From d1d8e440bafab55c4a05747e606bf1e0121aa6e3 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Mon, 18 Mar 2024 02:29:16 +0100
Subject: [PATCH] Update tools (#1230)

Co-authored-by: OlegZharkov <OlegZharkov@users.noreply.github.com>
---
 tools.md | 57 ++++++++++++++++++++++++++++++++++++--------------------
 1 file changed, 37 insertions(+), 20 deletions(-)

diff --git a/tools.md b/tools.md
index 65e591a10..c5f363903 100644
--- a/tools.md
+++ b/tools.md
@@ -2,7 +2,7 @@
 layout: default
 ---
 
-# European Galaxy tools (3364 and counting)
+# European Galaxy tools (3381 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>
@@ -216,12 +216,12 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=Grouping1" title="data by a column and perform aggregate operation on other columns."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Group</button></a>
 <hr/><h2>Genomic File Manipulation</h2>
 <h3>Convert Formats</h3>
+<a href="https://usegalaxy.eu/root?tool_id=biom_convert" title="between BIOM table formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bioext_bam2msa" title="to FASTA multiple sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_montage" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Image Montage</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_compare" title="with GraphicsMagick"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare two images</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gffread" title="Filters and/or converts GFF3/GTF2 records"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gffread</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_convert" title="with GraphicsMagick"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert image format</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biom_convert" title="between BIOM table formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=idpquery" title="Creates text reports from idpDB files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idpQuery</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tab2fasta" title="converts tabular file to FASTA format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tabular-to-FASTA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fasta2tab" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTA-to-Tabular</button></a>
@@ -245,6 +245,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=bax2bam" title="converts PacBio basecall format (bax.h5) into BAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bax2bam</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=galaxy_intermine_exchange" title="Dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create InterMine Interchange</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_bam_to_cram" title="convert BAM alignments to CRAM format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">samtools BAM to CRAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bam2fastx" title="PacBio BAM to Fastx"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PacBio bam2fastx</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hictk" title="convert cool to juicebox hic"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hictk</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=idconvert" title="Convert mass spectrometry identification files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idconvert</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=msconvert_subset" title="against list of scan numbers or indices."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">msconvert Subset Peak List</button></a>
@@ -279,6 +280,7 @@ 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=ncbi_fcs_gx" title="detects contamination from foreign organisms in genome sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI FCS GX</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fastp" title="fast all-in-one preprocessing for FASTQ files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fastp</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trimmomatic" title="flexible read trimming tool for Illumina NGS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trimmomatic</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=seqprep" title="Merge and Trim Adapter Sequences from Paired-End Illumina Reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merging paired-end Illumina reads (SeqPrep)</button></a>
@@ -392,6 +394,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=qualimap_counts" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QualiMap Counts QC</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fastq_info" title="validates single or paired fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ info</button></a>
 <h3>SAM/BAM</h3>
+<a href="https://usegalaxy.eu/root?tool_id=bamtools" title="datasets in various ways"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Operate on and transform BAM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mosdepth" title="- fast and flexible depth coverage calculation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mosdepth</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_ampliconclip" title="clip primer bases from bam files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools ampliconclip</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pileup_interval" title="condenses pileup format into ranges of bases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pileup-to-Interval</button></a>
@@ -407,7 +410,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=samtools_reheader" title="copy SAM/BAM header between datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools reheader</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qualimap_bamqc" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QualiMap BamQC</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qualimap_multi_bamqc" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QualiMap Multi-Sample BamQC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bamtools" title="datasets in various ways"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Operate on and transform BAM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tag_pileup_frequency" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tag pileup frequency</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_markdup" title="marks duplicate alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools markdup</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_merge" title="merge multiple sorted alignment files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools merge</button></a>
@@ -424,12 +426,12 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=ngsutils_bam_filter" title="Removes reads from a BAM file based on criteria"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BAM filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bamFilter" title="datasets on a variety of attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter BAM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_calmd" title="recalculate MD/NM tags"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools calmd</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_phase" title="call and phase heterozygous SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools phase</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bamhash" title="Hash BAM and FASTQ files to verify data integrity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BamHash</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bamtools_split_mapped" title="into a mapped and an unmapped dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by reads mapping status</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bamtools_split_paired" title="reads datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM into paired- and single-end</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bamtools_split_ref" title="into a dataset list collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by reference</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bamtools_split_mapped" title="into a mapped and an unmapped dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by reads mapping status</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bamtools_split_tag" title="into a dataset list collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by read tag value</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_phase" title="call and phase heterozygous SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools phase</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bamhash" title="Hash BAM and FASTQ files to verify data integrity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BamHash</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=varscan_mpileup" title="mutation caller for targeted, exome, and whole-genome resequencing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan mpileup</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=varscan_somatic" title="somatic mutation caller for cancer genomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan Somatic</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=varscan_somatic" title="somatic mutation caller for cancer genomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan Somatic</button></a>
@@ -597,6 +599,8 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=MAF_filter" title="by specified attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter MAF</button></a>
 <hr/><h2>Genomics Analysis</h2>
 <h3>Annotation</h3>
