the orthology-pairs/RBH files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteinortho summary</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=proteinortho_grab_proteins" title="finds genes/proteins in a given fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteinortho grab proteins</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=proteinortho" title="detects orthologous proteins/genes within different species"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteinortho</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=diann" title="is a software for DIA/SWATH data processing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DIA-NN</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pepquery2_show_sets" title="PepQueryDB datasets, Parameters, PTMs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PepQuery2 Show Sets</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pepquery2" title="Peptide-centric search engine for novel peptide identification and validation."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PepQuery2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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_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_illumina_pairend" title="Construct consensus reads from Illumina pair-end reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Illuminapairedend</button></a>
+<h3>Data and Metadata Management</h3>
+<a href="https://usegalaxy.eu/root?tool_id=makeeml" title="Create EML from EAL templates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make EML</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eml2eal" title="Create EAL templates from EML metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EML to EAL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eal_templates" title="for core features of a data package for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eal_table_template" title="attributes and categorical variables for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates for data tables</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=geo_cov_template" title="for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make geographic coverage template</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=taxo_cov_template" title="for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make taxonomic coverage template</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=raster_template" title="attributes for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates for raster files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vector_template" title="attributes for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates for vector files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=entities_template" title="for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make entities templates for raster, vector and other entities files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=annotations_template" title="from scratch or from EML metadata file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make annotations template</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eml_validate" title="check if your EML file is valid"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Eml validate:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=data_paper_from_EML" title="from EML"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make data paper sketches</button></a>
+<h3>Virology</h3>
+<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=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=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=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=freyja_variants" title="and get sequencing depth information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Freyja: Call variants</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=freyja_demix" title="lineage abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Freyja: Demix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=freyja_boot" title="method"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Freyja: Bootstrapping</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=freyja_aggregate_plot" title="demixed results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Freyja: Aggregate and visualize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cooc_mutbamscan" title="scans an alignment file for mutation co-occurrences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cojac: mutbamscan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cooc_pubmut" title="pretty-prints cojac mutbamscan co-occurrence results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cojac: pubmut</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cooc_tabmut" title="exports co-occurrence results from mutbamscan as a table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cojac: tabmut</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lineagespot" title="identifies SARS-CoV-2 lineages contributing to metagenomic samples from per-sample variant files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">lineagespot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=varvamp" title="design primers for highly diverse viruses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">varVAMP</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=virheat" title="from VCFs as a heatmap and map mutations to respective genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VirHEAT: visualize allele frequencies</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=irma" title="Construct robust assemblies of highly variable RNA viruses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IRMA</button></a>
+<hr/><h2>Proteomics, Metabolomics, Chemistry</h2>
+<h3>Proteomics</h3>
+<a href="https://usegalaxy.eu/root?tool_id=fragpipe" title="Data analysis for mass spectrometry-based proteomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FragPipe -  Academic Research and Education User License (Non-Commercial)</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=metaquantome_viz" title="taxonomic analysis, functional analysis, and function-taxonomy analysis results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaQuantome: visualize</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metaquantome_stat" title="differential analysis of functional expression and taxonomic abundance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaQuantome: stat</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metaquantome_filter" title="for quality, redundancy, and sample coverage"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaQuantome: filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metaquantome_expand" title="a set of functional or taxonomy annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaQuantome: expand</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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=eggnog_mapper" title="functional sequence annotation by orthology"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eggNOG Mapper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cardinal_combine" title="combine several mass spectrometry imaging datasets into one"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI combine</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=PSMFeatureExtractor" title="Computes extra features for each input PSM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PSMFeatureExtractor</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=meta_proteome_analyzer" title="functional and taxonomic characterization of proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaProteomeAnalyzer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metaquantome_sample" title="by specifying the experiment's groups and associated column names"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaQuantome: create samples file</button></a>
@@ -2360,6 +2339,10 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=cardinal_mz_images" title="mass spectrometry imaging m/z heatmaps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI mz images</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cardinal_preprocessing" title="mass spectrometry imaging preprocessing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI preprocessing</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=PeakPickerHiRes" title="Finds mass spectrometric peaks in profile mass spectra"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PeakPickerHiRes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=RNAMassCalculator" title="Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAMassCalculator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=QualityControl" title="Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QualityControl</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=RNPxlXICFilter" title="Remove MS2 spectra from treatment based on the fold change between control and treatment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNPxlXICFilter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=OpenSwathConfidenceScoring" title="Compute confidence scores for OpenSwath results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathConfidenceScoring</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MultiplexResolver" title="Completes peptide multiplets and resolves conflicts within them"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MultiplexResolver</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=psmvalidator" title="Validate PSMs against Ion Fragmentation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PSM-Fragment Validator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_remove_protonation_state" title="of every atom"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove protonation state</button></a>
@@ -2374,46 +2357,66 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=QCMerger" title="Merges two qcml files together"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCMerger</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=IDMapper" title="Assigns protein/peptide identifications to features or consensus features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDMapper</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=IDMassAccuracy" title="Calculates a distribution of the mass error from given mass spectra and IDs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDMassAccuracy</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=IDRTCalibration" title="Can be used to calibrate RTs of peptide hits linearly to standards"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDRTCalibration</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=IDSplitter" title="Splits protein/peptide identifications off of annotated data files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDSplitter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MRMTransitionGroupPicker" title="Picks peaks in SRM/MRM chromatograms"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MRMTransitionGroupPicker</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MapAlignerIdentification" title="Corrects retention time distortions between maps based on common peptide identifications"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MapAlignerIdentification</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=IsobaricAnalyzer" title="Calculates isobaric quantitative values for peptides"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IsobaricAnalyzer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ERPairFinder" title="Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ERPairFinder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ClusterMassTraces" title="Creates pseudo spectra"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ClusterMassTraces</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ClusterMassTracesByPrecursor" title="Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ClusterMassTracesByPrecursor</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CometAdapter" title="Annotates MS/MS spectra using Comet"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CometAdapter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CompNovo" 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">CompNovo</button></a>
 <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=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=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=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=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=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=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=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=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=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 identification run and annotated file origin"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDRipper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=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=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=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=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=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=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=PrecursorIonSelector" title="PrecursorIonSelector"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PrecursorIonSelector</button></a>
@@ -2429,8 +2432,11 @@ layout: default
 <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=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=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>
@@ -2438,25 +2444,35 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=FeatureFinderIdentification" title="Detects features in MS1 data based on peptide identifications"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureFinderIdentification</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FeatureFinderIsotopeWavelet" title="Detects two-dimensional features in LC-MS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureFinderIsotopeWavelet</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FeatureFinderMetabo" title="Assembles metabolite features from centroided (LC-)MS data using the mass trace approach"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureFinderMetabo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=FeatureFinderMetaboIdent" title="Detects features in MS1 data based on metabolite identifications"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureFinderMetaboIdent</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=FeatureFinderMRM" title="Detects two-dimensional features in LC-MS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureFinderMRM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FeatureFinderMultiplex" title="Determination of peak ratios in LC-MS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureFinderMultiplex</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FeatureLinkerUnlabeled" title="Groups corresponding features from multiple maps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureLinkerUnlabeled</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=FeatureLinkerUnlabeledKD" title="Groups corresponding features from multiple maps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureLinkerUnlabeledKD</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FeatureLinkerUnlabeledQT" title="Groups corresponding features from multiple maps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureLinkerUnlabeledQT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FFEval" title="Evaluation tool for feature detection algorithms."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FFEval</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FidoAdapter" title="Runs the protein inference engine Fido."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FidoAdapter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FileFilter" title="Extracts or manipulates portions of data from peak, feature or consensus-feature files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FileFilter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FileInfo" title="Shows basic information about the file, such as data ranges and file type"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FileInfo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=FileMerger" title="Merges several MS files into one file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FileMerger</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=GNPSExport" title="Tool to export representative consensus MS/MS scan per consensusElement into a .MGF file format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GNPSExport</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=AccurateMassSearch" title="Match MS signals to molecules from a database by mass"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AccurateMassSearch</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=DatabaseFilter" title="Filters a protein database (FASTA format) based on identified proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DatabaseFilter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=DeMeanderize" title="Orders the spectra of MALDI spotting plates correctly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeMeanderize</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=FeatureFinderSuperHirn" title="Finds mass spectrometric features in mass spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FeatureFinderSuperHirn</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cardinal_classification" title="spatial classification of mass spectrometry imaging data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI classification</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=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>
