From fb38d81783f6628cf44c099391e87b504a4e95d6 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Fri, 30 Aug 2024 04:59:00 +0000
Subject: [PATCH] Updated the data.yml sourced from
 australianbiocommons.github.io

---
 _data/data.yaml | 2617 +++++++++++++++++++++++++++++------------------
 1 file changed, 1617 insertions(+), 1000 deletions(-)

diff --git a/_data/data.yaml b/_data/data.yaml
index 00bb706..aad9048 100644
--- a/_data/data.yaml
+++ b/_data/data.yaml
@@ -1,4 +1,4 @@
-- biocontainers: 3d-dna
+- biocontainers: ''
   biotools: 3d-dna
   bunya:
   - '201008'
@@ -29,7 +29,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ABRicate
+- biocontainers: abricate
   biotools: ABRicate
   bunya:
   - 1.0.0-gompi-2021a
@@ -115,7 +115,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: AGAT
+- biocontainers: ''
   biotools: AGAT
   bunya: ''
   description: 'Another Gff Analysis Toolkit (AGAT)
@@ -128,7 +128,10 @@
   edam-outputs: []
   edam-topics:
   - Genomics
-  galaxy: ''
+  galaxy:
+  - description: 'AGAT: GTF/GFF analysis toolkit'
+    title: AGAT 1.4.0+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fagat%2Fagat%2F1.4.0%2Bgalaxy0
   homepage: https://github.com/NBISweden/AGAT
   id: agat
   license: GPL-3.0
@@ -143,7 +146,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: amber
+- biocontainers: ''
   biotools: amber
   bunya: ''
   description: 'The Assisted Model Building with Energy Refinement tool refers to
@@ -181,7 +184,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ambertools
+- biocontainers: ''
   biotools: ambertools
   bunya: ''
   description: Consists of several independently developed packages that work well
@@ -212,7 +215,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: anaconda
+- biocontainers: ''
   biotools: anaconda
   bunya:
   - '2022.05'
@@ -245,7 +248,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: anndata
+- biocontainers: ''
   biotools: anndata
   bunya: ''
   description: 'From https://anndata.readthedocs.io/en/latest/
@@ -282,7 +285,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: annotatemyids
+- biocontainers: ''
   biotools: annotatemyids
   bunya: ''
   description: This tool can get annotation for a generic set of IDs, using the Bioconductor
@@ -353,7 +356,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: any2fasta
+- biocontainers: ''
   biotools: any2fasta
   bunya:
   - 0.4.2-gcccore-10.3.0
@@ -378,7 +381,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: apollo
+- biocontainers: ''
   biotools: apollo
   bunya: ''
   description: Apollo is a genome annotation viewer and editor. Apollo allows researchers
@@ -410,7 +413,7 @@
   resources:
   - title: Apollo Portal
     url: https://apollo-portal.genome.edu.au/
-- biocontainers: aragorn
+- biocontainers: ''
   biotools: aragorn
   bunya: ''
   description: ARAGORN detects tRNA, mtRNA info about tmRNA, and tmRNA genes
@@ -459,7 +462,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: Arriba
+- biocontainers: ''
   biotools: Arriba
   bunya: ''
   description: Arriba is a command-line tool to detect gene fusions from RNA-Seq data
@@ -563,7 +566,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: autodock_vina
+- biocontainers: ''
   biotools: autodock_vina
   bunya: ''
   description: AutoDock Vina is a new open-source program for drug discovery, molecular
@@ -606,7 +609,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: bakta
+- biocontainers: ''
   biotools: bakta
   bunya: ''
   description: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
@@ -671,6 +674,13 @@
   - Data management
   - Sequence analysis
   galaxy:
+  - description: 'Operate on and transform BAM: datasets in various ways'
+    title: Operate on and transform BAM 2.5.2+galaxy2
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fbamtools%2Fbamtools%2F2.5.2%2Bgalaxy2
+  - description: 'Split BAM by reads mapping status: into a mapped and an unmapped
+      dataset'
+    title: Split BAM by reads mapping status 2.5.2+galaxy2
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbamtools_split_mapped%2Fbamtools_split_mapped%2F2.5.2%2Bgalaxy2
   - description: 'Split BAM by read tag value: into a dataset list collection'
     title: Split BAM by read tag value 2.5.2+galaxy2
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbamtools_split_tag%2Fbamtools_split_tag%2F2.5.2%2Bgalaxy2
@@ -695,7 +705,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: bamutil
+- biocontainers: ''
   biotools: bamutil
   bunya: ''
   description: Bamutil provides a serie of programs to work on SAM/BAM files.
@@ -840,8 +850,8 @@
   - RNA-Seq
   galaxy:
   - description: 'BBTools: BBduk: decontamination using kmers'
-    title: 'BBTools: BBduk 39.06+galaxy2'
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbbtools_bbduk%2Fbbtools_bbduk%2F39.06%2Bgalaxy2
+    title: 'BBTools: BBduk 39.08+galaxy0'
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbbtools_bbduk%2Fbbtools_bbduk%2F39.08%2Bgalaxy0
   homepage: https://jgi.doe.gov/data-and-tools/bbtools/
   id: bbmap
   license: BSD-3-Clause
@@ -855,7 +865,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: gff3_rebase
+- biocontainers: ''
   biotools: gff3_rebase
   bunya: ''
   description: A tool for filling the gap created by genomic data processing/analysis
@@ -920,112 +930,112 @@
   - GWAS study
   - Genotyping experiment
   galaxy:
-  - description: 'bcftools annotate: Annotate and edit VCF/BCF files'
-    title: bcftools annotate 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_annotate%2Fbcftools_annotate%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools call: SNP/indel variant calling from VCF/BCF'
-    title: bcftools call 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_call%2Fbcftools_call%2F1.15.1%2Bgalaxy3
+  - description: 'bcftools view: VCF/BCF conversion, view, subset and filter VCF/BCF
+      files'
+    title: bcftools view 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_view%2Fbcftools_view%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools roh: HMM model for detecting runs of homo/autozygosity'
+    title: bcftools roh 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_roh%2Fbcftools_roh%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools List Samples: in VCF/BCF file'
+    title: bcftools List Samples 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_query_list_samples%2Fbcftools_query_list_samples%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools gtcheck: Check sample identity'
+    title: bcftools gtcheck 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_gtcheck%2Fbcftools_gtcheck%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools concat: Concatenate or combine VCF/BCF files'
+    title: bcftools concat 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_concat%2Fbcftools_concat%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools stats: Parses VCF or BCF and produces stats which can be
+      plotted using plot-vcfstats'
+    title: bcftools stats 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_stats%2Fbcftools_stats%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools reheader: Modify header of VCF/BCF files, change sample
+      names'
+    title: bcftools reheader 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_reheader%2Fbcftools_reheader%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools query: Extracts fields from VCF/BCF file and prints them
+      in user-defined format'
+    title: bcftools query 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_query%2Fbcftools_query%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools tag2tag: plugin Convert between similar tags, such as GL
+      and GP'
+    title: bcftools tag2tag 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_tag2tag%2Fbcftools_plugin_tag2tag%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools setGT: plugin Sets genotypes'
+    title: bcftools setGT 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_setgt%2Fbcftools_plugin_setgt%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools mendelian: plugin Count Mendelian consistent / inconsistent
+      genotypes'
+    title: bcftools mendelian 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_mendelian%2Fbcftools_plugin_mendelian%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools fill-tags: plugin Set INFO tags AF, AN, AC, AC_Hom, AC_Het,
+      AC_Hemi'
+    title: bcftools fill-tags 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_fill_tags%2Fbcftools_plugin_fill_tags%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools dosage: plugin genotype dosage'
+    title: bcftools dosage 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_dosage%2Fbcftools_plugin_dosage%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools counts: plugin  counts number of samples, SNPs, INDELs,
+      MNPs and total sites'
+    title: bcftools counts 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_counts%2Fbcftools_plugin_counts%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools norm: Left-align and normalize indels; check if REF alleles
+      match the reference; split multiallelic sites into multiple rows; recover multiallelics
+      from multiple rows'
+    title: bcftools norm 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_norm%2Fbcftools_norm%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools mpileup: Generate VCF or BCF containing genotype likelihoods
+      for one or multiple alignment (BAM or CRAM) files'
+    title: bcftools mpileup 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_mpileup%2Fbcftools_mpileup%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools merge: Merge multiple VCF/BCF files from non-overlapping
+      sample sets to create one multi-sample file'
+    title: bcftools merge 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_merge%2Fbcftools_merge%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools filter: Apply fixed-threshold filters'
+    title: bcftools filter 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_filter%2Fbcftools_filter%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools csq: Haplotype aware consequence predictor'
+    title: bcftools csq 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_csq%2Fbcftools_csq%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools convert from vcf: Converts VCF/BCF to IMPUTE2/SHAPEIT formats'
+    title: bcftools convert from vcf 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_convert_from_vcf%2Fbcftools_convert_from_vcf%2F1.15.1%2Bgalaxy4
   - description: 'bcftools cnv: Call copy number variation from VCF B-allele frequency
       (BAF) and Log R Ratio intensity (LRR) values'
-    title: bcftools cnv 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_cnv%2Fbcftools_cnv%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools concat: Concatenate or combine VCF/BCF files'
-    title: bcftools concat 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_concat%2Fbcftools_concat%2F1.15.1%2Bgalaxy3
+    title: bcftools cnv 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_cnv%2Fbcftools_cnv%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools annotate: Annotate and edit VCF/BCF files'
+    title: bcftools annotate 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_annotate%2Fbcftools_annotate%2F1.15.1%2Bgalaxy4
+  - description: 'bcftools call: SNP/indel variant calling from VCF/BCF'
+    title: bcftools call 1.15.1+galaxy5
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_call%2Fbcftools_call%2F1.15.1%2Bgalaxy5
   - description: 'bcftools consensus: Create consensus sequence by applying VCF variants
       to a reference fasta file'
-    title: bcftools consensus 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_consensus%2Fbcftools_consensus%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools convert from vcf: Converts VCF/BCF to IMPUTE2/SHAPEIT formats'
-    title: bcftools convert from vcf 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_convert_from_vcf%2Fbcftools_convert_from_vcf%2F1.15.1%2Bgalaxy3
+    title: bcftools consensus 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_consensus%2Fbcftools_consensus%2F1.15.1%2Bgalaxy4
   - description: 'bcftools convert to vcf: Converts other formats to VCF/BCFk'
-    title: bcftools convert to vcf 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_convert_to_vcf%2Fbcftools_convert_to_vcf%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools csq: Haplotype aware consequence predictor'
-    title: bcftools csq 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_csq%2Fbcftools_csq%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools filter: Apply fixed-threshold filters'
-    title: bcftools filter 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_filter%2Fbcftools_filter%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools gtcheck: Check sample identity'