+<a href="https://usegalaxy.eu/root?tool_id=legsta" title="Legionella pneumophila sequence based typing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">legsta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=krocus" title="Multi-locus sequence typing (MLST) from uncorrected long reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">krocus</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=omark" title="proteome quality assessment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OMArk</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hmmer_jackhmmer" title="iteratively search a protein sequence against a protein database (PSIBLAST-like)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">jackhmmer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmemit" title="sample sequence(s) from a profile HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmemit</button></a>
@@ -724,6 +728,8 @@ layout: default
 <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=prodigal" title="A tool for gene prediction in microbial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prodigal Gene Predictor</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=aegean_gaeval" title="compute coverage and integrity scores for gene models using transcript alignments."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn GAEVAL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bg_find_subsequences" title="providing regions in BED format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nucleotide subsequence search</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rbc_gotohscan" title="Find subsequences in db"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GotohScan</button></a>
@@ -748,7 +754,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=list_spaln_tables" title="Given a query species, list the spaln settings tables that exist, from closest related species to most different"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">List spaln parameter tables</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gecco" title="is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GECCO</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interproscan" title="functional annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InterProScan</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=legsta" title="Legionella pneumophila sequence based typing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">legsta</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=te_finder" title="Transposable element insertions finder"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TEfinder</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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>
@@ -927,6 +932,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=srma_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Re-align with SRMA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mosaik_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with Mosaik</button></a>
 <h3>Variant Calling</h3>
+<a href="https://usegalaxy.eu/root?tool_id=cnv_vcf2json" title="Converts 1000hg structural variants VCF file to JSON"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNV VCF2JSON</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcfanno" title="VCF annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">vcfanno</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bbtools_callvariants" title="in aligned Bam files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: call variants</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=plink" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plink</button></a>
@@ -1028,6 +1034,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=snpEff_download" title="download a pre-built database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff download:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpEff" title="annotate variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff eff:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=manta" title="Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Manta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnv_phenopacket" title="Builds Phenopacket schema for the structural variants metadata from the 1000hg project"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNV Phenopacket</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=deepvariant" title="deep learning-based variant caller"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeepVariant</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=varscan_copynumber" title="Determine relative tumor copy number from tumor-normal pileups"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan copynumber</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=varscan" title="for variant detection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan</button></a>
@@ -1416,15 +1423,16 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=hgv_lps" title="LASSO-Patternsearch algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LPS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=master2pgSnp" title="Convert from MasterVar to pgSnp format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MasterVar to pgSnp</button></a>
 <h3>Single-cell</h3>
+<a href="https://usegalaxy.eu/root?tool_id=scanpy_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>
 <a href="https://usegalaxy.eu/root?tool_id=sceasy_convert" title="Convert between common single cell formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SCEasy Converter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=baredsc_1d" title="Compute distribution for a single gene"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">baredSC 1d</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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_normalize" title="with scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Normalize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scanpy_normalize" title="and impute with scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Normalize</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_inspect" title="with scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Inspect and manipulate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=anndata_inspect" title="object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Inspect AnnData</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=anndata_export" title="Interconvert AnnData and Loom formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Export AnnData and loom files</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_remove_confounders" title="with scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove confounders</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=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=baredsc_combine_2d" title="from baredSC"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Combine multiple 2D Models</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=baredsc_combine_1d" title="from baredSC"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Combine multiple 1D Models</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=anndata_import" title="from different format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Import Anndata and loom</button></a>
@@ -1435,7 +1443,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=dropletutils_empty_drops" title="Distinguish between droplets containing cells and ambient RNA in a droplet-based single-cell RNA sequencing experiment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DropletUtils emptyDrops</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=alevin" title="Quantification and analysis of 3-prime tagged-end single-cell sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Alevin</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_slice_image" title="into smaller patches"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slice Image</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_cluster_reduce_dimension" title="with scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster, infer trajectories and embed</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_parameter_iterator" title="produce an iteration over a defined parameter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy ParameterIterator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scater_plot_tsne" title="of two components"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: t-SNE plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scater_plot_pca" title="cell-level reduced dimension of a normalised SCE"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: PCA plot</button></a>
@@ -1802,6 +1809,11 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=mimodd_sort" title="takes a SAM/BAM dataset and generates a coordinate/name-sorted copy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MiModD Sort</button></a>
 <hr/><h2>Metagenomics</h2>
 <h3>Metagenomic Analysis</h3>