@@ -2472,6 +2488,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=encyclopedia_walnut" title="PeCAn-based Peptide Detection Directly from Data-Independent Acquisition (DIA) MS/MS Data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Walnut</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=encyclopedia_prosit_csv_to_library" title="Convert Prosit/Spectronaut CSV to EncyclopeDIA DLIB library"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ConvertPrositCSVToLibrary</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=OpenSwathChromatogramExtractor" title="Extract chromatograms (XIC) from a MS2 map file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathChromatogramExtractor</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=OpenSwathAnalyzer" title="Picks peaks and finds features in an SWATH-MS or SRM experiment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathAnalyzer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=encyclopedia_searchtolib" title="Build a Chromatogram Library from Data-Independent Acquisition (DIA) MS/MS Data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SearchToLib</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=OpenSwathFileSplitter" title="Splits SWATH files into n files, each containing one window"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenSwathFileSplitter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=encyclopedia_library_to_blib" title="Convert EncyclopeDIA Library to BLIB for Skyline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ConvertLibraryToBlib</button></a>
@@ -2479,21 +2496,17 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=PhosphoScoring" title="Scores potential phosphorylation sites in order to localize the most probable sites"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PhosphoScoring</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=HighResPrecursorMassCorrector" title="Corrects the precursor mass and charge determined by the instrument software"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HighResPrecursorMassCorrector</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=PrecursorMassCorrector" title="Corrects the precursor entries of MS/MS spectra, by using MS1 information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PrecursorMassCorrector</button></a>
+<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=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=LowMemPeakPickerHiRes" title="Finds mass spectrometric peaks in profile mass spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LowMemPeakPickerHiRes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=LowMemPeakPickerHiResRandomAccess" title="Finds mass spectrometric peaks in profile mass spectra."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LowMemPeakPickerHiResRandomAccess</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=maxquant_mqpar" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaxQuant (using mqpar.xml)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pepquery2_index" title="MS/MS data for faster search"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PepQuery2 index</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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=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=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=JSONExporter" title="Exports .oms (SQLite) files in JSON format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JSONExporter</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>
@@ -2512,6 +2525,9 @@ 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>
@@ -2545,6 +2561,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=TopPerc" title="Facilitate input to Percolator and reintegrate."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TopPerc</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=eden_protease_prediction" title="based on cleavage sites"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Protease prediction</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=decoyfasta" title="Creates a decoy search database by adding reverse    sequences to an existing database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create Decoy Database (reverse)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=morpheus" title="database search algorithm for high-resolution tandem mass spectra"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Morpheus</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fasta_cli" title="Appends decoy sequences to FASTA files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastaCLI</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ident_params" title="Sets the identification parameters to be used in SearchGUI and PeptideShaker apps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Identification Parameters</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=diffacto" title="Comparative Protein Abundance from Covariation of Peptide Abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diffacto</button></a>
@@ -2553,6 +2570,7 @@ 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=proteomiqon_psmstatistics" title="utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProteomIQon PSMStatistics</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=proteomiqon_proteininference" title="uses identified peptides to infere proteins explaining their presence in the sample."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProteomIQon ProteinInference</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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_psmbasedquantification" title="allows label-free quantification as well as quantification of full metabolic labeled samples."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteomiqon PSMBasedQuantification</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=proteomiqon_joinquantpepionswithproteins" title="combines the results from ProteinInference and PSMBasedQuantification."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteomiqon JoinQuantPepIonsWithProteins</button></a>
@@ -2560,46 +2578,27 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=proteomiqon_labelfreeproteinquantification" title="estimates protein abundances using quantified peptide ions."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteomiqon LabelFreeProteinQuantification</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=feature_alignment" title="integrates information from all available runs via a graph-based alignment strategy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRIC</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=proteomics_search_tandem_1" title="Run an X!Tandem Search"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">X!Tandem MSMS Search</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cardinal_single_ion_segmentation" title="mass spectrometry imaging spatial DGMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI single ion segmentation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cardinal_colocalization" title="mass spectrometry imaging colocalization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI colocalization</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metanovo" title="Produce targeted databases for mass spectrometry analysis."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaNovo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=prot_scriber" title="Protein annotation of short human readable descriptions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">prot-scriber</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=syndiva" title="diversity analysis of synthetic libraries of a Fibronectin domain"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">syndiva</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=proteomics_search_tandem_2" title="Run an X!Tandem Search - test"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">X!Tandem MSMS Search</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mqppep_preproc" title="Prep phosphoproteomic MaxQuant output for statistical anlaysis."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaxQuant Phosphopeptide Preprocessing</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mqppep_anova" title="Runs ANOVA and KSEA for phosphopeptides."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaxQuant Phosphopeptide ANOVA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qupath_roi_splitter" title="Split ROI coordinates of QuPath TMA annotation by cell type (classification)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QuPath ROI Splitter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pepquery2" title="Peptide-centric search engine for novel peptide identification and validation."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PepQuery2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pepquery2_show_sets" title="PepQueryDB datasets, Parameters, PTMs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PepQuery2 Show Sets</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pepquery2_index" title="MS/MS data for faster search"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PepQuery2 index</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=calisp" title="Estimate isotopic composition of peptides from proteomics mass spectrometry data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">calisp</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=diann" title="is a software for DIA/SWATH data processing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DIA-NN</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=eggnog_mapper_annotate" title="annotation phase"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eggNOG Mapper</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=eggnog_mapper_search" title="search phase"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eggNOG Mapper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=SageAdapter" title="Annotates MS/MS spectra using Sage"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SageAdapter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=OpenMSInfo" title="Prints configurations details of OpenMS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenMSInfo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=JSONExporter" title="Exports .oms (SQLite) files in JSON format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JSONExporter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ZeissLMDconverter" title="Converts tabular coordinates into a formatted text file readable by Zeiss laser-capture microdissection systems."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Zeiss laser-capture microdissection converter</button></a>
 <h3>Metabolomics</h3>
-<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_compute_template" title="compute retention time correction template feature table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - compute template</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_remove_noise" title="filter noise and detect peaks in high resolution mass spectrometry (HRMS) profile data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - remove noise</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_compute_clusters" title="compute clusters of mz and rt across samples and assign cluster IDs to individual features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - compute clusters</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_recover_weaker_signals" title="recover weaker signals from raw data using an aligned feature table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - recover weaker signals</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=matchms_split" title="split a large library into subsets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms split library</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=waveica" title="removal of batch effects for untargeted metabolomics data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WaveICA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dimet_timecourse_analysis" title="Differential analysis of tracer metabolomics data comparing consecutive time-points (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet timecourse analysis</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=matchms_remove_spectra" title="Filters spectra based on metadata presence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms remove spectra</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=matchms_subsetting" title="Extract spectra from a library given unique metadata identifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms subsetting</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=matchms_formatter" title="reformat scores object of matchms to long format table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms scores formatter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=matchms_fingerprint_similarity" title="calculate similarity between molecular fingerprints calculated from structural spectrum metadata descriptors"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms fingerprint similarity</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=msmetaenhancer" title="annotate MS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSMetaEnhancer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=matchms_add_key" title="Set metadata key in MSP to static value"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms add key</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dimet_pca_analysis" title="Principal Component Analysis for tracer metabolomics data, producing tables (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet pca analysis</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dimet_metabologram" title="Integration of transcriptomics and (tracer) metabolomics differential data (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet metabologram</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dimet_differential_analysis" title="Differential analysis of tracer metabolomics data comparing two groups (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet differential analysis</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=matchms_metadata_match" title="matchms metadata match calculation for numeric fields based on tolerance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms metadata match</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dimet_bivariate_analysis" title="Computation of the correlation of MDV profiles, or the metabolite time course profiles (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet bivariate analysis</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dimet_pca_plot" title="Figures of Principal Component Analysis for tracer metabolomics (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet pca plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dimet_enrichment_plot" title="Figures of mean enrichment by metabolite, as line-plots (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet enrichment plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dimet_abundance_plot" title="Figures of metabolites total abundance as barplots (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet abundance plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=matchms_metadata_export" title="extract all metadata from mass spectra file to tabular format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms metadata export</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=recetox_msfinder" title="Annotation of fragment peaks in mass spectral libraries."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RECETOX MsFinder</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=matchms_filtering" title="filter and normalize mass spectrometry data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms filtering</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=matchms_metadata_merge" title="Merge metadata csv into MSP by a specified column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms metadata merge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Transformation" title="Transforms the dataMatrix intensity values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Transformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=abims_anova" title="N-way anova. With ou Without interactions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Anova</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Multivariate" title="PCA, PLS and OPLS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Multivariate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biosigner" title="Molecular signature discovery from omics data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Biosigner</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Univariate" title="Univariate statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Univariate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mzmine_batch" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MZMine batch</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimspy_align_samples" title="- Align peaks across Peaklists"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align Samples</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimspy_replicate_filter" title="- Remove peaks that fail to appear in at least x-out-of-n (technical) replicates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replicate Filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimspy_process_scans" title="- Read, filter and average MS scans"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Process Scans (and SIM-Stitch)</button></a>
@@ -2622,7 +2621,7 @@ layout: default
 <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=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=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>
 <a href="https://usegalaxy.eu/root?tool_id=xcms_export_samplemetadata" title="which need to be filled with extra information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xcms get a sampleMetadata file</button></a>
@@ -2633,7 +2632,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=mixmodel" title="ANOVA for repeated measures statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mixmodel</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=asca" title="Splitting of the total variance into independent blocks according to the experimental factors and multivariate analysis (SCA) of each block"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ASCA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=corrtable" title="Correlation table between two tables and graphic representation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Between-table Correlation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=wsdl_hmdb" title="search by masses on HMDB online LCMS bank"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HMDB MS search</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=wsdl_hmdb" title="search by masses on HMDB v5 online LCMS bank"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HMDB MS search</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bank_inhouse" title="search by accurate mass (and by Retention time) on a local bank"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bank_inhouse</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lcmsmatching" title="Annotation of LCMS peaks using matching on a in-house spectra database or on PeakForest spectra database."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LCMS matching</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=golm_ws_lib_search" title=": GC-MS Mass Spectral Database."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Golm Metabolome Database search spectrum</button></a>