-    title: bcftools gtcheck 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_gtcheck%2Fbcftools_gtcheck%2F1.15.1%2Bgalaxy3
+    title: bcftools convert to vcf 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_convert_to_vcf%2Fbcftools_convert_to_vcf%2F1.15.1%2Bgalaxy4
   - description: 'bcftools isec: Create intersections, unions and complements of VCF
       files'
-    title: bcftools isec 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_isec%2Fbcftools_isec%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools merge: Merge multiple VCF/BCF files from non-overlapping
-      sample sets to create one multi-sample file'
-    title: bcftools merge 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_merge%2Fbcftools_merge%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools mpileup: Generate VCF or BCF containing genotype likelihoods
-      for one or multiple alignment (BAM or CRAM) files'
-    title: bcftools mpileup 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_mpileup%2Fbcftools_mpileup%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools norm: Left-align and normalize indels; check if REF alleles
-      match the reference; split multiallelic sites into multiple rows; recover multiallelics
-      from multiple rows'
-    title: bcftools norm 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_norm%2Fbcftools_norm%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools counts: plugin  counts number of samples, SNPs, INDELs,
-      MNPs and total sites'
-    title: bcftools counts 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_counts%2Fbcftools_plugin_counts%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools dosage: plugin genotype dosage'
-    title: bcftools dosage 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_dosage%2Fbcftools_plugin_dosage%2F1.15.1%2Bgalaxy3
+    title: bcftools isec 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_isec%2Fbcftools_isec%2F1.15.1%2Bgalaxy4
   - description: 'bcftools fill-AN-AC: plugin Fill INFO fields AN and AC'
-    title: bcftools fill-AN-AC 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_fill_an_ac%2Fbcftools_plugin_fill_an_ac%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools fill-tags: plugin Set INFO tags AF, AN, AC, AC_Hom, AC_Het,
-      AC_Hemi'
-    title: bcftools fill-tags 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_fill_tags%2Fbcftools_plugin_fill_tags%2F1.15.1%2Bgalaxy3
+    title: bcftools fill-AN-AC 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_fill_an_ac%2Fbcftools_plugin_fill_an_ac%2F1.15.1%2Bgalaxy4
   - description: 'bcftools fixploidy: plugin  Fix ploidy'
-    title: bcftools fixploidy 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_fixploidy%2Fbcftools_plugin_fixploidy%2F1.15.1%2Bgalaxy3
+    title: bcftools fixploidy 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_fixploidy%2Fbcftools_plugin_fixploidy%2F1.15.1%2Bgalaxy4
   - description: 'bcftools impute-info: plugin Add imputation information metrics
       to the INFO field'
-    title: bcftools impute-info 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_impute_info%2Fbcftools_plugin_impute_info%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools mendelian: plugin Count Mendelian consistent / inconsistent
-      genotypes'
-    title: bcftools mendelian 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_mendelian%2Fbcftools_plugin_mendelian%2F1.15.1%2Bgalaxy3
+    title: bcftools impute-info 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_impute_info%2Fbcftools_plugin_impute_info%2F1.15.1%2Bgalaxy4
   - description: 'bcftools missing2ref: plugin Set missing genotypes'
-    title: bcftools missing2ref 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_missing2ref%2Fbcftools_plugin_missing2ref%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools setGT: plugin Sets genotypes'
-    title: bcftools setGT 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_setgt%2Fbcftools_plugin_setgt%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools tag2tag: plugin Convert between similar tags, such as GL
-      and GP'
-    title: bcftools tag2tag 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_tag2tag%2Fbcftools_plugin_tag2tag%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools query: Extracts fields from VCF/BCF file and prints them
-      in user-defined format'
-    title: bcftools query 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_query%2Fbcftools_query%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools List Samples: in VCF/BCF file'
-    title: bcftools List Samples 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_query_list_samples%2Fbcftools_query_list_samples%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools reheader: Modify header of VCF/BCF files, change sample
-      names'
-    title: bcftools reheader 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_reheader%2Fbcftools_reheader%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools roh: HMM model for detecting runs of homo/autozygosity'
-    title: bcftools roh 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_roh%2Fbcftools_roh%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools stats: Parses VCF or BCF and produces stats which can be
-      plotted using plot-vcfstats'
-    title: bcftools stats 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_stats%2Fbcftools_stats%2F1.15.1%2Bgalaxy3
-  - description: 'bcftools view: VCF/BCF conversion, view, subset and filter VCF/BCF
-      files'
-    title: bcftools view 1.15.1+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_view%2Fbcftools_view%2F1.15.1%2Bgalaxy3
+    title: bcftools missing2ref 1.15.1+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_plugin_missing2ref%2Fbcftools_plugin_missing2ref%2F1.15.1%2Bgalaxy4
   homepage: http://www.htslib.org/
   id: bcftools
   license: MIT
@@ -1099,7 +1109,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: beagle-lib
+- biocontainers: ''
   biotools: beagle-lib
   bunya:
   - 3.1.2-gcc-11.3.0
@@ -1169,7 +1179,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: beast2
+- biocontainers: ''
   biotools: beast2
   bunya: ''
   description: Bayesian phylogenetic analysis of molecular sequences. It estimates
@@ -1203,7 +1213,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: bed_to_protein_map
+- biocontainers: ''
   biotools: bed_to_protein_map
   bunya: ''
   description: Convert a BED format file of the proteins from a proteomics search
@@ -1243,136 +1253,136 @@
   edam-topics:
   - Genomics
   galaxy:
-  - description: 'bedtools GroupByBed: group by common cols and summarize other cols'
-    title: bedtools GroupByBed 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_groupbybed%2F2.30.0
-  - description: 'bedtools ComplementBed: Extract intervals not represented by an
-      interval file'
-    title: bedtools ComplementBed 2.30.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_complementbed%2F2.30.0%2Bgalaxy1
-  - description: 'bedtools MergeBED: combine overlapping/nearby intervals into a single
-      interval'
-    title: bedtools MergeBED 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_mergebed%2F2.30.0
-  - description: 'bedtools WindowBed: find overlapping intervals within a window around
-      an interval'
-    title: bedtools WindowBed 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_windowbed%2F2.30.0
-  - description: 'bedtools SpacingBed: reports the distances between features'
-    title: bedtools SpacingBed 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_spacingbed%2F2.30.0
-  - description: 'bedtools getfasta: use intervals to extract sequences from a FASTA
-      file'
-    title: bedtools getfasta 2.30.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_getfastabed%2F2.30.0%2Bgalaxy1
   - description: 'bedtools RandomBed: generate random intervals in a genome'
-    title: bedtools RandomBed 2.30.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_randombed%2F2.30.0%2Bgalaxy1
-  - description: 'bedtools MultiCovBed: counts coverage from multiple BAMs at specific
-      intervals'
-    title: bedtools MultiCovBed 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_multicovtbed%2F2.30.0
-  - description: 'bedtools ReldistBed: calculate the distribution of relative distances'
-    title: bedtools ReldistBed 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_reldistbed%2F2.30.0
-  - description: 'bedtools SlopBed: adjust the size of intervals'
-    title: bedtools SlopBed 2.30.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_slopbed%2F2.30.0%2Bgalaxy1
-  - description: 'bedtools ExpandBed: replicate lines based on lists of values in
-      columns'
-    title: bedtools ExpandBed 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_expandbed%2F2.30.0
+    title: bedtools RandomBed 2.31.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_randombed%2F2.31.1%2Bgalaxy0
+  - description: 'bedtools MapBed: apply a function to a column for each overlapping
+      interval'
+    title: bedtools MapBed 2.31.1.3
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_map%2F2.31.1.3
   - description: 'bedtools Compute both the depth and breadth of coverage: of features
       in file B on the features in file A (bedtools coverage)'
-    title: bedtools Compute both the depth and breadth of coverage 2.30.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_coveragebed%2F2.30.0%2Bgalaxy1
-  - description: 'bedtools ShuffleBed: randomly redistrubute intervals in a genome'
-    title: bedtools ShuffleBed 2.30.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_shufflebed%2F2.30.0%2Bgalaxy1
-  - description: 'bedtools SortBED: order the intervals'
-    title: bedtools SortBED 2.30.0+galaxy2
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_sortbed%2F2.30.0%2Bgalaxy2
+    title: bedtools Compute both the depth and breadth of coverage 2.31.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_coveragebed%2F2.31.1%2Bgalaxy0
+  - description: 'bedtools ExpandBed: replicate lines based on lists of values in
+      columns'
+    title: bedtools ExpandBed 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_expandbed%2F2.31.1
+  - description: 'bedtools FisherBed: calculate Fisher statistic between two feature
+      files'
+    title: bedtools FisherBed 2.31.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_fisher%2F2.31.1%2Bgalaxy0
+  - description: 'bedtools SlopBed: adjust the size of intervals'
+    title: bedtools SlopBed 2.31.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_slopbed%2F2.31.1%2Bgalaxy0
+  - description: 'bedtools TagBed: tag BAM alignments based on overlaps with interval
+      files'
+    title: bedtools TagBed 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_tagbed%2F2.31.1
+  - description: 'bedtools Genome Coverage: compute the coverage over an entire genome'
+    title: bedtools Genome Coverage 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_genomecoveragebed%2F2.31.1
+  - description: 'bedtools SubtractBed: remove intervals based on overlaps'
+    title: bedtools SubtractBed 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_subtractbed%2F2.31.1
+  - description: 'bedtools MultiCovBed: counts coverage from multiple BAMs at specific
+      intervals'
+    title: bedtools MultiCovBed 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_multicovtbed%2F2.31.1
   - description: 'bedtools AnnotateBed: annotate coverage of features from multiple
       files'
-    title: bedtools AnnotateBed 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_annotatebed%2F2.30.0
-  - description: 'bedtools MapBed: apply a function to a column for each overlapping
+    title: bedtools AnnotateBed 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_annotatebed%2F2.31.1
+  - description: 'bedtools GroupByBed: group by common cols and summarize other cols'
+    title: bedtools GroupByBed 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_groupbybed%2F2.31.1
+  - description: 'bedtools WindowBed: find overlapping intervals within a window around
+      an interval'
+    title: bedtools WindowBed 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_windowbed%2F2.31.1
+  - description: 'bedtools JaccardBed: calculate the distribution of relative distances
+      between two files'
+    title: bedtools JaccardBed 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_jaccard%2F2.31.1
+  - description: 'bedtools MergeBED: combine overlapping/nearby intervals into a single
       interval'
-    title: bedtools MapBed 2.30.0.3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_map%2F2.30.0.3
+    title: bedtools MergeBED 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_mergebed%2F2.31.1
+  - description: 'bedtools NucBed: profile the nucleotide content of intervals in
+      a FASTA file'
