From 6fdf92c14a068bca88ec749cf21b885e99a0a607 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Mon, 20 May 2024 10:00:49 +0200
Subject: [PATCH] Update tools (#1258)

Co-authored-by: OlegZharkov <OlegZharkov@users.noreply.github.com>
---
 tools.md | 118 +++++++++++++++++++++++++++++--------------------------
 1 file changed, 63 insertions(+), 55 deletions(-)

diff --git a/tools.md b/tools.md
index 622d5a17..909adc8e 100644
--- a/tools.md
+++ b/tools.md
@@ -2,9 +2,10 @@
 layout: default
 ---
 
-# European Galaxy tools (3484 and counting)
+# European Galaxy tools (3492 and counting)
 <hr/>
 <h3>Get Data</h3>
+<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>
@@ -285,6 +286,9 @@ 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=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>
@@ -851,10 +855,10 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=shasta" title="De novo assembly of long read sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Shasta</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lordec" title="is a set a programs for correcting sequencing errors in PacBio reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Lordec</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=novoplasty" title="de novo assembler for short circular genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NOVOplasty</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=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=megahit" title="for metagenomics assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAHIT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=idba_tran" title="Iterative de Bruijn Graph Assembler for transcriptome data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDBA-TRAN</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=shovill" title="Faster SPAdes assembly of Illumina reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Shovill</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=flye" title="de novo assembler for single molecule sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flye</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=racon" title="Consensus module for raw de novo DNA assembly of long uncorrected reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Racon</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=minia" title="Short-read assembler based on a de Bruijn graph"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Minia</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=quast" title="Genome assembly Quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Quast</button></a>
@@ -973,7 +977,6 @@ layout: default
 <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=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=snpfreqplot" title="Generates a heatmap of allele frequencies grouped by variant type for SnpEff-annotated SARS-CoV-2 data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Variant Frequency Plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mut2read" title="Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DCS mutations to tags/reads:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_filter" title="Filter variants using arbitrary expressions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mut2sscs" title="Extracts all tags from the single stranded consensus sequence (SSCS) bam file that carry a mutation at the same position a mutation is called in the duplex consensus sequence (DCS) and calculates their frequencies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DCS mutations to SSCS stats:</button></a>
@@ -1446,6 +1449,8 @@ 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=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_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_plot" title="with scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_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_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>
@@ -1477,6 +1482,7 @@ layout: default
 <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=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=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>
@@ -2208,6 +2214,7 @@ layout: default
 <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=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>
@@ -2510,7 +2517,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=eggnog_mapper_annotate" title="annotation phase"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eggNOG Mapper</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=eggnog_mapper_search" title="search phase"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eggNOG Mapper</button></a>
 <h3>Metabolomics</h3>
-<a href="https://usegalaxy.eu/root?tool_id=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=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=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>
@@ -2614,6 +2620,7 @@ layout: default
 <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=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=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=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>
@@ -2718,6 +2725,7 @@ layout: default
 <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=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>
@@ -2764,7 +2772,6 @@ 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>
@@ -2845,6 +2852,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=decontaminator" title="Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">decontaminator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=deepmicro" title="Representation learning and classification framework"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeepMicro</button></a>
 <h3>Graph/Display Data</h3>
+<a href="https://usegalaxy.eu/root?tool_id=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=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>
@@ -2870,7 +2878,6 @@ 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>
@@ -3070,11 +3077,11 @@ 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=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=ip_points_to_binaryimage" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert point coordinates to binary image</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=label_to_binary" title="with NumPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert label map to binary image</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=orientationpy" title="with OrientationPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute image orientation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gate_finder" title="with Vitessce"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform gating</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cellpose" title="with Cellpose"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run generalist cell and nucleus segmentation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bia_download" title="Download images from Bioimage Archive"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FTP Link for Bioimage Archive</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_binary_to_labelimage" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to label map</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_curve_fitting" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform curve fitting</button></a>
@@ -3345,6 +3352,7 @@ layout: default
 <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>
@@ -3516,64 +3524,64 @@ 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=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=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_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_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_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_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_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_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_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_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_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_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=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_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=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_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_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_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=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_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=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=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_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_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_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_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_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_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_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_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_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_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_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_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_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=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_mdconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert XTC, DCD, and TRR</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bed_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_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=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_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_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_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_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=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_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_interval_to_bed12_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Strict BED12</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_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_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_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_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_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_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_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_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_gff_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BED to GFF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_sam_to_unsorted_bam" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SAM to BAM without sorting</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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=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_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_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_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_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_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_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=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_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_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_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_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_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_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_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_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_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_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_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_parquet_to_csv" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Parquet to csv</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_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_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_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_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_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_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_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=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_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>