@@ -2651,8 +2650,10 @@ layout: default
 <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=abims_anova" title="N-way anova. With ou Without interactions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Anova</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Multivariate" title="PCA, PLS and OPLS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Multivariate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biosigner" title="Molecular signature discovery from omics data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Biosigner</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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=ramclustr_define_experiment" title="Definition of experimental design used for record keeping and writing spectra data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RAMClustR define experiment</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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>
@@ -2661,41 +2662,87 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=Batch_correction" title="Corrects intensities for signal drift and batch-effects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Batch_correction</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=massbank_ws_searchspectrum" title=": Search by pseudo-spectra on a High Quality Mass Spectral Database."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MassBank spectrum searches</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=Univariate" title="Univariate statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Univariate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=abims_CAMERA_combinexsAnnos" title="Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CAMERA.combinexsAnnos</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=profia" title="Preprocessing of FIA-HRMS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">proFIA</button></a>
 <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=xcms_plot_raw" title="Plot raw data filtered by m/z range and retention time (RT) range"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xcms plot raw</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xcms_plot_eic" title="Plot the extracted ion chromatogram (EIC) from mzML file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xcms plot eic</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=abims_xcms_refine" title="Remove or merge chromatographic peaks based on specific criteria."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xcms refineChromPeaks (refine)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=isoplot" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Isoplot: Generate plots from isocor output</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_generate_feature_table" title="generate feature table from noise-removed HRMS profile data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - generate feature table</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_recover_weaker_signals" title="recover weaker signals from raw data using an aligned feature table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - recover weaker signals</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_correct_time" title="correct retention time across samples for peak alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - correct time</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_compute_clusters" title="compute clusters of mz and rt across samples and assign cluster IDs to individual features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - compute clusters</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_remove_noise" title="filter noise and detect peaks in high resolution mass spectrometry (HRMS) profile data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - remove noise</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_merge_known_table" title="join knowledge from aligned features and known table."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - merge known table</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_compute_template" title="compute retention time correction template feature table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - compute template</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_align_features" title="align peaks across samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - align features</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rmassbank" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RMassBank</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biotransformer" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BioTransformer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=msmetaenhancer" title="annotate MS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSMetaEnhancer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=riassigner" title="compute retention indices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RIAssigner</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ramclustr" title="A feature clustering algorithm for non-targeted mass spectrometric metabolomics data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RAMClustR</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ramclustr_define_experiment" title="Definition of experimental design used for record keeping and writing spectra data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RAMClustR define experiment</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_xmsannotator_advanced" title="annotate peak intensity table including scores and confidence levels"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-xMSannotator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=matchms_convert" title="convert between mass spectral library formats (.mgf/.msp/.json) using matchms"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms convert</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_filtering" title="filter and normalize mass spectrometry data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms filtering</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_fingerprint_similarity" title="calculate similarity between molecular fingerprints calculated from structural spectrum metadata descriptors"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms fingerprint similarity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_formatter" title="reformat scores object of matchms to long format table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms scores formatter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_metadata_export" title="extract all metadata from mass spectra file to tabular format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms metadata export</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_metadata_match" title="matchms metadata match calculation for numeric fields based on tolerance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms metadata match</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=matchms_networking" title="create similarity network graph from matchms similarity scores"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms networking</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_similarity" title="calculate the similarity score and matched peaks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms similarity</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=matchms_spectral_similarity" title="matchms spectral similarity calculation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms spectral similarity</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=matchms_remove_key" title="Remove metadata entry for all spectra in a library"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms remove key</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_split" title="split a large library into subsets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms split library</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=waveica" title="removal of batch effects for untargeted metabolomics data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WaveICA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dimet_abundance_plot" title="Figures of metabolites total abundance as barplots (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet abundance plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dimet_differential_analysis" title="Differential analysis of tracer metabolomics data comparing two groups (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet differential analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimet_differential_multigroup_analysis" title="Differential analysis of 3 or more chosen groups of tracer metabolomics data (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet differential multigroup analysis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dimet_enrichment_plot" title="Figures of mean enrichment by metabolite, as line-plots (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet enrichment plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimet_isotopologues_plot" title="Figures of isotopologues proportions by metabolite, as stacked barplots (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet isotopologues plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=riassigner" title="compute retention indices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RIAssigner</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dimet_metabologram" title="Integration of transcriptomics and (tracer) metabolomics differential data (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet metabologram</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dimet_pca_analysis" title="Principal Component Analysis for tracer metabolomics data, producing tables (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet pca analysis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dimet_pca_plot" title="Figures of Principal Component Analysis for tracer metabolomics (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet pca plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dimet_timecourse_analysis" title="Differential analysis of tracer metabolomics data comparing consecutive time-points (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet timecourse analysis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mzmine_batch" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MZMine batch</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_subsetting" title="Extract spectra from a library given unique metadata identifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms subsetting</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_metadata_merge" title="Merge metadata csv into MSP by a specified column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms metadata merge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_add_key" title="Set metadata key in MSP to static value"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms add key</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_remove_key" title="Remove metadata entry for all spectra in a library"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms remove key</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=recetox_msfinder" title="Annotation of fragment peaks in mass spectral libraries."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RECETOX MsFinder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dimet_bivariate_analysis" title="Computation of the correlation of MDV profiles, or the metabolite time course profiles (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet bivariate analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=use_theoretical_mz_annotations" title="Overwrite experimentally measured mz values for peaks with theoretical values from peak comments."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">use theoretical m/z values</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=riassigner_from_comment" title="Assign different retention indices from unstructured comment metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RIAssigner init from comment</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tracegroomer" title="TraceGroomer is a solution to format and normalize files for DIMet tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tracegroomer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sirius_csifingerid" title="is used to identify metabolites using single and        tandem mass spectrometry"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SIRIUS-CSI:FingerID</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ramclustr" title="A feature clustering algorithm for non-targeted mass spectrometric metabolomics data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RAMClustR</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=isolib" title="create an isotopic pattern library for given compounds and adducts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">isolib</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=isolib" title="create an isotopic pattern library for given compounds and adducts based on enviPat"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">isolib</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gc_derivatization" title="In silico MeOX and TMS derivatization tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GC derivatization</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_correct_time" title="correct retention time across samples for peak alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - correct time</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_generate_feature_table" title="generate feature table from noise-removed HRMS profile data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - generate feature table</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_merge_known_table" title="join knowledge from aligned features and known table."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - merge known table</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_remove_spectra" title="Filters spectra based on metadata presence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms remove spectra</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=skyline2isocor" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Skyline2Isocor: converting skyling outputs into IsoCor inputs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_align_features" title="align peaks across samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - align features</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=abims_xcms_refine" title="Remove or merge chromatographic peaks based on specific criteria."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xcms refineChromPeaks (refine)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=isoplot" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Isoplot: Generate plots from isocor output</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rmassbank" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RMassBank</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biotransformer" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BioTransformer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=recetox_xmsannotator_advanced" title="annotate peak intensity table including scores and confidence levels"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-xMSannotator</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=matchms_similarity" title="calculate the similarity score and matched peaks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms similarity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rename_annotated_feature" title="Rename columns in abundance table based on annotations table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Rename Annotated Feature</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spec2vec_similarity" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">spec2vec similarity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spec2vec_training" title="Train a Spec2Vec model for mass spectra similarity scoring"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">spec2vec model training</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfassignr_snplot" title="Noise level assessment using the SNplot function."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFAssignR SNplot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfassignr_histnoise" title="Noise level assessment using the HistNoise"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFAssignR HistNoise</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfassignr_kmdnoise" title="Noise level assessment using the KMDNoise."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFAssignR KMDNoise</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfassignr_isofiltr" title="Separates likely isotopic masses from monoisotopic masses in a mass list"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFAssignR IsoFiltR</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfassignr_mfassign" title="Molecular formula assignment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFAssignR MFAssign</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfassignr_mfassignCHO" title="Molecular formula assignment (only with CHO)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFAssignR MFAssignCHO</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfassignr_recal" title="Internal mass recalibration using a recalibrant series."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFAssignR Recal</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfassignr_recallist" title="Identification of candidate series for recalibration."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFAssignR RecalList</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rcx-tk" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rcx-tk</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfassignr_findRecalSeries" title="Selects most suitable series for recalibration"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFAssignR FindRecalSeries</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ms2deepscore_config_generator" title="Generates model parameters for MS2DeepScore in JSON format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MS2DeepScore Configuration Generator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ms2deepscore_similarity" title="Compute similarity scores using a pre-trained MS2DeepScore model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MS2DeepScore Similarity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ms2deepscore_training" title="Compute similarity scores using a pre-trained MS2DeepScore model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MS2DeepScore Model Training</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=target_screen" title="Extract peaks from recetox-aplcms tables using a list of target ions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MS target screening</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mixmodel4repeated_measures" title="ANOVA for repeated measures statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mixmodel</button></a>