+    title: bedtools NucBed 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_nucbed%2F2.31.1
+  - description: 'bedtools BED12 to BED6: converter'
+    title: bedtools BED12 to BED6 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_bed12tobed6%2F2.31.1
+  - description: 'bedtools SpacingBed: reports the distances between features'
+    title: bedtools SpacingBed 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_spacingbed%2F2.31.1
+  - description: 'bedtools FlankBed: create new intervals from the flanks of existing
+      intervals'
+    title: bedtools FlankBed 2.31.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_flankbed%2F2.31.1%2Bgalaxy0
+  - description: 'bedtools SortBED: order the intervals'
+    title: bedtools SortBED 2.31.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_sortbed%2F2.31.1%2Bgalaxy0
+  - description: 'bedtools Intersect intervals: find overlapping intervals in various
+      ways'
+    title: bedtools Intersect intervals 2.31.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_intersectbed%2F2.31.1%2Bgalaxy0
+  - description: 'bedtools ReldistBed: calculate the distribution of relative distances'
+    title: bedtools ReldistBed 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_reldistbed%2F2.31.1
+  - description: 'bedtools MakeWindowsBed: make interval windows across a genome'
+    title: bedtools MakeWindowsBed 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_makewindowsbed%2F2.31.1
+  - description: 'bedtools LinksBed: create a HTML page of links to UCSC locations'
+    title: bedtools LinksBed 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_links%2F2.31.1
+  - description: 'bedtools ClusterBed: cluster overlapping/nearby intervals'
+    title: bedtools ClusterBed 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_clusterbed%2F2.31.1
+  - description: 'bedtools getfasta: use intervals to extract sequences from a FASTA
+      file'
+    title: bedtools getfasta 2.31.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_getfastabed%2F2.31.1%2Bgalaxy0
   - description: 'bedtools BED to BAM: converter'
-    title: bedtools BED to BAM 2.30.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_bedtobam%2F2.30.0%2Bgalaxy1
+    title: bedtools BED to BAM 2.31.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_bedtobam%2F2.31.1%2Bgalaxy0
   - description: 'bedtools MaskFastaBed: use intervals to mask sequences from a FASTA
       file'
-    title: bedtools MaskFastaBed 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_maskfastabed%2F2.30.0
-  - description: 'bedtools NucBed: profile the nucleotide content of intervals in
-      a FASTA file'
-    title: bedtools NucBed 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_nucbed%2F2.30.0
+    title: bedtools MaskFastaBed 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_maskfastabed%2F2.31.1
+  - description: 'bedtools ComplementBed: Extract intervals not represented by an
+      interval file'
+    title: bedtools ComplementBed 2.31.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_complementbed%2F2.31.1%2Bgalaxy0
+  - description: 'bedtools Merge BedGraph files: combines coverage intervals from
+      multiple BEDGRAPH files'
+    title: bedtools Merge BedGraph files 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_unionbedgraph%2F2.31.1
   - description: 'bedtools BED to IGV: create batch script for taking IGV screenshots'
-    title: bedtools BED to IGV 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_bedtoigv%2F2.30.0
+    title: bedtools BED to IGV 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_bedtoigv%2F2.31.1
+  - description: 'bedtools ShuffleBed: randomly redistrubute intervals in a genome'
+    title: bedtools ShuffleBed 2.31.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_shufflebed%2F2.31.1%2Bgalaxy0
+  - description: 'bedtools BAM to BED: converter'
+    title: bedtools BAM to BED 2.31.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_bamtobed%2F2.31.1%2Bgalaxy0
+  - description: 'bedtools BEDPE to BAM: converter'
+    title: bedtools BEDPE to BAM 2.31.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_bedpetobam%2F2.31.1%2Bgalaxy0
+  - description: 'bedtools OverlapBed: computes the amount of overlap from two intervals'
+    title: bedtools OverlapBed 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_overlapbed%2F2.31.1
   - description: 'bedtools ClosestBed: find the closest, potentially non-overlapping
       interval'
-    title: bedtools ClosestBed 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_closestbed%2F2.30.0
-  - description: 'bedtools SubtractBed: remove intervals based on overlaps'
-    title: bedtools SubtractBed 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_subtractbed%2F2.30.0
-  - description: 'bedtools TagBed: tag BAM alignments based on overlaps with interval
-      files'
-    title: bedtools TagBed 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_tagbed%2F2.30.0
-  - description: 'bedtools Genome Coverage: compute the coverage over an entire genome'
-    title: bedtools Genome Coverage 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_genomecoveragebed%2F2.30.0
-  - description: 'bedtools OverlapBed: computes the amount of overlap from two intervals'
-    title: bedtools OverlapBed 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_overlapbed%2F2.30.0
+    title: bedtools ClosestBed 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_closestbed%2F2.31.1
   - description: 'bedtools Multiple Intersect: identifies common intervals among multiple
       interval files'
-    title: bedtools Multiple Intersect 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_multiintersectbed%2F2.30.0
-  - description: 'bedtools BEDPE to BAM: converter'
-    title: bedtools BEDPE to BAM 2.30.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_bedpetobam%2F2.30.0%2Bgalaxy1
-  - description: 'bedtools MakeWindowsBed: make interval windows across a genome'
-    title: bedtools MakeWindowsBed 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_makewindowsbed%2F2.30.0
-  - description: 'bedtools JaccardBed: calculate the distribution of relative distances
-      between two files'
-    title: bedtools JaccardBed 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_jaccard%2F2.30.0
-  - description: 'bedtools LinksBed: create a HTML page of links to UCSC locations'
-    title: bedtools LinksBed 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_links%2F2.30.0
-  - description: 'bedtools Intersect intervals: find overlapping intervals in various
-      ways'
-    title: bedtools Intersect intervals 2.30.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_intersectbed%2F2.30.0%2Bgalaxy1
-  - description: 'bedtools BED12 to BED6: converter'
-    title: bedtools BED12 to BED6 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_bed12tobed6%2F2.30.0
-  - description: 'bedtools BAM to BED: converter'
-    title: bedtools BAM to BED 2.30.0+galaxy2
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_bamtobed%2F2.30.0%2Bgalaxy2
-  - description: 'bedtools FisherBed: calculate Fisher statistic between two feature
-      files'
-    title: bedtools FisherBed 2.30.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_fisher%2F2.30.0%2Bgalaxy1
-  - description: 'bedtools Merge BedGraph files: combines coverage intervals from
-      multiple BEDGRAPH files'
-    title: bedtools Merge BedGraph files 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_unionbedgraph%2F2.30.0
-  - description: 'bedtools ClusterBed: cluster overlapping/nearby intervals'
-    title: bedtools ClusterBed 2.30.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_clusterbed%2F2.30.0
-  - description: 'bedtools FlankBed: create new intervals from the flanks of existing
-      intervals'
-    title: bedtools FlankBed 2.30.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_flankbed%2F2.30.0%2Bgalaxy1
+    title: bedtools Multiple Intersect 2.31.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_multiintersectbed%2F2.31.1
   - description: 'bedtools Convert from BAM to FastQ: '
     title: bedtools Convert from BAM to FastQ 2.27.1
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbedtools%2Fbedtools_bamtofastq%2F2.27.1
@@ -1395,7 +1405,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: Bellerophon
+- biocontainers: ''
   biotools: Bellerophon
   bunya: ''
   description: 'The Bellerophon pipeline, improving de novo transcriptomes and removing
@@ -1439,7 +1449,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: berokka
+- biocontainers: ''
   biotools: berokka
   bunya: ''
   description: Trim, circularise, orient and filter long read bacterial genome assemblies
@@ -1478,12 +1488,12 @@
   edam-outputs: ''
   edam-topics: ''
   galaxy:
-  - description: 'Convert image format: with Bioformats'
-    title: Convert image format 6.7.0+galaxy2
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2Fbfconvert%2Fip_convertimage%2F6.7.0%2Bgalaxy2
   - description: 'Show image info: with Bioformats'
-    title: Show image info 5.7.1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2Fimage_info%2Fip_imageinfo%2F5.7.1
+    title: Show image info 5.7.1+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2Fimage_info%2Fip_imageinfo%2F5.7.1%2Bgalaxy1
+  - description: 'Convert image format: with Bioformats'
+    title: Convert image format 6.7.0+galaxy3
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2Fbfconvert%2Fip_convertimage%2F6.7.0%2Bgalaxy3
   homepage: ''
   id: bftools
   license: ''
@@ -1517,7 +1527,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: bio3d
+- biocontainers: ''
   biotools: bio3d
   bunya: ''
   description: Bio3D is an R package containing utilities for the analysis of protein
@@ -1582,7 +1592,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: biobambam
+- biocontainers: ''
   biotools: biobambam
   bunya: ''
   description: Tools for early stage NGS alignment file processing including fast
@@ -1629,7 +1639,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: biomformat
+- biocontainers: bioconductor-biomformat
   biotools: biomformat
   bunya: ''
   description: This package includes basic tools for reading biom-format files, accessing
@@ -1719,7 +1729,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: biopython
+- biocontainers: ''
   biotools: biopython
   bunya:
   - 1.79-foss-2021a
@@ -1765,7 +1775,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: biotransformer
+- biocontainers: ''
   biotools: biotransformer
   bunya: ''
   description: BioTransformer is a freely available web server that supports accurate,
@@ -1790,8 +1800,8 @@
   - NMR
   galaxy:
   - description: 'BioTransformer: '
-    title: BioTransformer 3.0_20230403+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fbiotransformer%2Fbiotransformer%2F3.0_20230403%2Bgalaxy1
+    title: BioTransformer 3.0.20230403+galaxy3
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fbiotransformer%2Fbiotransformer%2F3.0.20230403%2Bgalaxy3
   homepage: https://biotransformer.ca
   id: biotransformer
   license: LGPL-3.0
@@ -1849,7 +1859,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: blast
+- biocontainers: ''
   biotools: blast
   bunya:
   - 2.11.0-linux_x86_64
@@ -1903,7 +1913,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: blast
+- biocontainers: ''
   biotools: blast
   bunya:
   - 2.11.0-gompi-2021a
@@ -2009,7 +2019,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: blat
+- biocontainers: ''
   biotools: blat
   bunya:
   - 3.7-gcc-11.3.0
@@ -2035,7 +2045,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: blockbuster
+- biocontainers: ''
   biotools: blockbuster
   bunya: ''
   description: detect blocks of overlapping reads using a gaussian-distribution approach
@@ -2114,7 +2124,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: boost
+- biocontainers: ''
   biotools: boost
   bunya:
   - 1.76.0-gcc-10.3.0
@@ -2264,7 +2274,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: bracken
+- biocontainers: ''
   biotools: bracken
   bunya: ''
   description: Statistical method that computes the abundance of species in DNA sequences
@@ -2279,8 +2289,8 @@
   galaxy:
   - description: 'Bracken: to re-estimate abundance at a taxonomic level from kraken
       output'
-    title: Bracken 2.9+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbracken%2Fest_abundance%2F2.9%2Bgalaxy0
+    title: Bracken 3.0+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbracken%2Fest_abundance%2F3.0%2Bgalaxy0
   homepage: https://ccb.jhu.edu/software/bracken/
   id: bracken
   license: GPL-3.0
@@ -2294,7 +2304,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: braker1
+- biocontainers: ''
   biotools: braker1
   bunya:
   - 3.0.3
@@ -2326,7 +2336,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: breseq
+- biocontainers: ''
   biotools: breseq
   bunya: ''
   description: Runs Breseq software on a set of fastq files.