+<a href="https://usegalaxy.eu/root?tool_id=bigscape" title="Construct sequence similarity networks of BGCs and group them into GCF"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BiG-SCAPE</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phyloseq_plot_ordination" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq: plot ordination</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_otu_network" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 OTU network plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_frequency" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 frequency plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kraken_taxonomy_report" title="view report of classification for multiple samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken taxonomic report</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=recentrifuge" title="Robust comparative analysis and contamination removal for metagenomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Recentrifuge</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=das_tool" title="for genome-resolved metagenomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DAS Tool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ampvis2_core" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 core community analysis</button></a>
@@ -1811,7 +1823,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=polypolish" title="Short-read polishing of long-read bacterial genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Polypolish</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ampvis2_alpha_diversity" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 alpha diversity</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=taxonomy_krona_chart" title="from taxonomic profile"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krona pie chart</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kraken_taxonomy_report" title="view report of classification for multiple samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken taxonomic report</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=kraken-filter" title="filter classification by confidence score"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken-filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=kraken-translate" title="convert taxonomy IDs to names"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken-translate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=semibin_generate_cannot_links" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Contig annotations</button></a>
@@ -1902,14 +1913,12 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=metabat2" title="metagenome binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaBAT2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ampvis2_boxplot" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 boxplot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ampvis2_export_fasta" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 export fasta</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_frequency" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 frequency plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ampvis2_heatmap" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 heatmap</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ampvis2_load" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 load</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ampvis2_merge_ampvis2" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 merge ampvis2 data sets</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ampvis2_mergereplicates" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 merge replicates</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ampvis2_octave" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 octave plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ampvis2_ordinate" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 ordination plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_otu_network" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 OTU network plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ampvis2_rankabundance" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 rank abundance plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ampvis2_rarecurve" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 rarefaction curve</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ampvis2_setmetadata" title="types"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 set metadata</button></a>
@@ -1922,6 +1931,8 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=coverm_contig" title="Calculate read coverage per contig"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CoverM contig</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=coverm_genome" title="Calculate coverage of individual genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CoverM genome</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Fasta_to_Contig2Bin" title="to scaffolds-to-bin table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Converts genome bins in fasta format</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phyloseq_from_dada2" title="from dada2 sequence and taxonomy tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create phyloseq object</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phyloseq_plot_richness" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq: plot alpha diverstiy measure</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metabat2_jgi_summarize_bam_contig_depths" title="for MetaBAT2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate contig depths</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=semibin" title="for Semi-supervised Metagenomic Binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=semibin_bin" title="into bins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Group the contigs</button></a>
@@ -1936,9 +1947,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=megan_blast2rma" title="from BLAST output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAN: Generate RMA files</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=megan_blast2lca" title="to produce a taxonomic classification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEGAN Blast2LCA: apply LCA alignment</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bin_refiner" title="refines metagenome bins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Binning refiner</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=phyloseq_from_dada2" title="from dada2 sequence and taxonomy tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create phyloseq object</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=phyloseq_plot_ordination" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq: plot ordination</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=phyloseq_plot_richness" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq: plot alpha diverstiy measure</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=concoct" title="for metagenome binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CONCOCT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=concoct_coverage_table" title="for CONCOCT"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CONCOCT: Generate the input coverage table</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=concoct_cut_up_fasta" title="in non-overlapping or overlapping parts of equal length"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CONCOCT: Cut up contigs</button></a>
@@ -2472,6 +2480,7 @@ 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=matchms_add_key" title="Set metadata key in MSP to static value"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms add key</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimet_timecourse_analysis" title="Differential analysis of tracer metabolomics data comparing consecutive time-points (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet timecourse analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimet_pca_analysis" title="Principal Component Analysis for tracer metabolomics data, producing tables (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet pca analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimet_metabologram" title="Integration of transcriptomics and (tracer) metabolomics differential data (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet metabologram</button></a>
@@ -2483,7 +2492,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=dimet_abundance_plot" title="Figures of metabolites total abundance as barplots (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet abundance plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=matchms_subsetting" title="Extract spectra from a library given unique metadata identifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms subsetting</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=matchms_metadata_export" title="extract all metadata from mass spectra file to tabular format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms metadata export</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=matchms_add_key" title="Set metadata key in MSP to static value"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms add key</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=recetox_msfinder" title="Annotation of fragment peaks in mass spectral libraries."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RECETOX MsFinder</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=matchms_filtering" title="filter and normalize mass spectrometry data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms filtering</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=matchms_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>