 <h3>ChemicalToolBox</h3>
-<a href="https://usegalaxy.eu/root?tool_id=xtb_molecular_optimization" title="Semiempirical quantum mechanical molecular optimization method"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xtb molecular optimization</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biopdb_align_and_rmsd" title="using Biopython"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align structures and compute relative RMSDs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qcxms_neutral_run" title="required as first step to prepare for the production runs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCxMS neutral run</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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>
@@ -2711,7 +2758,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=gmx_sim" title="for system equilibration or data collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS simulation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gmx_em" title="of the system prior to equilibration and production MD"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS energy minimization</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gmx_setup" title="of topology and GRO structure file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS initial setup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=OpenPepXL" title="Tool for protein-protein cross-linking identification using labeled linkers."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenPepXL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_subsearch" title="of fingerprint data sets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Substructure Search</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=biomd_rmsd_clustering" title="from MD RMSD matrix data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hierarchical clustering</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=biomd_extract_clusters" title="from linkage matrix data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract clusters of MD trajectories</button></a>
@@ -2728,6 +2774,7 @@ 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>
@@ -2779,12 +2826,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=ctb_im_xcos" title="scoring"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">XCos</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=featurestein" title="feature overlay scoring"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">'FeatureStein' fragment overlay scoring</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gmx_merge_topology_files" title="and GRO files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge GROMACS topologies</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rem_complex" title="Remove molecular coordination complexes from a list of structure representations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove coordination complexes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qcxms_production_run" title="Production run to obtain a QCxMS simulated mass spectrum"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCxMS production run</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qcxms_getres" title="Get result of the Production run to obtain a QCxMS simulated mass spectrum"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCxMS get results</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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=qiskit_xyz2pdb" title="alpha carbon PDB files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Qiskit's XYZ files to</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pulchra" title="from reduced representations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PULCHRA recontruction of all atom proteins</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>
@@ -2831,6 +2872,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=gmx_rg" title="of a molecular structure"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS Radius of Gyration</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=acpype_Amber2Gromacs" title="using acpype"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Amber topology and coordinate files to GROMACS format</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tleap" title="interactively build and run tLEaP files to set up systems with AmberTools"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build tLEaP</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=alphafold" title="- AI-guided 3D structural prediction of proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Alphafold 2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gromacs_modify_topology" title="to a GROMACS topology file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Adding New Topology Information</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gromacs_extract_topology" title="from a GROMACS topology file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extracting Topology Information</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gmx_get_builtin_file" title="from built-in datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS copy file</button></a>
@@ -2838,6 +2880,14 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=gmx_check" title="to provide information about GROMACS input files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS check</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gmx_rmsd" title="of molecular structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS RMSD calculation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gmx_rmsf" title="of molecular structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS RMSF calculation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xtb_molecular_optimization" title="Semiempirical quantum mechanical molecular optimization method"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xtb molecular optimization</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rem_complex" title="Remove molecular coordination complexes from a list of structure representations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove coordination complexes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qcxms_neutral_run" title="required as first step to prepare for the production runs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCxMS neutral run</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qcxms_production_run" title="Production run to obtain a QCxMS simulated mass spectrum"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCxMS production run</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qcxms_getres" title="Get result of the Production run to obtain a QCxMS simulated mass spectrum"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCxMS get results</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiskit_xyz2pdb" title="alpha carbon PDB files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Qiskit's XYZ files to</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pulchra" title="from reduced representations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PULCHRA recontruction of all atom proteins</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biopdb_align_and_rmsd" title="using Biopython"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align structures and compute relative RMSDs</button></a>
 <hr/><h2>Statistics and Visualisation</h2>
 <h3>Statistics</h3>
 <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>
@@ -2849,10 +2899,10 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=BestSubsetsRegression1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform Best-subsets Regression</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pca1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Principal Component Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=kpca1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kernel Principal Component Analysis</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scipy_sparse" title="for manipulating 2-D Scipy sparse numeric data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sparse Matrix Functions</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=kcca1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kernel Canonical Correlation Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cca1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Canonical Correlation Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=t_test_two_samples" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">T Test for Two Samples</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scipy_sparse" title="for manipulating 2-D Scipy sparse numeric data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sparse Matrix Functions</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=create_tool_recommendation_model" title="using deep learning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a model to recommend tools</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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>
@@ -2866,24 +2916,19 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=seq_composition" title="Count bases or amino-acids"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sequence composition</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rgcca" title="performs multiblock data analysis of several sets of variables (blocks) observed on the same group of individuals."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RGCCA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bg_statistical_hypothesis_testing" title="computes several descriptive statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Statistical hypothesis testing</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=clustering_from_distmat" title="using Scipy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Distance matrix-based hierarchical clustering</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=deepmicro" title="Representation learning and classification framework"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeepMicro</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biomodels_biomd0000001066" title="to predict efficacy of immune checkpoint blockade across multiple cancer patient cohorts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Random Forest model</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biomodels_biomd0000001076" title="proteins involved in cancer immunotherapy using molecular descriptors and Multi Layer Perceptron (MLP) neural network"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prediction of Breast Cancer (BC)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mcl" title="Markov Cluster Algorithm for graphs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MCL</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_train_test_split" title="into training and test subsets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split Dataset</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_train_test_eval" title="fit a model using part of dataset and evaluate using the rest"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Train, Test and Evaluation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_pca" title="with scikit-learn"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Principal component analysis</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_fitted_model_eval" title="using a new batch of labeled data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Evaluate a Fitted Model</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=model_prediction" title="predicts on new data using a preffited model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Model Prediction</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ml_visualization_ex" title="includes several types of plotting for machine learning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Machine Learning Visualization Extension</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_lightgbm" title="- train and apply LightGBM models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LightGBM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_numeric_clustering" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Numeric Clustering</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_stacking_ensemble_models" title="builds stacking, voting ensemble models with numerous base options"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacking Ensembles</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=keras_train_and_eval" title="conduct deep training and evaluation either implicitly or explicitly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Deep learning training and evaluation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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_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_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=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_sample_generator" title="random samples with controlled size and complexity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_estimator_attributes" title="get important attributes from an estimator or scikit object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Estimator attributes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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>
@@ -2898,24 +2943,29 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_discriminant_classifier" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Discriminant Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_generalized_linear" title="for classification and regression"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generalized linear models</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_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_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_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_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=keras_batch_models" title="with online data generator for Genomic/Protein sequences and images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build Deep learning Batch Training Models</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=keras_model_builder" title="with an optimizer, loss function and fit parameters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create deep learning model</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=keras_model_config" title="using Keras"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a deep learning model architecture</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scipy_sparse" title="for manipulating 2-D Scipy sparse numeric data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sparse Matrix Functions</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=create_tool_recommendation_model" title="using deep learning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a model to recommend tools</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sklearn_label_encoder" title="Encode target labels with value between 0 and n_classes-1"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Label encoder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=black_forest_labs_flux" title="text-to-image model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FLUX</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_to_categorical" title="Converts a class vector (integers) to binary class matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">To categorical</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=colorize_labels" title="with NetworkX"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Colorize label map</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=whisper" title="Transcribe audio or video files to text using the OpenAI Whisper"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Speech to Text</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=virhunter" title="Deep learning method to identify viruses in sequencing datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virhunter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=decontaminator" title="Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">decontaminator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deepmicro" title="Representation learning and classification framework"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeepMicro</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sklearn_label_encoder" title="Encode target labels with value between 0 and n_classes-1"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Label encoder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=colorize_labels" title="with NetworkX"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Colorize label map</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biomodels_biomd0000001076" title="proteins involved in cancer immunotherapy using molecular descriptors and Multi Layer Perceptron (MLP) neural network"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prediction of Breast Cancer (BC)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biomodels_biomd0000001066" title="to predict efficacy of immune checkpoint blockade across multiple cancer patient cohorts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Random Forest model</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=whisper" title="Transcribe audio or video files to text using the OpenAI Whisper"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Speech to Text</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=flexynesis" title="A deep-learning based multi-omics bulk sequencing data integration suite"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flexynesis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chatgpt_openai_api" title="Integrating OpenAI's ChatGPT into Galaxy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chatGPT</button></a>
