From 755ff750a03899984045a25bd8e2226494c823b1 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Mon, 1 Apr 2024 01:19:30 +0200
Subject: [PATCH] Update tools (#1235)

Co-authored-by: OlegZharkov <OlegZharkov@users.noreply.github.com>
---
 tools.md | 153 ++++++++++++++++++++++++++++---------------------------
 1 file changed, 77 insertions(+), 76 deletions(-)

diff --git a/tools.md b/tools.md
index bde0a30ec..6c0d02fd8 100644
--- a/tools.md
+++ b/tools.md
@@ -2,7 +2,7 @@
 layout: default
 ---
 
-# European Galaxy tools (3448 and counting)
+# European Galaxy tools (3449 and counting)
 <hr/>
 <h3>Get Data</h3>
 <a href="https://usegalaxy.eu/root?tool_id=fasterq_dump" title="format from NCBI SRA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Faster Download and Extract Reads in FASTQ</button></a>
@@ -72,7 +72,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=hbvar" title="Human Hemoglobin Variants and Thalassemias"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HbVar</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=omicsdi" title="Sync dataset's files from OmicsDI"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OmicsDI</button></a>
 <h3>Send Data</h3>
-<a href="https://usegalaxy.eu/root?tool_id=ena_upload" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ENA Upload tool</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ena_upload" title="Submission of (meta)data to the European Nucleotide Archive (ENA)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ENA Upload tool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=curl_post" title="send cURL POST requests"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cURL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=send_to_cloud" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Send to cloud</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=export_remote" title="to remote files source"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Export datasets</button></a>
@@ -106,6 +106,26 @@ 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>
@@ -118,37 +138,17 @@ 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=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=gops_cluster_1" title="the intervals of a dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gff3.rebase" title="against parent features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Rebase GFF3 features</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=column_remove_by_header" title="by heading"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove columns</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=column_order_header_sort" title="by heading"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort Column Order</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_easyjoin_tool" title="two files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_tac" title="reverse a file (reverse cat)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tac</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_cat" title="tail-to-head (cat)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate datasets</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_multijoin_tool" title="(combine multiple files)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Multi-Join</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_uniq_tool" title="assuming sorted input file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unique lines</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_cut_tool" title="columns from a table (cut)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Advanced Cut</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_tail_tool" title="lines from a dataset (tail)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select last</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_sort_rows" title="according to their columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort a row</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_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=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_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_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=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>
@@ -722,13 +722,15 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=aegean_canongff3" title="pre-process GFF3 files, removing all features not directly related to protein-coding genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn CanonGFF3</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=aegean_parseval" title="compare two sets of gene annotations for the same sequence."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn ParsEval</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.intersect_and_adjacent" title="Outputs nearby top-level GFF features from two GFF3 files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Intersect and Adjacent</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=helixer" title="gene calling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Helixer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=integron_finder" title="is a program that detects integrons in DNA sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Integron Finder</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmfetch" title="retrieve profile HMM(s) from a file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmfetch</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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=hamronize_summarize" title="Concatenate and summarize AMR detection reports"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hamronize summarize:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hamronize_tool" title="Antimicrobial Resistance Analysis Reports into a common data structure"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hAMRonize</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mirmachine" title="A tool to detect miRNA homologs in genome sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MirMachine</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=abritamr" title="AMR gene detection with AMRFinderPlus"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">abriTAMR</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=miniprot" title="align a protein sequence against a genome with affine gap penalty, splicing and frameshift"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Miniprot align</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=miniprot_index" title="build a genome index for miniprot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Miniprot index</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=prodigal" title="A tool for gene prediction in microbial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prodigal Gene Predictor</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=aegean_gaeval" title="compute coverage and integrity scores for gene models using transcript alignments."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn GAEVAL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bg_find_subsequences" title="providing regions in BED format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nucleotide subsequence search</button></a>
@@ -755,10 +757,8 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=gecco" title="is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GECCO</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interproscan" title="functional annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InterProScan</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=te_finder" title="Transposable element insertions finder"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TEfinder</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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=edta" title="Whole-genome de-novo TE annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">edta</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gffcompare" title="compare assembled transcripts to a reference annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GffCompare</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pfamscan" title="search a FASTA sequence against a library of Pfam HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PfamScan</button></a>
@@ -1371,6 +1371,7 @@ layout: default
 <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=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>
@@ -1387,7 +1388,6 @@ 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>
@@ -2935,7 +2935,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=rnalfoldz" title="calculates locally stable secondary structures of RNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNALfoldz</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=re_he_maldi_image_registration" title="Registration of MALDI and HE Image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HE/ MALDI Image Registration</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=netcdf2zarr" title="Rewrite a netCDF to Zarr"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF to Zarr</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=jbrowse2" title="genome browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">jbrowse2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=jbrowse2" title="genome browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JBrowse2</button></a>
 <h3>GIS Data Handling</h3>
 <a href="https://usegalaxy.eu/root?tool_id=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>
@@ -3178,6 +3178,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=ecoregion_eco_map" title="Create map from cluster to visualize ecoregions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EcoMap</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ecoregion_cluster_estimate" title="Find an optimal number of cluster with SIH index"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ClusterEstimate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ecoregion_clara_cluster" title="Make cluster from BRT prediction with Clara algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ClaraClust</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ecoregion_GeoNearestNeighbor" title="Merge two data tables by finding the closest points based on latitude and longitude coordinates (WGS84 projection)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GeoNearestNeighbor</button></a>
 <h3>Indicators from geometric mean</h3>
 <a href="https://usegalaxy.eu/root?tool_id=Map_shp" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make a map with a shapefile</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Mean_geom" title="- calcul of the geometric means for the 'bois mort' indicator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Geometric means</button></a>
@@ -3480,64 +3481,64 @@ 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_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_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_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_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_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_bed_gff_or_vcf_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BED, GFF, or VCF to BigWig</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gz_to_uncompressed" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert compressed file to uncompressed.</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_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_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_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=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_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_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_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_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_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_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_fasta_to_len" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to len file</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_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_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=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_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_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_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_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_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_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_maf_to_interval_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert MAF to Genomic Intervals</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_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=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_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_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_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_bam_to_qname_sorted_bam" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM to queryname-sorted BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bed_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_Gro_to_Pdb_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GRO to PDB</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_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_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_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_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_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=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=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_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_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_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_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_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=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_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=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_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_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_cram_to_bam_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert CRAM to BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bam_to_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=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_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_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_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_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_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_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_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_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_sam_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SAM to BigWig</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=lped2fpedconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert lped to fped</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_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_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_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_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_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_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_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_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_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_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_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_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_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_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=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_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_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=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_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_fasta_to_len" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to len file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_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_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_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_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_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_maf_to_interval_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert MAF to Genomic Intervals</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_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_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_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_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_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_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=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_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_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_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_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=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_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_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>