@@ -2570,6 +2578,8 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=dimet_differential_multigroup_analysis" title="Differential analysis of 3 or more chosen groups of tracer metabolomics data (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet differential multigroup analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimet_isotopologues_plot" title="Figures of isotopologues proportions by metabolite, as stacked barplots (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet isotopologues plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=riassigner" title="compute retention indices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RIAssigner</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=use_theoretical_mz_annotations" title="Overwrite experimentally measured mz values for peaks with theoretical values from peak comments."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">use theoretical m/z values</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=riassigner_from_comment" title="Assign different retention indices from unstructured comment metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RIAssigner init from comment</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=abims_xcms_refine" title="Remove or merge chromatographic peaks based on specific criteria."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xcms refineChromPeaks (refine)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=isoplot" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Isoplot: Generate plots from isocor output</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_generate_feature_table" title="generate feature table from noise-removed HRMS profile data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - generate feature table</button></a>
@@ -2589,6 +2599,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=matchms_similarity" title="calculate the similarity score and matched peaks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms similarity</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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>
 <h3>ChemicalToolBox</h3>
+<a href="https://usegalaxy.eu/root?tool_id=qcxms_neutral_run" title="required as first step to prepare for the production runs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCxMS neutral run</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=xtb_molecular_optimization" title="Semiempirical quantum mechanical molecular optimization method"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xtb molecular optimization</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ambertools_acpype" title="using acpype"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate MD topologies for small molecules</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=chembl" title="for compounds which are similar to a SMILES string"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Search ChEMBL database</button></a>
@@ -2674,6 +2685,8 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=featurestein" title="feature overlay scoring"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">'FeatureStein' fragment overlay scoring</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gmx_merge_topology_files" title="and GRO files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge GROMACS topologies</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rem_complex" title="Remove molecular coordination complexes from a list of structure representations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove coordination complexes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qcxms_production_run" title="Production run to obtain a QCxMS simulated mass spectrum"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCxMS production run</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qcxms_getres" title="Get result of the Production run to obtain a QCxMS simulated mass spectrum"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCxMS get results</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=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>
@@ -2746,7 +2759,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=create_tool_recommendation_model" title="using deep learning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a model to recommend tools</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dwt_var1" title="using Discrete Wavelet Transfoms"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Wavelet variance</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=graphembed" title="Compute and plot a 2D embedding of a data matrix given supervised class information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GraphEmbed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_landmark_registration" title="Landmark Registration"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Landmark Registration</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=plotly_regression_performance_plots" title="of tabular data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Plot actual vs predicted curves and residual plots</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=plotly_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=pandas_rolling_window" title="over a dataframe (e.g. for data smoothing)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Rolling window</button></a>
@@ -2795,6 +2807,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=create_tool_recommendation_model" title="using deep learning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a model to recommend tools</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_label_encoder" title="Encode target labels with value between 0 and n_classes-1"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Label encoder</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_to_categorical" title="Converts a class vector (integers) to binary class matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">To categorical</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=colorize_labels" title="with NetworkX"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Colorize label map</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=virhunter" title="Deep learning method to identify viruses in sequencing datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virhunter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=decontaminator" title="Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">decontaminator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=deepmicro" title="Representation learning and classification framework"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeepMicro</button></a>
@@ -2918,6 +2931,7 @@ layout: default
 <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>
 <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>
 <a href="https://usegalaxy.eu/root?tool_id=xarray_metadata_info" title="summarize content of a Netcdf file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Metadata Info</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=xarray_select" title="extracts variable values with custom conditions on dimensions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Selection</button></a>
@@ -2929,6 +2943,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=gdal_gdalinfo" title="lists information about a raster dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL Informations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gdal_gdalbuildvrt" title="builds a VRT from a list of datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL Build VRT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gdal_gdaladdo" title="builds or rebuilds overview images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL addo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=otb_band_math" title="outputs a monoband image as a result of a mathematical operation on several multi-band images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OTB.BandMath</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=xarray_netcdf2netcdf" title="manipulate xarray from netCDF and save back to netCDF"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray operations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=xarray_mapplot" title="Visualize netCDF variables on a geographical map"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray map plotting</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=xarray_coords_info" title="Get values for each coordinate of a Netcdf file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Coordinate Info</button></a>
@@ -3019,6 +3034,9 @@ 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=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>
@@ -3124,7 +3142,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_convert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Image Converter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_localthreshold" title="applies a local threshold algorithm to an image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Local Threshold</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_2d_split_binaryimage_by_watershed" title="Split binary image by using watershed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split objects</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_points_to_binaryimage" title="Converts points to a binary image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Points to Binary Image</button></a>
 <h3>Species abundance</h3>
 <a href="https://usegalaxy.eu/root?tool_id=pampa_glmsp" title="Compute a GLM of your choice on population data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute GLM on population data</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pampa_glmcomm" title="Compute a GLM of your choice on community data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute GLM on community data</button></a>