 <h3>Graph/Display Data</h3>
-<a href="https://usegalaxy.eu/root?tool_id=jbrowse2" title="genome browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JBrowse2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=volcanoplot" title="create a volcano plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Volcano Plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=plotly_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=ggplot2_heatmap2" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">heatmap2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pretext_snapshot" title="image generator for Pretext contact maps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pretext Snapshot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=wordcloud" title="with highly customizable appearance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate a word cloud</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=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>
@@ -2939,14 +2989,18 @@ layout: default
 <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=intervene_pairwise" title="and heatmap for genomic intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairwise intersection</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pathview" title="for pathway based data integration and visualization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pathview</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=jbrowse2" title="genome browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JBrowse2</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>
@@ -2959,6 +3013,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=mummerplot_wrapper" title="Combine mummer/nucmer/promer with mummerplot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MUMmer dotplot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=karyotype_Plot_1" title="for multiple series"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Karyotype Plotting tool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pe_histogram" title="of insert size frequency"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Paired-end histogram</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=circos" title="visualizes data in a circular layout"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=barchart_gnuplot" title="for multiple columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bar chart</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pathifier" title=": Quantify deregulation of pathways in cancer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pathifier</button></a>
@@ -2976,10 +3031,11 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=pm_uep_opt" title="run UEP optimisation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyMuonSuite AIRSS UEP Optimise</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pm_muairss_read" title="run clustering for optimised structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyMuonSuite AIRSS Cluster</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=muspinsim_combine" title="combine datafiles generated from MuSpinSim"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MuSpinSim Combine</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mudirac" title="Muonic atom Dirac equation solver"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MuDirac</button></a>
 <hr/><h2>Miscellaneous Tools</h2>
 <h3>Evolution</h3>
-<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=mutate_snp_codon_1" title="with SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Mutate Codons</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=iqtree" title="Phylogenomic / evolutionary tree construction from multiple sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IQ-TREE</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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>
@@ -2989,6 +3045,7 @@ layout: default
 <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=revoluzer_crex" title="reconstruct pairwise gene order rearrangement"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CREx</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=revoluzer_distmat" title="for gene orders"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute distance matrix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=quicktree" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Quicktree</button></a>
 <h3>Motif Tools</h3>
 <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>
@@ -3000,6 +3057,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=chipeakanno_annopeaks" title="annotate peaks by annoGR object in the given range"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChIPpeakAnno annoPeaks</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=clusterprofiler_bitr" title="converting ID types"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster Profiler Bitr</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=clusterprofiler_go" title="run GO Analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster Profiler GO</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=netcdf2zarr" title="Rewrite a netCDF to Zarr"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF to Zarr</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_zeppelin_notebook" title="Zeppelin Notebook"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">zeppelin</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=concatenate_icenet_data" title="for concatenating yearly sea ice concentration netcdf files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate Icenet Data</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=icenet_forecast" title="for forecasting sea ice concentration with IceNet"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Icenet Forecast</button></a>
@@ -3026,11 +3084,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=sequence_convert" title="for various sequence formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sequence converter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=translate_nucleotides" title="to amino acids"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Translate nucleotides</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rnalfoldz" title="calculates locally stable secondary structures of RNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNALfoldz</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=netcdf2zarr" title="Rewrite a netCDF to Zarr"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF to Zarr</button></a>
 <h3>GIS Data Handling</h3>
-<a href="https://usegalaxy.eu/root?tool_id=zoo_project_ogc_api_processes" title="executes remote OTB processes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Zoo Project OGC API Processes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=otb_mean_shift_smoothing" title="smooths an image using the MeanShift algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OTB.MeanShiftSmoothing</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=interpolation_run_idw_interpolation" title="based on Inverse Distance Weighting (IDW)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run interpolation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=xarray_metadata_info" title="summarize content of a Netcdf file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Metadata Info</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=xarray_select" title="extracts variable values with custom conditions on dimensions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Selection</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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>
@@ -3041,11 +3095,16 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=gdal_gdalinfo" title="lists information about a raster dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL Informations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gdal_gdalbuildvrt" title="builds a VRT from a list of datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL Build VRT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gdal_gdaladdo" title="builds or rebuilds overview images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL addo</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=otb_band_math" title="outputs a monoband image as a result of a mathematical operation on several multi-band images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OTB.BandMath</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hirondelle_crim" title="executes remote processes."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hirondelle CRIM OGC API Processes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=xarray_netcdf2netcdf" title="manipulate xarray from netCDF and save back to netCDF"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray operations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=xarray_mapplot" title="Visualize netCDF variables on a geographical map"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray map plotting</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=xarray_coords_info" title="Get values for each coordinate of a Netcdf file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Coordinate Info</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interpolation_run_idw_interpolation" title="based on Inverse Distance Weighting (IDW)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run interpolation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=otb_band_math" title="outputs a monoband image as a result of a mathematical operation on several multi-band images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OTB.BandMath</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=otb_mean_shift_smoothing" title="smooths an image using the MeanShift algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OTB.MeanShiftSmoothing</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=terrabyte_ogc_api_processes" title="Water quality EO Application Package"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Terrabyte OGC API Processes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=zoo_project_ogc_api_processes" title="executes remote OTB processes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Zoo Project OGC API Processes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hirondelle_crim" title="executes remote processes."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hirondelle CRIM OGC API Processes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=aquainfra_ogc_api_processes" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AquaINFRA OGC API Processes</button></a>
 <h3>Animal Detection on Acoustic Recordings</h3>
 <a href="https://usegalaxy.eu/root?tool_id=spocc_occ" title="from GBIF, ALA, iNAT and others"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get species occurrences data</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vigiechiro_bilanenrichipf" title="from Animal Detection on Acoustic Recordings"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Advanced restitution: 'Point fixe' protocol</button></a>
@@ -3109,22 +3168,24 @@ 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=c3s" title="for retrieving climate data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Climate Data Store</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=harmonize_insitu_to_netcdf" title="and aggregator of insitu marine physical and biogeochemical data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCV harmonizer</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=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 retrieving climate data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Climate Data Store</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cesm" title="Community Earth System Model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CESM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cads" title="for retrieving data from the Atmosphere Monitoring Service"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Atmosphere Data Store</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=eodie" title="converts simple features data between file formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EODIE</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cdo_operations" title="Climate Data Manipulation Operators operations for standard processing of climate and NWP model output."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CDO Operations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cdo_info" title="Climate Data Information Operators to get information on Climate and NWP model data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CDO get info</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=timeseries_extraction" title="Extract and plot time series"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF timeseries Extractor</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=landcover_subindicator" title="subindicator to track land changes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Land cover degradation</button></a>
 <h3>Apollo</h3>
-<a href="https://usegalaxy.eu/root?tool_id=create_account" title="with Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Register Account</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=list_organism" title="in Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">List Organisms</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=iframe" title="opens an IFrame to Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Annotate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fetch_jbrowse" title="for an organism, from Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Retrieve JBrowse</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=feat_from_gff3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF3 to Apollo Annotations</button></a>
@@ -3133,32 +3194,6 @@ layout: default
 <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=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=bioimage_inference" title="with PyTorch"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Process image using a BioImage.IO model</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=background_removal" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove image background</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=plantseg" title="with PlantSeg"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform segmentation in densely packed 3-D volumetric images</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scimap_anndata_to_csv" title="with Scimap"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Anndata to CSV</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_imageinfo" title="with Bioformats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Show image info</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_points_to_binaryimage" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert point coordinates to binary image</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=squidpy_spatial" title="with Squidpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Analyze and visualize spatial multi-omics data</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gate_finder" title="with Vitessce"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform gating</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cellpose" title="with Cellpose"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run generalist cell and nucleus segmentation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=label_to_binary" title="with NumPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert label map to binary image</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=orientationpy" title="with OrientationPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute image orientation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bia_download" title="Download images from Bioimage Archive"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FTP Link for Bioimage Archive</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_binary_to_labelimage" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to label map</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_curve_fitting" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform curve fitting</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_image_registration" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform affine image registration (intensity-based)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_landmark_registration" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform affine image registration (landmark-based)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_segmetrics" title="with SegMetrics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute image segmentation and object detection performance measures</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_color_deconvolution" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform color decomposition</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_overlay_images" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Overlay images</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spyboat" title="with SpyBOAT"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform wavelet transformation on 3D-image stack</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rfove" title="with RFOVE"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform segmentation using region-based fitting of overlapping ellipses</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=idr_download_by_ids" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Download IDR/OMERO</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_visceral_evaluatesegmentation" title="with EvaluateSegmentation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Evaluate segmentation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_2d_feature_extraction" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract image features</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_scale_image" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scale image</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_binary_to_edm" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to EDM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cp_cellprofiler" title="with CellProfiler 3"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run CellProfiler pipeline</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cp_common" title="Load images and metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Starting Modules</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cp_color_to_gray" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ColorToGray</button></a>