@@ -2423,7 +2433,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: buttery_eel
+- biocontainers: ''
   biotools: buttery_eel
   bunya: ''
   description: Accelerated nanopore basecalling with SLOW5 data format.
@@ -2509,7 +2519,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: bwa-mem2
+- biocontainers: ''
   biotools: bwa-mem2
   bunya: ''
   description: Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces
@@ -2589,7 +2599,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: bx-python
+- biocontainers: ''
   biotools: bx-python
   bunya: ''
   description: Tools for manipulating biological data, particularly multiple sequence
@@ -2651,45 +2661,30 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: C3
-  biotools: C3
+- biocontainers: ''
+  biotools: ''
   bunya: ''
-  description: Consensus Cancer Driver Gene Caller | Next-generation sequencing has
-    allowed identification of millions of somatic mutations in human cancer cells.
-    A key challenge in interpreting cancer genomes is to distinguish drivers of cancer
-    development among available genetic mutations. To address this issue, we present
-    the first web-based application, consensus cancer driver gene caller (C3), to
-    identify the consensus driver genes using six different complementary strategies,
-    i.e., frequency-based, machine learning-based, functional bias-based, clustering-based,
-    statistics model-based, and network-based strategies. This application allows
-    users to specify customized operations when calling driver genes, and provides
-    solid statistical evaluations and interpretable visualizations on the integration
-    results
+  description: ''
   edam-inputs: ''
   edam-operations: ''
   edam-outputs: ''
-  edam-topics:
-  - Genetic variation
-  - Oncology
-  - Sequencing
+  edam-topics: ''
   galaxy:
   - description: 'Copernicus Climate Data Store: for retrieveing climate data'
     title: Copernicus Climate Data Store 0.1.0
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fclimate%2Fc3s%2Fc3s%2F0.1.0
-  homepage: http://drivergene.rwebox.com/c3/index.html
+  homepage: ''
   id: c3s
   license: ''
   name: c3s
   nci-gadi: ''
   nci-if89: ''
   pawsey: ''
-  publications:
-  - title: 'C3: Consensus Cancer Driver Gene Caller'
-    url: https://doi.org/10.1016/J.GPB.2018.10.004
+  publications: ''
   resources:
   - title: .nan
     url: .nan
-- biocontainers: cactus
+- biocontainers: ''
   biotools: cactus
   bunya: ''
   description: Cactus is a reference-free whole-genome multiple alignment program.
@@ -2732,7 +2727,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: camera
+- biocontainers: ''
   biotools: camera
   bunya: ''
   description: Annotation of peaklists generated by xcms, rule based annotation of
@@ -2804,7 +2799,7 @@
   resources:
   - title: Testing & optimisation on Gadi (NCI)
     url: https://github.com/AustralianBioCommons/Canu
-- biocontainers: cap3
+- biocontainers: ''
   biotools: cap3
   bunya: ''
   description: Web-based contig assembly.
@@ -2837,7 +2832,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: cardinal
+- biocontainers: ''
   biotools: cardinal
   bunya: ''
   description: Implements statistical and computational tools for analyzing mass spectrometry
@@ -2861,35 +2856,35 @@
   - Proteomics
   - Data visualisation
   galaxy:
-  - description: 'MSI classification: spatial classification of mass spectrometry
-      imaging data'
-    title: MSI classification 2.10.0.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcardinal_classification%2Fcardinal_classification%2F2.10.0.0
+  - description: 'MSI plot spectra: mass spectrometry imaging mass spectra plots'
+    title: MSI plot spectra 3.4.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcardinal_spectra_plots%2Fcardinal_spectra_plots%2F3.4.3%2Bgalaxy0
+  - description: 'MSI Qualitycontrol: mass spectrometry imaging QC'
+    title: MSI Qualitycontrol 3.4.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcardinal_quality_report%2Fcardinal_quality_report%2F3.4.3%2Bgalaxy0
+  - description: 'MSI preprocessing: mass spectrometry imaging preprocessing'
+    title: MSI preprocessing 3.4.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcardinal_preprocessing%2Fcardinal_preprocessing%2F3.4.3%2Bgalaxy0
+  - description: 'MSI mz images: mass spectrometry imaging m/z heatmaps'
+    title: MSI mz images 3.4.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcardinal_mz_images%2Fcardinal_mz_images%2F3.4.3%2Bgalaxy0
+  - description: 'MSI data exporter: exports imzML and Analyze7.5 to tabular files'
+    title: MSI data exporter 3.4.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcardinal_data_exporter%2Fcardinal_data_exporter%2F3.4.3%2Bgalaxy0
   - description: 'MSI combine: combine several mass spectrometry imaging datasets
       into one'
-    title: MSI combine 2.10.0.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcardinal_combine%2Fcardinal_combine%2F2.10.0.0
-  - description: 'MSI data exporter: exports imzML and Analyze7.5 to tabular files'
-    title: MSI data exporter 2.10.0.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcardinal_data_exporter%2Fcardinal_data_exporter%2F2.10.0.0
+    title: MSI combine 3.4.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcardinal_combine%2Fcardinal_combine%2F3.4.3%2Bgalaxy0
+  - description: 'MSI classification: spatial classification of mass spectrometry
+      imaging data'
+    title: MSI classification 3.4.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcardinal_classification%2Fcardinal_classification%2F3.4.3%2Bgalaxy0
   - description: 'MSI filtering: tool for filtering mass spectrometry imaging data'
-    title: MSI filtering 2.10.0.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcardinal_filtering%2Fcardinal_filtering%2F2.10.0.0
-  - description: 'MSI mz images: mass spectrometry imaging m/z heatmaps'
-    title: MSI mz images 2.10.0.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcardinal_mz_images%2Fcardinal_mz_images%2F2.10.0.0
-  - description: 'MSI preprocessing: mass spectrometry imaging preprocessing'
-    title: MSI preprocessing 2.10.0.1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcardinal_preprocessing%2Fcardinal_preprocessing%2F2.10.0.1
-  - description: 'MSI Qualitycontrol: mass spectrometry imaging QC'
-    title: MSI Qualitycontrol 2.10.0.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcardinal_quality_report%2Fcardinal_quality_report%2F2.10.0.0
+    title: MSI filtering 3.4.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcardinal_filtering%2Fcardinal_filtering%2F3.4.3%2Bgalaxy0
   - description: 'MSI segmentation: mass spectrometry imaging spatial clustering'
-    title: MSI segmentation 2.10.0.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcardinal_segmentations%2Fcardinal_segmentations%2F2.10.0.0
-  - description: 'MSI plot spectra: mass spectrometry imaging mass spectra plots'
-    title: MSI plot spectra 2.10.0.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcardinal_spectra_plots%2Fcardinal_spectra_plots%2F2.10.0.0
+    title: MSI segmentation 3.4.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcardinal_segmentations%2Fcardinal_segmentations%2F3.4.3%2Bgalaxy0
   homepage: http://bioconductor.org/packages/release/bioc/html/Cardinal.html
   id: cardinal
   license: Artistic-2.0
@@ -2903,7 +2898,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: cat_bins
+- biocontainers: ''
   biotools: cat_bins
   bunya: ''
   description: Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines
@@ -2926,8 +2921,8 @@
   - Sequence assembly
   galaxy:
   - description: 'CAT bins: annotate with taxonomic classification'
-    title: CAT bins 5.0.3.1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcat_bins%2Fcat_bins%2F5.0.3.1
+    title: CAT bins 5.2.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcat_bins%2Fcat_bins%2F5.2.3%2Bgalaxy0
   - description: 'CAT summarise: the number of contigs or bins assigned to each taxonomic
       name'
     title: CAT summarise 5.2.3+galaxy0
@@ -2999,7 +2994,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: celseq2
+- biocontainers: ''
   biotools: celseq2
   bunya:
   - 0.5.3
@@ -3027,7 +3022,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: CellProfiler
+- biocontainers: cellprofiler
   biotools: CellProfiler
   bunya: ''
   description: Tool for quantifying data from biological images, particularly in high-throughput
@@ -3150,7 +3145,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: cellxgene
+- biocontainers: ''
   biotools: cellxgene
   bunya: ''
   description: cellxgene (pronounced "cell-by-gene") is an interactive data explorer
@@ -3181,7 +3176,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: checkm
+- biocontainers: ''
   biotools: checkm
   bunya:
   - 1.1.3-foss-2021a
@@ -3218,7 +3213,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: checkm
+- biocontainers: ''
   biotools: checkm
   bunya:
   - '2015_01_16'
@@ -3254,7 +3249,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: chembl
+- biocontainers: ''
   biotools: chembl
   bunya: ''
   description: Database of bioactive compounds, their quantitative properties and
@@ -3299,7 +3294,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: chemfp
+- biocontainers: ''
   biotools: chemfp
   bunya: ''
   description: 'Fast cheminformatics fingerprint search, at your fingertips.
@@ -3352,7 +3347,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: chemicaltoolbox
+- biocontainers: ''
   biotools: chemicaltoolbox
   bunya: ''
   description: ChemicalToolbox is a publicly available web server for performing cheminformatics
@@ -3400,7 +3395,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: chipseeker
+- biocontainers: bioconductor-chipseeker
   biotools: chipseeker
   bunya: ''
   description: This package implements functions to retrieve the nearest genes around
@@ -3447,7 +3442,46 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: chromeister
+- biocontainers: ''
+  biotools: chira
+  bunya: ''
+  description: ChiRA is a tool suite to analyze RNA-RNA interactome experimental data
+    such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.
+  edam-inputs: ''
+  edam-operations: ''
+  edam-outputs: ''
+  edam-topics:
+  - RNA
+  - Molecular interactions, pathways and networks
+  - Functional, regulatory and non-coding RNA
+  galaxy:
+  - description: 'ChiRA qauntify: quantify aligned loci to score the alignments'
+    title: ChiRA qauntify 1.4.30
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fchira_quantify%2Fchira_quantify%2F1.4.30
+  - description: 'ChiRA merge: merge aligned positions'
+    title: ChiRA merge 1.4.30
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fchira_merge%2Fchira_merge%2F1.4.30
+  - description: 'ChiRA extract: extrat the chimeras'
+    title: ChiRA extract 1.4.31
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fchira_extract%2Fchira_extract%2F1.4.31
+  - description: 'ChiRA collapse: deduplicate fastq reads'
+    title: ChiRA collapse 1.4.31
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fchira_collapse%2Fchira_collapse%2F1.4.31
+  - description: 'ChiRA map: map reads to trascriptome'
+    title: ChiRA map 1.4.30
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fchira_map%2Fchira_map%2F1.4.30
+  homepage: https://github.com/pavanvidem/chira
+  id: chira
+  license: GPL-3.0
+  name: ChiRA
+  nci-gadi: ''
+  nci-if89: ''
+  pawsey: ''
+  publications: ''
+  resources:
+  - title: .nan
+    url: .nan
+- biocontainers: ''
   biotools: chromeister
   bunya: ''
   description: An ultra fast, heuristic approach to detect conserved signals in extremely
@@ -3647,7 +3681,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: clinker
+- biocontainers: ''
   biotools: clinker
   bunya: ''
   description: 'Automatic generation of gene cluster comparison figures.