@@ -3182,7 +3217,11 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=cp_relate_objects" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RelateObjects</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cp_save_images" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SaveImages</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cp_image_math" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ImageMath</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_landmark_registration" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform affine image registration (landmark-based)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_projective_transformation_points" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Performs projective transformation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_image_registration" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform affine image registration (intensity-based)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spyboat" title="with SpyBOAT"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform wavelet transformation on 3D-image stack</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_binary_to_edm" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to EDM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=imagej2_skeletonize3d" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Skeletonize</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=imagej2_find_edges" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Find edges</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=imagej2_shadows" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add shadow effect</button></a>
@@ -3192,63 +3231,85 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_raw_transform" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Apply raw transformation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=imagej2_math" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Operate on pixels</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_elastic_transform" title="with ImageJ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Apply elastic transformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cp_cellprofiler4" title="with CellProfiler 4"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run CellProfiler pipeline</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compare_elastic_raw" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare elastic and raw deformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compose_raw_elastic" title="into a raw transformation with bUnwarpJ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compose a raw and an elastic transformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_analyze_particles_binary" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Analyze particles</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_create_image" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create new image</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_noise" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add or remove noise</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compose_raw" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compose two raw transformations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_align" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align two images</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_smooth" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Smooth image</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_analyze_skeleton" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Analyze skeleton</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compare_elastic" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare opposite elastic deformations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compare_raw" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare two raw deformations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_convert_to_raw" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert elastic transformation to raw</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_make_binary" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert to binary</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_sharpen" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sharpen</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compose_elastic" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compose two elastic transformations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=imagej2_adjust_threshold_binary" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Adjust threshold</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=idr_download_by_ids" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Download IDR/OMERO</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_wsi_extract_top_view" title="with OpenSlide"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract top view from whole-slide image</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_convert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Image Converter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_adapt_transform" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Adapt an elastic transformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_filter_standard" title="with scipy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter 2-D image</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_mahotas_features" title="with Mahotas"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute image features</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_adjust_threshold_binary" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Adjust threshold</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compose_elastic" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compose two elastic transformations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_sharpen" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sharpen</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_make_binary" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert to binary</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_convert_to_raw" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert elastic transformation to raw</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compare_raw" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare two raw deformations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compare_elastic" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare opposite elastic deformations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_analyze_skeleton" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Analyze skeleton</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_smooth" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Smooth image</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_align" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align two images</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compose_raw" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compose two raw transformations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_noise" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add or remove noise</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_create_image" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create new image</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_analyze_particles_binary" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Analyze particles</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compose_raw_elastic" title="into a raw transformation with bUnwarpJ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compose a raw and an elastic transformation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagej2_bunwarpj_compare_elastic_raw" title="with ImageJ2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare elastic and raw deformation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_imageinfo" title="with Bioformats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Show image info</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_detection_viz" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Visualize detections</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_threshold" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Threshold image</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_convertimage" title="with Bioformats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert image format</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_histogram_equalization" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform histogram equalization</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_superdsm" title="with SuperDSM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform segmentation using deformable shape models</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_convertimage" title="with Bioformats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert image format</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_2d_feature_extraction" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract image features</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_permutate_axis" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Permutate image axes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_labelimage_to_points" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert label map to points (center of masses)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_points_to_label" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert point coordinates to label map</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_concat_channels" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate images or channels</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_scale_image" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scale image</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_merge_neighbours_in_label" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge neighbors in label map</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_binary_to_labelimage" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to label map</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_2d_filter_segmentation_by_features" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter label map by rules</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_anisotropic_diffusion" title="with MedPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Apply anisotropic diffusion</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_projective_transformation" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Performs projective transformation with/without labels</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_spot_detection_2d" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform 2D spot detection</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_points_association_nn" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform linking in time series (nearest neighbors)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_filter_standard" title="with scipy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter 2-D image</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=imagecoordinates_flipaxis" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Switch axis coordinates</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_2d_filter_segmentation_by_features" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter label map by rules</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_coordinates_of_roi" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to points (point coordinates)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_count_objects" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Count objects in label map</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_color_deconvolution" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform color decomposition</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_mahotas_features" title="with Mahotas"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute image features</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_projective_transformation" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Performs projective transformation with/without labels</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_visceral_evaluatesegmentation" title="with EvaluateSegmentation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Evaluate segmentation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_binaryimage_to_points" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to points (center of masses)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_merge_neighbours_in_label" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge neighbors in label map</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_slice_image" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slice image into patches</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_split_labelmap" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split label map using morphological operators</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_concat_channels" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate images or channels</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_points_to_label" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert point coordinates to label map</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_labelimage_to_points" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert label map to points (center of masses)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_permutate_axis" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Permutate image axes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_count_objects" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Count objects in label map</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_coordinates_of_roi" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to points (point coordinates)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bf2raw" title="with Bioformats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert to OME-Zarr</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=woundhealing_scratch_assay" title="image analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Wound healing scratch assay</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=background_removal" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove image background</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_viz_overlay_moving_and_fixed_image" title="moving and fixed image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Overlay</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_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=plantseg" title="with PlantSeg"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform segmentation in densely packed 3-D volumetric images</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_curve_fitting" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform curve fitting</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_points_association_nn" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform linking in time series (nearest neighbors)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_spot_detection_2d" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform 2-D spot detection</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_overlay_images" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Overlay images</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cp_cellprofiler4" title="with CellProfiler 4"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run CellProfiler pipeline</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_segmetrics" title="with SegMetrics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute image segmentation and object detection performance measures</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gate_finder" title="with Vitessce"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform gating</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vitessce_spatial" title="with Vitessce"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run multi-modal single-cell visualization</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=squidpy_spatial" title="with Squidpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Analyze and visualize spatial multi-omics data</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rename_tiff_channels" title="with ome-types"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Rename OME-TIFF channels</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cell_intensity_processing" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Process single-cell intensities</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_superdsm" title="with SuperDSM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform segmentation using deformable shape models</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rfove" title="with RFOVE"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform segmentation using region-based fitting of overlapping ellipses</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bia_download" title="Download images from Bioimage Archive"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FTP Link for Bioimage Archive</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=woundhealing_scratch_assay" title="image analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Wound healing scratch assay</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cellpose" title="with Cellpose"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run generalist cell and nucleus segmentation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bf2raw" title="with Bioformats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert to OME-Zarr</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=voronoi_tessellation" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute Voronoi tessellation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=morphological_operations" title="with SciPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Apply a morphological operation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=colorize_labels" title="with NetworkX"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Colorize label map</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=image_math" title="with NumPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Process images using arithmetic expressions</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=orientationpy" title="with OrientationPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute image orientation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=label_to_binary" title="with NumPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert label map to binary image</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=colorize_labels" title="with NetworkX"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Colorize label map</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=repeat_channels" title="with NumPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert single-channel to multi-channel image</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=squidpy_scatter" title="with Squidpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create spatial scatterplot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=squidpy_spatial" title="with Squidpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Analyze and visualize spatial multi-omics data</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_detection_viz" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Visualize detections</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_wsi_extract_top_view" title="with OpenSlide"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract top view from whole-slide image</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_convert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Image Converter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_localthreshold" title="applies a local threshold algorithm to an image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Local Threshold</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_2d_split_binaryimage_by_watershed" title="Split binary image by using watershed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split objects</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scimap_anndata_to_csv" title="with Scimap"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Anndata to CSV</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bioimage_inference" title="with PyTorch"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Process image using a BioImage.IO model</button></a>