@@ -3807,7 +3841,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: colabfold
+- biocontainers: ''
   biotools: colabfold
   bunya: ''
   description: ColabFold databases are MMseqs2 expandable profile databases to generate
@@ -3930,8 +3964,8 @@
   - Transcription factors and regulatory sites
   galaxy:
   - description: 'CPAT: coding potential assessment'
-    title: CPAT 3.0.5+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcpat%2Fcpat%2F3.0.5%2Bgalaxy0
+    title: CPAT 3.0.5+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcpat%2Fcpat%2F3.0.5%2Bgalaxy1
   homepage: http://lilab.research.bcm.edu/cpat/
   id: cpat
   license: GPL-3.0
@@ -3946,7 +3980,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: Crisflash
+- biocontainers: ''
   biotools: Crisflash
   bunya:
   - 1.2.0        star-ccm+
@@ -4022,7 +4056,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: cuDNN
+- biocontainers: ''
   biotools: cuDNN
   bunya: ''
   description: "The NVIDIA CUDA\xAE Deep Neural Network library (cuDNN) is a GPU-accelerated\
@@ -4118,7 +4152,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: cummerbund
+- biocontainers: bioconductor-cummerbund
   biotools: cummerbund
   bunya: ''
   description: Allows for persistent storage, access, exploration, and manipulation
@@ -4149,7 +4183,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: customprodb
+- biocontainers: ''
   biotools: customprodb
   bunya: ''
   description: Generate customized protein sequence database from RNA-Seq data for
@@ -4215,7 +4249,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: cutadapt
+- biocontainers: ''
   biotools: cutadapt
   bunya:
   - 3.4-gcccore-10.3.0
@@ -4248,8 +4282,8 @@
   - Sequencing
   galaxy:
   - description: 'Cutadapt: Remove adapter sequences from FASTQ/FASTA'
-    title: Cutadapt 4.8+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Flparsons%2Fcutadapt%2Fcutadapt%2F4.8%2Bgalaxy1
+    title: Cutadapt 4.9+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Flparsons%2Fcutadapt%2Fcutadapt%2F4.9%2Bgalaxy1
   homepage: https://pypi.org/project/cutadapt/
   id: cutadapt
   license: MIT
@@ -4267,7 +4301,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: cuteSV
+- biocontainers: ''
   biotools: cuteSV
   bunya: ''
   description: Long Read based Human Genomic Structural Variation Detection with cuteSV
@@ -4310,7 +4344,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: dada2
+- biocontainers: ''
   biotools: dada2
   bunya: ''
   description: This package infers exact sequence variants (SVs) from amplicon data,
@@ -4354,8 +4388,8 @@
     title: 'dada2: filterAndTrim 1.30.0+galaxy0'
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_filterandtrim%2Fdada2_filterAndTrim%2F1.30.0%2Bgalaxy0
   - description: 'dada2: assignTaxonomy and addSpecies: Learn Error rates'
-    title: 'dada2: assignTaxonomy and addSpecies 1.28+galaxy0'
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_assigntaxonomyaddspecies%2Fdada2_assignTaxonomyAddspecies%2F1.28%2Bgalaxy0
+    title: 'dada2: assignTaxonomy and addSpecies 1.30.0+galaxy0'
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_assigntaxonomyaddspecies%2Fdada2_assignTaxonomyAddspecies%2F1.30.0%2Bgalaxy0
   - description: 'dada2: dada: Remove sequencing errors'
     title: 'dada2: dada 1.30.0+galaxy0'
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_dada%2Fdada2_dada%2F1.30.0%2Bgalaxy0
@@ -4635,7 +4669,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: deseq2
+- biocontainers: ''
   biotools: deseq2
   bunya: ''
   description: R/Bioconductor package for differential gene expression analysis based
@@ -4674,7 +4708,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: dexseq
+- biocontainers: bioconductor-dexseq
   biotools: dexseq
   bunya: ''
   description: The package is focused on finding differential exon usage using RNA-seq
@@ -4714,7 +4748,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: dfam
+- biocontainers: ''
   biotools: dfam
   bunya:
   - 3.3--hdfd78af_0
@@ -4747,7 +4781,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: DIA-NN
+- biocontainers: ''
   biotools: DIA-NN
   bunya: ''
   description: 'Neural networks and interference correction enable deep proteome coverage
@@ -4791,7 +4825,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: DIA-Umpire
+- biocontainers: ''
   biotools: DIA-Umpire
   bunya: ''
   description: DIA-Umpire is an open source Java program for computational analysis
@@ -4833,7 +4867,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: diamond
+- biocontainers: ''
   biotools: diamond
   bunya:
   - 2.0.13-gcc-10.3.0
@@ -4876,7 +4910,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: diapasef
+- biocontainers: ''
   biotools: diapasef
   bunya: ''
   description: diaPASEF is an appproch for parallel accumulation-serial fragmentation
@@ -4912,7 +4946,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: diffbind
+- biocontainers: ''
   biotools: diffbind
   bunya: ''
   description: Compute differentially bound sites from multiple ChIP-seq experiments
@@ -4926,8 +4960,8 @@
   - ChIP-seq
   galaxy:
   - description: 'DiffBind: differential binding analysis of ChIP-Seq peak data'
-    title: DiffBind 2.10.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdiffbind%2Fdiffbind%2F2.10.0%2Bgalaxy1
+    title: DiffBind 3.12.0+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdiffbind%2Fdiffbind%2F3.12.0%2Bgalaxy0
   homepage: http://bioconductor.org/packages/release/bioc/html/DiffBind.html
   id: diffbind
   license: Artistic-2.0
@@ -4941,6 +4975,36 @@
   resources:
   - title: .nan
     url: .nan
+- biocontainers: ''
+  biotools: dorado
+  bunya: ''
+  description: Dorado is a high-performance, easy-to-use, open source basecaller for
+    Oxford Nanopore reads.
+  edam-inputs: []
+  edam-operations:
+  - Base-calling
+  - Sequence generation
+  edam-outputs: []
+  edam-topics:
+  - Sequence analysis
+  galaxy:
+  - description: 'Dorado: basecaller for raw Oxford Nanopore data'
+    title: Dorado 0.7.3+6e6c45c+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxy-australia%2Fdorado%2Fdorado%2F0.7.3%2B6e6c45c%2Bgalaxy0
+  - description: 'fast5 to pod5: converter for raw Oxford Nanopore data'
+    title: fast5 to pod5 0.7.3+6e6c45c+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxy-australia%2Fdorado_pod5_convert%2Fdorado_pod5_convert%2F0.7.3%2B6e6c45c%2Bgalaxy0
+  homepage: https://github.com/nanoporetech/dorado
+  id: dorado
+  license: ''
+  name: Dorado
+  nci-gadi: ''
+  nci-if89: ''
+  pawsey: ''
+  publications: ''
+  resources:
+  - title: .nan
+    url: .nan
 - biocontainers: ''
   biotools: ''
   bunya: ''
@@ -4963,7 +5027,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: dropletutils
+- biocontainers: ''
   biotools: dropletutils
   bunya: ''
   description: Provides a number of utility functions for handling single-cell (RNA-seq)
@@ -5039,7 +5103,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: eagleimp
+- biocontainers: ''
   biotools: eagleimp
   bunya:
   - '1.10'
@@ -5071,7 +5135,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: easybuild
+- biocontainers: ''
   biotools: easybuild
   bunya:
   - 4.8.0
@@ -5096,7 +5160,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: edger
+- biocontainers: bioconductor-edger
   biotools: edger
   bunya: ''
   description: Differential expression analysis of RNA-seq expression profiles with
@@ -5148,7 +5212,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: edger
+- biocontainers: ''
   biotools: edger
   bunya: ''
   description: Differential expression analysis of RNA-seq expression profiles with
@@ -5201,7 +5265,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: edirect
+- biocontainers: ''
   biotools: edirect
   bunya:
   - '16.2'
@@ -5227,7 +5291,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: eggnog-mapper
+- biocontainers: ''
   biotools: eggnog-mapper
   bunya: ''
   description: 'For fast functional annotation of novel sequences. It uses precomputed
@@ -5276,7 +5340,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: egsea
+- biocontainers: bioconductor-egsea
   biotools: egsea
   bunya: ''
   description: This package implements the Ensemble of Gene Set Enrichment Analyses
@@ -5311,7 +5375,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: elastix
+- biocontainers: ''
   biotools: elastix
   bunya: ''
   description: 'Evaluation of an Open Source Registration Package for Automatic Contour
@@ -5718,7 +5782,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ena
+- biocontainers: ''
   biotools: ena
   bunya: ''
   description: A globally comprehensive data resource for nucleotide sequence, spanning
@@ -5762,7 +5826,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: EncyclopeDIA
+- biocontainers: ''
   biotools: EncyclopeDIA
   bunya: ''
   description: EncyclopeDIA is library search engine comprised of several algorithms
@@ -5782,22 +5846,22 @@
   - Proteomics
   - Proteomics experiment
   galaxy:
+  - description: 'Walnut: PeCAn-based Peptide Detection Directly from Data-Independent
+      Acquisition (DIA) MS/MS Data'
+    title: Walnut 1.12.34+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fencyclopedia_walnut%2Fencyclopedia_walnut%2F1.12.34%2Bgalaxy0
   - description: 'SearchToLib: Build a Chromatogram Library from Data-Independent
       Acquisition (DIA) MS/MS Data'
     title: SearchToLib 1.12.34+galaxy0
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fencyclopedia_searchtolib%2Fencyclopedia_searchtolib%2F1.12.34%2Bgalaxy0
   - description: 'EncyclopeDIA: Library Searching Directly from Data-Independent Acquisition
       (DIA) MS/MS Data'
-    title: EncyclopeDIA 1.2.2+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fencyclopedia_encyclopedia%2Fencyclopedia_encyclopedia%2F1.2.2%2Bgalaxy0
+    title: EncyclopeDIA 1.12.34+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fencyclopedia_encyclopedia%2Fencyclopedia_encyclopedia%2F1.12.34%2Bgalaxy0
   - description: 'EncyclopeDIA Quantify: samples from Data-Independent Acquisition
       (DIA) MS/MS Data'
     title: EncyclopeDIA Quantify 1.12.34+galaxy0
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fencyclopedia_quantify%2Fencyclopedia_quantify%2F1.12.34%2Bgalaxy0
-  - description: 'Walnut: PeCAn-based Peptide Detection Directly from Data-Independent
-      Acquisition (DIA) MS/MS Data'
-    title: Walnut 1.2.2+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fencyclopedia_walnut%2Fencyclopedia_walnut%2F1.2.2%2Bgalaxy0
   homepage: https://bitbucket.org/searleb/encyclopedia/
   id: encyclopedia
   license: Apache-2.0
@@ -5854,7 +5918,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ete
+- biocontainers: ''
   biotools: ete
   bunya: ''
   description: The Environment for Tree Exploration (ETE) is a computational framework
@@ -5909,7 +5973,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: eupathdb
+- biocontainers: ''
   biotools: eupathdb
   bunya: ''
   description: Integrated database covering the eukaryotic pathogens of the genera
@@ -5946,7 +6010,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: exabayes
+- biocontainers: ''
   biotools: exabayes
   bunya: ''
   description: ExaBayes is a software package for Bayesian phylogenetic tree inference.
@@ -5972,7 +6036,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ExaML
+- biocontainers: ''
   biotools: ExaML
   bunya: ''
   description: Tool for phylogenomic analyses on supercomputers.
@@ -6057,7 +6121,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: export2graphlan
+- biocontainers: ''
   biotools: export2graphlan
   bunya: ''
   description: export2graphlan is a conversion software tool for producing both annotation
@@ -6089,7 +6153,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: express
+- biocontainers: ''
   biotools: express
   bunya: ''
   description: Streaming tool for quantifying the abundances of a set of target sequences
@@ -6140,7 +6204,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: f5c
+- biocontainers: ''
   biotools: f5c
   bunya:
   - 1.1--h0326b38_1
@@ -6178,7 +6242,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: falcon
+- biocontainers: ''
   biotools: falcon
   bunya:
   - 0.0.8--hdfd78af_1
@@ -6203,7 +6267,7 @@
   resources:
   - title: Install, optimisation and testing at Pawsey
     url: https://github.com/AustralianBioCommons/falcon
-- biocontainers: compute_sequence_length
+- biocontainers: ''
   biotools: compute_sequence_length
   bunya: ''
   description: Add length of sequence to fasta header.
@@ -6262,7 +6326,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: fastani
+- biocontainers: ''
   biotools: fastani
   bunya:
   - 1.33-gcc-10.3.0
@@ -6290,7 +6354,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: fastool
+- biocontainers: ''
   biotools: fastool
   bunya:
   - 0.1.4--h7132678_6
@@ -6331,8 +6395,8 @@
   - Probes and primers
   galaxy:
   - description: 'fastp: fast all-in-one preprocessing for FASTQ files'
-    title: fastp 0.23.4+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffastp%2Ffastp%2F0.23.4%2Bgalaxy0
+    title: fastp 0.23.4+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffastp%2Ffastp%2F0.23.4%2Bgalaxy1
   homepage: https://github.com/OpenGene/fastp
   id: fastp
   license: MIT
@@ -6379,8 +6443,8 @@
   - Sequence analysis
   galaxy:
   - description: 'FastQC: Read Quality reports'
-    title: FastQC 0.74+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastqc%2Ffastqc%2F0.74%2Bgalaxy0
+    title: FastQC 0.74+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastqc%2Ffastqc%2F0.74%2Bgalaxy1
   homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
   id: fastqc
   license: GPL-3.0
@@ -6397,7 +6461,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: fastqe
+- biocontainers: ''
   biotools: fastqe
   bunya: ''
   description: Compute quality stats for FASTQ files and print those stats as emoji...
@@ -6411,8 +6475,8 @@
   - Sequencing
   galaxy:
   - description: "FASTQE: visualize fastq files with emoji's \U0001F9EC\U0001F60E"
-    title: FASTQE 0.2.6+galaxy2
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffastqe%2Ffastqe%2F0.2.6%2Bgalaxy2
+    title: FASTQE 0.3.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffastqe%2Ffastqe%2F0.3.1%2Bgalaxy0
   homepage: https://fastqe.com/
   id: fastqe
   license: ''
@@ -6511,7 +6575,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: fastx-toolkit
+- biocontainers: ''
   biotools: fastx-toolkit
   bunya: ''
   description: Collection of command line tools for Short-Reads FASTA/FASTQ files
@@ -6552,7 +6616,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: feelnc
+- biocontainers: ''
   biotools: feelnc
   bunya: ''
   description: A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.
@@ -6602,7 +6666,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: featurecounts
+- biocontainers: ''
   biotools: featurecounts
   bunya: ''
   description: featureCounts is a very efficient read quantifier. It can be used to
@@ -6650,7 +6714,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: fgenesh
+- biocontainers: ''
   biotools: fgenesh
   bunya: ''
   description: HMM-based gene structure prediction (multiple genes, both chains);
@@ -6678,7 +6742,7 @@
   resources:
   - title: Fgenesh++
     url: https://support.pawsey.org.au/documentation/pages/viewpage.action?pageId=68818716
-- biocontainers: fgsea
+- biocontainers: ''
   biotools: fgsea
   bunya: ''
   description: The package implements an algorithm for fast gene set enrichment analysis.
@@ -6731,7 +6795,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: filtlong
+- biocontainers: ''
   biotools: filtlong
   bunya: ''
   description: Filtlong is a tool for filtering long reads by quality. It can take
@@ -6759,7 +6823,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: flashlfq
+- biocontainers: ''
   biotools: flashlfq
   bunya: ''
   description: FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry
@@ -6818,7 +6882,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: Flye
+- biocontainers: ''
   biotools: Flye
   bunya:
   - 2.9-gcc-10.3.0
@@ -6841,8 +6905,8 @@
   - Genomics
   galaxy:
   - description: 'Flye: de novo assembler for single molecule sequencing reads'
-    title: Flye 2.9.3+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fflye%2Fflye%2F2.9.3%2Bgalaxy0
+    title: Flye 2.9.4+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fflye%2Fflye%2F2.9.4%2Bgalaxy0
   homepage: https://github.com/fenderglass/Flye
   id: flye
   license: ''
@@ -6864,7 +6928,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: flymine
+- biocontainers: ''
   biotools: flymine
   bunya: ''
   description: An integrated database for Drosophila and Anopheles genomics.
@@ -6909,7 +6973,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: foldseek
+- biocontainers: ''
   biotools: foldseek
   bunya: ''
   description: Foldseek enables fast and sensitive comparisons of large structure
@@ -6944,7 +7008,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: fpocket
+- biocontainers: ''
   biotools: fpocket
   bunya: ''
   description: Web server which detects small molecule pockets by relying on the geometric
@@ -6985,7 +7049,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: fraggenescan
+- biocontainers: ''
   biotools: fraggenescan
   bunya: ''
   description: Application for finding (fragmented) genes in short reads
@@ -7086,7 +7150,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: funannotate
+- biocontainers: ''
   biotools: funannotate
   bunya: ''
   description: funannotate is a pipeline for genome annotation (built specifically
@@ -7098,21 +7162,21 @@
   edam-topics:
   - Genomics
   galaxy:
+  - description: 'Funannotate predict annotation: '
+    title: Funannotate predict annotation 1.8.15+galaxy5
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffunannotate_predict%2Ffunannotate_predict%2F1.8.15%2Bgalaxy5
+  - description: 'Sort assembly: '
+    title: Sort assembly 1.8.15+galaxy5
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffunannotate_sort%2Ffunannotate_sort%2F1.8.15%2Bgalaxy5
+  - description: 'Funannotate assembly clean: '
+    title: Funannotate assembly clean 1.8.15+galaxy5
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffunannotate_clean%2Ffunannotate_clean%2F1.8.15%2Bgalaxy5
   - description: 'Funannotate functional: annotation'
     title: Funannotate functional 1.8.15+galaxy5
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffunannotate_annotate%2Ffunannotate_annotate%2F1.8.15%2Bgalaxy5
-  - description: 'Funannotate assembly clean: '
-    title: Funannotate assembly clean 1.8.15+galaxy4
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffunannotate_clean%2Ffunannotate_clean%2F1.8.15%2Bgalaxy4
   - description: 'Funannotate compare: annotations'
     title: Funannotate compare 1.8.15+galaxy4
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffunannotate_compare%2Ffunannotate_compare%2F1.8.15%2Bgalaxy4
-  - description: 'Funannotate predict annotation: '
-    title: Funannotate predict annotation 1.8.15+galaxy4
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffunannotate_predict%2Ffunannotate_predict%2F1.8.15%2Bgalaxy4
-  - description: 'Sort assembly: '
-    title: Sort assembly 1.8.15+galaxy4
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffunannotate_sort%2Ffunannotate_sort%2F1.8.15%2Bgalaxy4
   homepage: https://github.com/nextgenusfs/funannotate
   id: funannotate
   license: BSD-2-Clause
@@ -7124,7 +7188,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: gaeval
+- biocontainers: ''
   biotools: gaeval
   bunya: ''
   description: Gene Annotation EVAluation.