 <h3>Species abundance</h3>
 <a href="https://usegalaxy.eu/root?tool_id=pampa_glmsp" title="Compute a GLM of your choice on population data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute GLM on population data</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pampa_glmcomm" title="Compute a GLM of your choice on community data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute GLM on community data</button></a>
@@ -3284,11 +3345,12 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=Map_shp" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make a map with a shapefile</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Mean_geom" title="- calcul of the geometric means for the 'bois mort' indicator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Geometric means</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bar_plot" title="for simple discrete data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bar plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=divand_full_analysis" title="Data-Interpolating Variational Analysis in n dimensions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DIVAnd</button></a>
 <h3>Astronomy</h3>
-<a href="https://usegalaxy.eu/root?tool_id=astronomical_archives" title="queries astronomical archives through Virtual Observatory protocols"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Astronomical Archives (IVOA)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=astropy_fits2bitmap" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">astropy fits2bitmap</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=astropy_fits2csv" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">astropy fits2csv</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=astropy_fitsinfo" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">astropy fitsinfo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=astronomical_archives" title="queries astronomical archives through Virtual Observatory protocols"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Astronomical Archives (IVOA)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sgwb_astro_tool" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SGWB</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hess_astro_tool" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HESS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cta_astro_tool" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CTA</button></a>
@@ -3299,20 +3361,24 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_tadviewer" title="interactive table viewer with SQL enginer for filtering"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tadviewer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_qgis" title="interactive geographic information system (GIS)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QGIS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_qupath" title="interactive Open Software for Bioimage Analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QuPath</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_pampa" title="Performance Indicators of Marine Protected Areas for the management of coastal ecosystems, resources and their uses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pampa</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_odv" title="interactive plotting tool for geo-referenced data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ODV</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_ilastik" title="interactive learning and segmentation toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Ilastik</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_metashrimps" title="Metadata Shiny for Retroactive Information Management and Production of data paper Sketches"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metashrimps</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_hdfview" title="Desktop application to display netcdf, hdf4 or hdf5 files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive Hdfview tool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_scoop3_argo" title="Interactive visual quality control of Argo netCDF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scoop3-Argo</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_divand" title="Data-Interpolating Variational Analysis in n dimensions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive DIVAnd Notebooks</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_rstudio_askor" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RStudio AskoR</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_blobtoolkit" title="genome assembly QC viewer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive BlobToolKit</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_pavian" title="Interactive analysis of metagenomics data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pavian</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_mgnify_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive MGnify Notebook</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_jupyter_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive JupyterLab Notebook</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_ml_jupyter_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GPU-enabled Interactive Jupyter Notebook for Machine Learning</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_climate_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive Climate Notebook</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_jupytergis_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive JupyterGIS Notebook</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_pangeo_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive Pangeo Notebook</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_pangeo_ml_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive Pangeo Machine Learning Notebook</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_cellpose" title="a generalist algorithm for cellular segmentation and restoration"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CellPose Interactive</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_rstudio" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RStudio</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_pyiron" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyIron Interactive Jupyter Notebook</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_higlass" title="an interactive Hi-C data visualizer."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HiGlass</button></a>
@@ -3333,6 +3399,8 @@ 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_ideal" title="Interactive Differential Expression AnaLysis in RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDEAL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_phyloseq" title="Explore microbiome profiles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_metashark" title="Metadata Shiny Automated Resource and Knowledge"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metashark</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_audiolabeler" title="Nature+Energy Audio Labeller audio data annotation tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NEAL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_genenotebook" title="viewer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GeneNoteBook</button></a>
@@ -3340,8 +3408,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook" title="sample notebooks to access and discover data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Data Space Ecosystem</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_qiskit_jupyter_notebook" title="interactive tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Qiskit Jupyter notebook</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_stac" title="for searching, aggregating and downloading data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">STAC catalog</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_ideal" title="Interactive Differential Expression AnaLysis in RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDEAL</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_phyloseq" title="Explore microbiome profiles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq</button></a>
 <h3>OBO Ontology manipulation</h3>
 <a href="https://usegalaxy.eu/root?tool_id=onto_tk_get_ancestor_terms" title="Collects the ancestor terms from a given term in the given OBO ontology"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get the ancestor terms of a given OBO term</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=onto_tk_get_relationship_types" title="from the given OBO ontology"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get all the relationship types</button></a>
@@ -3409,14 +3475,11 @@ layout: default
 <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=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=length_and_gc_content" title="from GTF and FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gene length and GC content</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=parse_mito_blast" title="overlap-conscious coverage calculation between scaffold-accession number pairs from blast output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Parse mitochondrial blast</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=orfipy" title="a versatile ORF finder"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ORFipy</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=b2btools_single_sequence" title="from their amino-acid sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">b2bTools: Biophysical predictors for single sequences</button></a>
 <h3>QIIME 2</h3>
-<a href="https://usegalaxy.eu/root?tool_id=qiime_extract_viz" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QIIME vizualisation extractor</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qiime2__deblur__denoise_16S" title="Deblur sequences using a 16S positive filter."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 deblur denoise-16S</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__first_differences" title="Compute first differences or difference from baseline between sequential states"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal first-differences</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__alignment__mafft" title="De novo multiple sequence alignment with MAFFT"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 alignment mafft</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__alignment__mafft_add" title="Add sequences to multiple sequence alignment with MAFFT."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 alignment mafft-add</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__alignment__mask" title="Positional conservation and gap filtering."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 alignment mask</button></a>
@@ -3455,6 +3518,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__core_metrics" title="Core diversity metrics (non-phylogenetic)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity core-metrics</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__core_metrics_phylogenetic" title="Core diversity metrics (phylogenetic and non-phylogenetic)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity core-metrics-phylogenetic</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__filter_distance_matrix" title="Filter samples from a distance matrix."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity filter-distance-matrix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__filter_alpha_diversity" title="Filter samples from an alpha diversity metric."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity filter-alpha-diversity</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__mantel" title="Apply the Mantel test to two distance matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity mantel</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__pcoa" title="Principal Coordinate Analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity pcoa</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__pcoa_biplot" title="Principal Coordinate Analysis Biplot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity pcoa-biplot</button></a>
@@ -3517,6 +3581,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__gneiss__ilr_phylogenetic_ordination" title="Ordination through a phylogenetic Isometric Log Ratio transform."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 gneiss ilr-phylogenetic-ordination</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__anova" title="ANOVA test"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal anova</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__feature_volatility" title="Feature volatility analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal feature-volatility</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__first_differences" title="Compute first differences or difference from baseline between sequential states"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal first-differences</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__first_distances" title="Compute first distances or distance from baseline between sequential states"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal first-distances</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__linear_mixed_effects" title="Linear mixed effects modeling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal linear-mixed-effects</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__maturity_index" title="Microbial maturity index prediction."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal maturity-index</button></a>
@@ -3576,6 +3641,35 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__vsearch__uchime_ref" title="Reference-based chimera filtering with vsearch."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 vsearch uchime-ref</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2_core__tools__export" title="Export data from a QIIME 2 artifact"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 tools export</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2_core__tools__import" title="Import data into a QIIME 2 artifact"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 tools import</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__deblur__denoise_16S" title="Deblur sequences using a 16S positive filter."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 deblur denoise-16S</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime_extract_viz" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QIIME vizualisation extractor</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__vizard__lineplot" title="Lineplot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 vizard lineplot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__vizard__heatmap" title="Heatmap"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 vizard heatmap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__vizard__scatterplot_2d" title="2D Scatterplot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 vizard scatterplot-2d</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__vizard__boxplot" title="Boxplot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 vizard boxplot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__stats__collate_stats" title="Combine and FDR correct multiple stats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 stats collate-stats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__stats__wilcoxon_srt" title="Wilcoxon Signed Rank Test"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 stats wilcoxon-srt</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__stats__plot_rainclouds" title="Raincloud plots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 stats plot-rainclouds</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__stats__wilcoxon_srt_facet" title="Per-facet Wilcoxon Signed Rank Test"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 stats wilcoxon-srt-facet</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__stats__facet_across" title="Facet across outer group"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 stats facet-across</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__stats__facet_within" title="Facet within outer group"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 stats facet-within</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__stats__prep_alpha_distribution" title="Alpha diversity to Dist1D"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 stats prep-alpha-distribution</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__stats__mann_whitney_u_facet" title="Per-facet Mann-Whitney U Test"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 stats mann-whitney-u-facet</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__stats__alpha_group_significance" title="Alpha group significance test and plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 stats alpha-group-significance</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__rescript__get_bv_brc_genome_features" title="Fetch genome features from BV-BRC."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 rescript get-bv-brc-genome-features</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__rescript__get_bv_brc_genomes" title="Get genome sequences from the BV-BRC database."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 rescript get-bv-brc-genomes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__rescript__get_bv_brc_metadata" title="Fetch BV-BCR metadata."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 rescript get-bv-brc-metadata</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2_core__tools__import_fastq" title="Import fastq data into a QIIME 2 artifact"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 tools import-fastq</button></a>