@@ -7172,6 +7236,9 @@
   edam-outputs: ''
   edam-topics: ''
   galaxy:
+  - description: 'Split by group: '
+    title: Split by group 0.6
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsplit_file_on_column%2Ftp_split_on_column%2F0.6
   - description: 'Split file: to dataset collection'
     title: Split file 0.5.2
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsplit_file_to_collection%2Fsplit_file_to_collection%2F0.5.2
@@ -7290,190 +7357,190 @@
   - description: 'LAV to BED: Converts a LAV formatted file to BED format'
     title: LAV to BED 1.0.0
     url: https://usegalaxy.org.au/root?tool_id=lav_to_bed1
-  - description: 'Convert plink pbed to ld reduced format: '
-    title: Convert plink pbed to ld reduced format 0.02
-    url: https://usegalaxy.org.au/root?tool_id=pbed2ldindepconvert
-  - description: 'Convert Biom datasets: '
-    title: Convert Biom datasets 2.1.5
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_biom
+  - description: 'Convert SAM to BAM without sorting: '
+    title: Convert SAM to BAM without sorting 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_unsorted_bam
+  - description: 'Convert FASTQ files to seek locations: '
+    title: Convert FASTQ files to seek locations 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fastq_to_fqtoc0
+  - description: 'Convert Wiggle to BigWig: '
+    title: Convert Wiggle to BigWig 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wig_to_bigwig
+  - description: 'Convert GRO to PDB: '
+    title: Convert GRO to PDB 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Gro_to_Pdb_0
+  - description: 'Convert uncompressed file to compressed: '
+    title: Convert uncompressed file to compressed 1.16+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_uncompressed_to_gz
+  - description: 'Convert Interval to BGZIP: '
+    title: Convert Interval to BGZIP 1.0.3
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bgzip_0
+  - description: 'Convert BAM to coordinate-sorted BAM: '
+    title: Convert BAM to coordinate-sorted BAM 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam
+  - description: 'Convert BAM to BigWig: '
+    title: Convert BAM to BigWig 1.0.2
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_bigwig_0
   - description: 'OpenBabel converter for molecular formats: '
     title: OpenBabel converter for molecular formats 2.4.1
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_molecules
-  - description: 'Convert BedGraph to BigWig: '
-    title: Convert BedGraph to BigWig 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bedgraph_to_bigwig
+  - description: 'Convert Picard Interval List to BED6: converter'
+    title: Convert Picard Interval List to BED6 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_picard_interval_list_to_bed6
+  - description: 'Convert tabular to CSV: '
+    title: Convert tabular to CSV 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=tabular_to_csv
+  - description: 'Convert compressed file to uncompressed.: '
+    title: Convert compressed file to uncompressed. 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bz2_to_uncompressed
+  - description: 'Convert Genomic Intervals To Strict BED12: '
+    title: Convert Genomic Intervals To Strict BED12 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed12_0
+  - description: 'Convert MAF to Genomic Intervals: '
+    title: Convert MAF to Genomic Intervals 1.0.3
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_interval_0
+  - description: 'Convert XTC, DCD, and TRR: '
+    title: Convert XTC, DCD, and TRR 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mdconvert
+  - description: 'Convert lped to plink pbed: '
+    title: Convert lped to plink pbed 0.02
+    url: https://usegalaxy.org.au/root?tool_id=lped2pbedconvert
+  - description: 'Convert BED, GFF, or VCF to BigWig: '
+    title: Convert BED, GFF, or VCF to BigWig 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0
+  - description: 'Convert CML to SMILES: '
+    title: Convert CML to SMILES 2.4.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cml_to_smiles
+  - description: 'Convert compressed file to uncompressed.: '
+    title: Convert compressed file to uncompressed. 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gz_to_uncompressed
+  - description: 'Convert FASTA to Tabular: '
+    title: Convert FASTA to Tabular 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular
   - description: 'Convert Interval to tabix: '
     title: Convert Interval to tabix 1.0.2
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_tabix_0
-  - description: 'Convert Genomic Intervals To Strict BED: '
-    title: Convert Genomic Intervals To Strict BED 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0
-  - description: 'Convert CRAM to BAM: '
-    title: Convert CRAM to BAM 1.0.2
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cram_to_bam_0
+  - description: 'Convert Len file to Linecount: '
+    title: Convert Len file to Linecount 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_len_to_linecount
+  - description: 'Convert MOL2 to MOL: '
+    title: Convert MOL2 to MOL 2.4.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mol2_to_mol
   - description: 'Convert SMILES to MOL: '
     title: Convert SMILES to MOL 2.4.1
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_SMILES_to_MOL
+  - description: 'Convert GFF to Interval Index: '
+    title: Convert GFF to Interval Index 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_interval_index_0
+  - description: 'Convert InChI to MOL: '
+    title: Convert InChI to MOL 2.4.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_inchi_to_mol
   - description: 'Convert BigWig to Wiggle: Convert bigWig to wig'
     title: Convert BigWig to Wiggle 377+galaxy0
     url: https://usegalaxy.org.au/root?tool_id=bigwigtowig
+  - description: 'Convert compressed and uncompressed BCF files: '
+    title: Convert compressed and uncompressed BCF files 0.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf
+  - description: 'Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence
+      taxonomy file to a 2 column mothur taxonomy_outline format'
+    title: Convert Ref taxonomy to Seq Taxonomy 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_ref_to_seq_taxomony
+  - description: 'Convert tar to directory: '
+    title: Convert tar to directory 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_tar_to_directory
+  - description: 'Convert Genomic Intervals To BED: '
+    title: Convert Genomic Intervals To BED 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed_0
+  - description: 'Convert SAM to BigWig: '
+    title: Convert SAM to BigWig 1.0.3
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_bigwig_0
+  - description: 'Convert BAM to queryname-sorted BAM: '
+    title: Convert BAM to queryname-sorted BAM 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_qname_sorted_bam
   - description: 'Convert FASTA to Bowtie base space Index: '
     title: Convert FASTA to Bowtie base space Index 1.3.1
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_base_index
-  - description: 'Convert FASTQ files to seek locations: '
-    title: Convert FASTQ files to seek locations 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fastq_to_fqtoc0
+  - description: 'Convert plink pbed to ld reduced format: '
+    title: Convert plink pbed to ld reduced format 0.02
+    url: https://usegalaxy.org.au/root?tool_id=pbed2ldindepconvert
   - description: 'Convert FASTA to fai file: '
     title: Convert FASTA to fai file 1.0.1
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_fai
-  - description: 'Convert Genomic Intervals To Coverage: '
-    title: Convert Genomic Intervals To Coverage 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bigwig_0
-  - description: 'Convert PDB to GRO: '
-    title: Convert PDB to GRO 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Pdb_to_Gro_0
-  - description: 'Convert BAM to queryname-sorted BAM: '
-    title: Convert BAM to queryname-sorted BAM 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_qname_sorted_bam
-  - description: 'Convert FASTA to Tabular: '
-    title: Convert FASTA to Tabular 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular
-  - description: 'Convert CML to SMILES: '
-    title: Convert CML to SMILES 2.4.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cml_to_smiles
-  - description: 'Convert Bam to Bai: '
-    title: Convert Bam to Bai 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Bam_Bai_0
-  - description: 'Convert tabular to CSV: '
-    title: Convert tabular to CSV 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=tabular_to_csv
-  - description: 'Convert lped to plink pbed: '
-    title: Convert lped to plink pbed 0.02
-    url: https://usegalaxy.org.au/root?tool_id=lped2pbedconvert
-  - description: 'Convert BED to Feature Location Index: '
-    title: Convert BED to Feature Location Index 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_fli_0
-  - description: 'Convert GFF to Interval Index: '
-    title: Convert GFF to Interval Index 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_interval_index_0
-  - description: 'Convert GFF to Feature Location Index: '
-    title: Convert GFF to Feature Location Index 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_fli_0
-  - description: 'Convert Interval to BGZIP: '
-    title: Convert Interval to BGZIP 1.0.3
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bgzip_0
-  - description: 'Convert MOL2 to MOL: '
-    title: Convert MOL2 to MOL 2.4.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mol2_to_mol
-  - description: 'Convert Genomic Intervals To Strict BED12: '
-    title: Convert Genomic Intervals To Strict BED12 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed12_0
-  - description: 'Convert MAF to Genomic Intervals: '
-    title: Convert MAF to Genomic Intervals 1.0.3
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_interval_0
-  - description: 'Convert BAM to coordinate-sorted BAM: '
-    title: Convert BAM to coordinate-sorted BAM 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam
-  - description: 'Convert InChI to MOL: '
-    title: Convert InChI to MOL 2.4.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_inchi_to_mol
-  - description: 'Convert FASTA to len file: '
-    title: Convert FASTA to len file 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_len
-  - description: 'Convert SAM to BAM without sorting: '
-    title: Convert SAM to BAM without sorting 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_unsorted_bam
-  - description: 'Convert compressed file to uncompressed.: '
-    title: Convert compressed file to uncompressed. 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bz2_to_uncompressed
-  - description: 'Convert lped to fped: '
-    title: Convert lped to fped 0.02
-    url: https://usegalaxy.org.au/root?tool_id=lped2fpedconvert
+  - description: 'Convert BGZ VCF to tabix: '
+    title: Convert BGZ VCF to tabix 1.0.2
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0
   - description: 'Convert neostore.zip files to neostore: '
     title: Convert neostore.zip files to neostore 1.0.0
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_neostorezip_to_neostore
-  - description: 'Convert BED, GFF, or VCF to BigWig: '
-    title: Convert BED, GFF, or VCF to BigWig 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0
-  - description: 'Convert uncompressed file to compressed: '
-    title: Convert uncompressed file to compressed 1.16+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_uncompressed_to_gz
-  - description: 'Convert GFF to BED: '
-    title: Convert GFF to BED 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_bed_0
   - description: 'Convert plink pbed to linkage lped: '
     title: Convert plink pbed to linkage lped 0.02
     url: https://usegalaxy.org.au/root?tool_id=pbed2lpedconvert
-  - description: 'Convert XTC, DCD, and TRR: '
-    title: Convert XTC, DCD, and TRR 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mdconvert
-  - description: 'Convert BAM to BigWig: '
-    title: Convert BAM to BigWig 1.0.2
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_bigwig_0
-  - description: 'Convert Genomic Intervals To Strict BED6: '
-    title: Convert Genomic Intervals To Strict BED6 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed6_0
-  - description: 'Convert BGZ VCF to tabix: '
-    title: Convert BGZ VCF to tabix 1.0.2
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0
-  - description: 'Convert CSV to tabular: '
-    title: Convert CSV to tabular 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=csv_to_tabular
+  - description: 'Convert BedGraph to BigWig: '
+    title: Convert BedGraph to BigWig 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bedgraph_to_bigwig
+  - description: 'SMILES to SMILES: '
+    title: SMILES to SMILES 2.4.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_smiles_to_smiles
   - description: 'Convert Wiggle to Interval: '
     title: Convert Wiggle to Interval 1.0.1
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wiggle_to_interval_0
-  - description: 'Convert Parquet to csv: '
-    title: Convert Parquet to csv 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_parquet_to_csv
-  - description: 'Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence
-      taxonomy file to a 2 column mothur taxonomy_outline format'
-    title: Convert Ref taxonomy to Seq Taxonomy 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_ref_to_seq_taxomony
-  - description: 'Convert FASTA to 2bit: '
-    title: Convert FASTA to 2bit 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_2bit
-  - description: 'Convert tar to directory: '
-    title: Convert tar to directory 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_tar_to_directory