+<h3>Data Managers</h3>
+<a href="https://usegalaxy.eu/root?tool_id=checkv_end_to_end" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckV end to end</button></a>
+<h3>XAS (X-ray Absorption Spectroscopy)</h3>
+<a href="https://usegalaxy.eu/root?tool_id=larch_select_paths" title="select FEFF paths for XAFS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch Select Paths</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=larch_plot" title="plot Athena projects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch Plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=larch_athena" title="generate Athena projects from XAFS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch Athena</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=larch_artemis" title="generate Artemis projects from XAFS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch Artemis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=larch_feff" title="generate FEFF paths from XAFS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch FEFF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=larch_lcf" title="perform linear combination fit on XAS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch LCF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=larch_criteria_report" title="generate reports on Artemis fitting from XAFS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch Criteria Report</button></a>
 <h3>Metagenomic Analysis</h3>
 <a href="https://usegalaxy.eu/root?tool_id=t2t_report" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Summarize taxonomy</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Draw_phylogram" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Draw phylogeny</button></a>
@@ -3586,64 +3680,64 @@ layout: default
 <h3>GATK Tools</h3>
 <a href="https://usegalaxy.eu/root?tool_id=gatk_count_covariates" title="on BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Count Covariates</button></a>
 <h3>Built-in Converters</h3>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_SMILES_to_MOL" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SMILES to MOL</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bed_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To BED</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Coverage</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_neostorezip_to_neostore" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert neostore.zip files to neostore</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bam_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM to BigWig</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_bowtie_base_index" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to Bowtie base space Index</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bedgraph_to_bigwig" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BedGraph to BigWig</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BGZ VCF to tabix</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_cml_to_smiles" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert CML to SMILES</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bgzip_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Interval to BGZIP</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_molecules" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenBabel converter for molecular formats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bz2_to_uncompressed" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert compressed file to uncompressed.</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gz_to_uncompressed" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert compressed file to uncompressed.</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BED, GFF, or VCF to BigWig</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_uncompressed_to_gz" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert uncompressed file to compressed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_picard_interval_list_to_bed6" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Picard Interval List to BED6</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_mdconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert XTC, DCD, and TRR</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_maf_to_fasta_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert MAF to Fasta</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_wiggle_to_interval_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Wiggle to Interval</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pbed2ldindepconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert plink pbed to ld reduced format</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_2bit" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to 2bit</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gff_to_bed_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GFF to BED</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bedstrict_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Strict BED</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_inchi_to_mol" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert InChI to MOL</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert compressed and uncompressed BCF files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bed_to_gff_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BED to GFF</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bed12_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Strict BED12</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gff_to_interval_index_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GFF to Interval Index</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_cram_to_bam_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert CRAM to BAM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bed_to_fli_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BED to Feature Location Index</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_smiles_to_smiles" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SMILES to SMILES</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tabular_to_dbnsfp" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert tabular to dbnsfp</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_Bam_Bai_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Bam to Bai</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bam_to_qname_sorted_bam" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM to queryname-sorted BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_mol2_to_mol" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert MOL2 to MOL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_biom" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Biom datasets</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BED, GFF, or VCF to BigWig</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM to coordinate-sorted BAM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_tabix_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Interval to tabix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fastq_to_fqtoc0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTQ files to seek locations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tabular_to_csv" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert tabular to CSV</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_tabix_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Interval to tabix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bedgraph_to_bigwig" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BedGraph to BigWig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gff_to_fli_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GFF to Feature Location Index</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Coverage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_ref_to_seq_taxomony" title="converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Ref taxonomy to Seq Taxonomy</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_Pdb_to_Gro_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert PDB to GRO</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_tabular" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to Tabular</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_2bit" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to 2bit</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=csv_to_tabular" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert CSV to tabular</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bed6_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Strict BED6</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM to coordinate-sorted BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bigwigtowig" title="Convert bigWig to wig"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BigWig to Wiggle</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bed_to_fli_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BED to Feature Location Index</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BGZ VCF to tabix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_cram_to_bam_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert CRAM to BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_bowtie_base_index" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to Bowtie base space Index</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_smiles_to_smiles" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SMILES to SMILES</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_cml_to_smiles" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert CML to SMILES</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_neostorezip_to_neostore" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert neostore.zip files to neostore</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert compressed and uncompressed BCF files</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lped2pbedconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert lped to plink pbed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_fai" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to fai file</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_sam_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SAM to BigWig</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gz_to_uncompressed" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert compressed file to uncompressed.</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bam_to_qname_sorted_bam" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM to queryname-sorted BAM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_tar_to_directory" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert tar to directory</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_wig_to_bigwig" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Wiggle to BigWig</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bigwigtowig" title="Convert bigWig to wig"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BigWig to Wiggle</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_len" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to len file</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=lped2fpedconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert lped to fped</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_Bam_Bai_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Bam to Bai</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_bowtie_color_index" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to Bowtie color space Index</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fastq_to_fqtoc0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTQ files to seek locations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_mol2_to_mol" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert MOL2 to MOL</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gff_to_fli_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GFF to Feature Location Index</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pbed2lpedconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert plink pbed to linkage lped</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_mdconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert XTC, DCD, and TRR</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bed6_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Strict BED6</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_SMILES_to_MOL" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SMILES to MOL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bed12_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Strict BED12</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bed_to_gff_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BED to GFF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bedstrict_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Strict BED</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_parquet_to_csv" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Parquet to csv</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bz2_to_uncompressed" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert compressed file to uncompressed.</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_inchi_to_mol" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert InChI to MOL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bam_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM to BigWig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_tabular" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to Tabular</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gff_to_bed_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GFF to BED</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gff_to_interval_index_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GFF to Interval Index</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_maf_to_interval_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert MAF to Genomic Intervals</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tabular_to_dbnsfp" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert tabular to dbnsfp</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=csv_to_tabular" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert CSV to tabular</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_ref_to_seq_taxomony" title="converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Ref taxonomy to Seq Taxonomy</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_fai" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to fai file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lped2fpedconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert lped to fped</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_wiggle_to_interval_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Wiggle to Interval</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_len_to_linecount" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Len file to Linecount</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_len" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to len file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pbed2ldindepconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert plink pbed to ld reduced format</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_wig_to_bigwig" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Wiggle to BigWig</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_Gro_to_Pdb_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GRO to PDB</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_picard_interval_list_to_bed6" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Picard Interval List to BED6</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_tar_to_directory" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert tar to directory</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_sam_to_unsorted_bam" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SAM to BAM without sorting</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bgzip_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Interval to BGZIP</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_len_to_linecount" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Len file to Linecount</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_molecules" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenBabel converter for molecular formats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bed_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To BED</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pbed2lpedconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert plink pbed to linkage lped</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_bowtie_color_index" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to Bowtie color space Index</button></a>