-  - description: 'Convert SAM to BigWig: '
-    title: Convert SAM to BigWig 1.0.3
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_bigwig_0
-  - description: 'Convert GRO to PDB: '
-    title: Convert GRO to PDB 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Gro_to_Pdb_0
-  - description: 'Convert compressed file to uncompressed.: '
-    title: Convert compressed file to uncompressed. 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gz_to_uncompressed
-  - description: 'Convert tabular to dbnsfp: '
-    title: Convert tabular to dbnsfp 1.0.2
-    url: https://usegalaxy.org.au/root?tool_id=tabular_to_dbnsfp
-  - description: 'Convert Len file to Linecount: '
-    title: Convert Len file to Linecount 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_len_to_linecount
-  - description: 'Convert Genomic Intervals To BED: '
-    title: Convert Genomic Intervals To BED 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed_0
-  - description: 'Convert Wiggle to BigWig: '
-    title: Convert Wiggle to BigWig 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wig_to_bigwig
-  - description: 'Convert Picard Interval List to BED6: converter'
-    title: Convert Picard Interval List to BED6 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_picard_interval_list_to_bed6
   - description: 'Convert MAF to Fasta: '
     title: Convert MAF to Fasta 1.0.2
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_fasta_0
-  - description: 'Convert compressed and uncompressed BCF files: '
-    title: Convert compressed and uncompressed BCF files 0.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf
   - description: 'Convert FASTA to Bowtie color space Index: '
     title: Convert FASTA to Bowtie color space Index 1.2.3
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_color_index
+  - description: 'Convert Genomic Intervals To Strict BED6: '
+    title: Convert Genomic Intervals To Strict BED6 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed6_0
+  - description: 'Convert Genomic Intervals To Coverage: '
+    title: Convert Genomic Intervals To Coverage 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bigwig_0
+  - description: 'Convert GFF to Feature Location Index: '
+    title: Convert GFF to Feature Location Index 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_fli_0
+  - description: 'Convert PDB to GRO: '
+    title: Convert PDB to GRO 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Pdb_to_Gro_0
+  - description: 'Convert CRAM to BAM: '
+    title: Convert CRAM to BAM 1.0.2
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cram_to_bam_0
+  - description: 'Convert FASTA to 2bit: '
+    title: Convert FASTA to 2bit 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_2bit
+  - description: 'Convert BED to Feature Location Index: '
+    title: Convert BED to Feature Location Index 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_fli_0
+  - description: 'Convert Biom datasets: '
+    title: Convert Biom datasets 2.1.5
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_biom
+  - description: 'Convert Bam to Bai: '
+    title: Convert Bam to Bai 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Bam_Bai_0
+  - description: 'Convert CSV to tabular: '
+    title: Convert CSV to tabular 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=csv_to_tabular
+  - description: 'Convert tabular to dbnsfp: '
+    title: Convert tabular to dbnsfp 1.0.2
+    url: https://usegalaxy.org.au/root?tool_id=tabular_to_dbnsfp
+  - description: 'Convert Parquet to csv: '
+    title: Convert Parquet to csv 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_parquet_to_csv
+  - description: 'Convert GFF to BED: '
+    title: Convert GFF to BED 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_bed_0
+  - description: 'Convert lped to fped: '
+    title: Convert lped to fped 0.02
+    url: https://usegalaxy.org.au/root?tool_id=lped2fpedconvert
   - description: 'Convert BED to GFF: '
     title: Convert BED to GFF 2.0.1
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_gff_0
-  - description: 'SMILES to SMILES: '
-    title: SMILES to SMILES 2.4.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_smiles_to_smiles
+  - description: 'Convert FASTA to len file: '
+    title: Convert FASTA to len file 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_len
+  - description: 'Convert Genomic Intervals To Strict BED: '
+    title: Convert Genomic Intervals To Strict BED 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0
   homepage: ''
   id: Galaxy CONVERTER
   license: ''
@@ -7494,6 +7561,9 @@
   edam-outputs: ''
   edam-topics: ''
   galaxy:
+  - description: 'EGA Download Client: '
+    title: EGA Download Client 5.0.2+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fega_download_client%2Fpyega3%2F5.0.2%2Bgalaxy0
   - description: 'UCSC Main: table browser'
     title: UCSC Main 1.0.0
     url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=ucsc_table_direct1
@@ -7545,15 +7615,15 @@
   edam-outputs: ''
   edam-topics: ''
   galaxy:
+  - description: 'Sub-sample sequences files: e.g. to reduce coverage'
+    title: Sub-sample sequences files 0.2.6
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fpeterjc%2Fsample_seqs%2Fsample_seqs%2F0.2.6
   - description: 'Filter sequences by ID: from a tabular file'
     title: Filter sequences by ID 0.2.9
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fpeterjc%2Fseq_filter_by_id%2Fseq_filter_by_id%2F0.2.9
   - description: 'Filter FASTA: on the headers and/or the sequences'
     title: Filter FASTA 2.3
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Ffilter_by_fasta_ids%2Ffilter_by_fasta_ids%2F2.3
-  - description: 'Sub-sample sequences files: e.g. to reduce coverage'
-    title: Sub-sample sequences files 0.2.5
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fpeterjc%2Fsample_seqs%2Fsample_seqs%2F0.2.5
   - description: 'Filter: data on any column using simple expressions'
     title: Filter 1.1.1
     url: https://usegalaxy.org.au/root?tool_id=Filter1
@@ -7595,6 +7665,10 @@
   edam-outputs: ''
   edam-topics: ''
   galaxy:
+  - description: 'Plot confusion matrix, precision, recall and ROC and AUC curves:
+      of tabular data'
+    title: Plot confusion matrix, precision, recall and ROC and AUC curves 0.4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fplotly_ml_performance_plots%2Fplotly_ml_performance_plots%2F0.4
   - description: 'Volcano Plot: create a volcano plot'
     title: Volcano Plot 0.0.6
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvolcanoplot%2Fvolcanoplot%2F0.0.6
@@ -7604,10 +7678,6 @@
   - description: 'Histogram: of a numeric column'
     title: Histogram 1.0.4
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fhistogram%2Fhistogram_rpy%2F1.0.4
-  - description: 'Plot confusion matrix, precision, recall and ROC and AUC curves:
-      of tabular data'
-    title: Plot confusion matrix, precision, recall and ROC and AUC curves 0.3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fplotly_ml_performance_plots%2Fplotly_ml_performance_plots%2F0.3
   - description: 'Parallel Coordinates Plot: of tabular data'
     title: Parallel Coordinates Plot 0.2
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fplotly_parallel_coordinates_plot%2Fplotly_parallel_coordinates_plot%2F0.2
@@ -7768,6 +7838,12 @@
   edam-outputs: ''
   edam-topics: ''
   galaxy:
+  - description: 'Add input name as column: to an existing tabular file'
+    title: Add input name as column 0.2.0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fmvdbeek%2Fadd_input_name_as_column%2FaddName%2F0.2.0
+  - description: 'SQLite to tabular: for SQL query'
+    title: SQLite to tabular 3.2.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsqlite_to_tabular%2Fsqlite_to_tabular%2F3.2.1
   - description: 'Filter Tabular: '
     title: Filter Tabular 3.3.1
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffilter_tabular%2Ffilter_tabular%2F3.3.1
@@ -7813,9 +7889,6 @@
   - description: 'Replace column: by values which are defined in a convert file'
     title: Replace column 0.2
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Freplace_column_by_key_value_file%2Freplace_column_with_key_value_file%2F0.2
-  - description: 'SQLite to tabular: for SQL query'
-    title: SQLite to tabular 3.2.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsqlite_to_tabular%2Fsqlite_to_tabular%2F3.2.0
   - description: 'Table Compute: computes operations on table data'
     title: Table Compute 1.2.4+galaxy0
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftable_compute%2Ftable_compute%2F1.2.4%2Bgalaxy0
@@ -8056,7 +8129,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: gblocks
+- biocontainers: ''
   biotools: gblocks
   bunya: ''
   description: Cleaning aligned sequences.
@@ -8129,7 +8202,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: gecko
+- biocontainers: ''
   biotools: gecko
   bunya: ''
   description: Software aimed at pairwise sequence comparison generating high quality
@@ -8167,7 +8240,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: gemini
+- biocontainers: ''
   biotools: gemini
   bunya: ''
   description: GEMINI (GEnome MINIng) is a flexible framework for exploring genetic
@@ -8276,7 +8349,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: gemoma
+- biocontainers: ''
   biotools: gemoma
   bunya: ''
   description: Gene Model Mapper is a homology-based gene prediction program. GeMoMa
@@ -8308,7 +8381,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: gene.iobio
+- biocontainers: ''
   biotools: gene.iobio
   bunya: ''
   description: 'An interactive web tool for versatile, clinically-driven variant interrogation
@@ -8417,7 +8490,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: GenomeScope_2.0
+- biocontainers: ''
   biotools: GenomeScope_2.0
   bunya: ''
   description: Reference-free profiling of polyploid genomes | We have developed GenomeScope
@@ -8436,8 +8509,8 @@
   - Mapping
   galaxy:
   - description: 'GenomeScope: reference-free genome profiling'
-    title: GenomeScope 2.0+galaxy2
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgenomescope%2Fgenomescope%2F2.0%2Bgalaxy2
+    title: GenomeScope 2.0.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgenomescope%2Fgenomescope%2F2.0.1%2Bgalaxy0
   homepage: https://github.com/tbenavi1/genomescope2.0
   id: genomescope
   license: Apache-2.0
@@ -8526,7 +8599,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: getorganelle
+- biocontainers: ''
   biotools: getorganelle
   bunya: ''
   description: 'A fast and versatile toolkit for accurate de novo assembly of organelle
@@ -8593,7 +8666,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: gfastats
+- biocontainers: ''
   biotools: gfastats
   bunya: ''
   description: gfastats is a single fast and exhaustive tool for summary statistics
@@ -8667,7 +8740,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: gffcompare
+- biocontainers: ''
   biotools: gffcompare
   bunya:
   - 0.12.2-gcc-10.3.0
@@ -8718,7 +8791,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: gffread
+- biocontainers: ''
   biotools: gffread
   bunya:
   - 0.12.7-gcccore-10.3.0
@@ -8746,7 +8819,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ggplot2
+- biocontainers: ''
   biotools: ggplot2
   bunya: ''
   description: Plotting system for R, based on the grammar of graphics.
@@ -8883,7 +8956,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: parallel
+- biocontainers: ''
   biotools: parallel
   bunya:
   - 20210622-gcccore-10.3.0
@@ -8914,7 +8987,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: gsl
+- biocontainers: ''
   biotools: gsl
   bunya:
   - 2.7-gcc-10.3.0
@@ -8938,7 +9011,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: goenrichment
+- biocontainers: ''
   biotools: goenrichment
   bunya: ''
   description: "GOEnrichment is a tool for performing GO enrichment analysis of gene\
@@ -8987,7 +9060,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: goseq
+- biocontainers: bioconductor-goseq
   biotools: goseq
   bunya: ''
   description: Detect Gene Ontology and/or other user defined categories which are
@@ -9038,7 +9111,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: graphlan
+- biocontainers: ''
   biotools: graphlan
   bunya: ''
   description: GraPhlAn is a software tool for producing high-quality circular representations
@@ -9078,7 +9151,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: gromacs
+- biocontainers: ''
   biotools: gromacs
   bunya:
   - 2021.3-foss-2021a
@@ -9185,7 +9258,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: GTDB-Tk
+- biocontainers: ''
   biotools: GTDB-Tk
   bunya:
   - 2.0.0-foss-2021a
@@ -9280,7 +9353,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: gubbins
+- biocontainers: ''
   biotools: gubbins
   bunya: ''
   description: Gubbins is a tool for rapid phylogenetic analysis of large samples
@@ -9337,7 +9410,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: hapcut2
+- biocontainers: ''
   biotools: hapcut2
   bunya: ''
   description: 'HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes
@@ -9401,7 +9474,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: heinz
+- biocontainers: ''
   biotools: heinz
   bunya: ''
   description: Tool for single-species active module discovery.
@@ -9440,7 +9513,37 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: hgv_david
+- biocontainers: ''
+  biotools: helixer
+  bunya: ''
+  description: Deep Learning to predict gene annotations
+  edam-inputs: []
+  edam-operations:
+  - Gene prediction
+  - Genome annotation
+  edam-outputs: []
+  edam-topics:
+  - Sequence analysis
+  - Gene transcripts
+  galaxy:
+  - description: 'Helixer: gene calling'
+    title: Helixer 0.3.2
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgenouest%2Fhelixer%2Fhelixer%2F0.3.2
+  homepage: https://github.com/weberlab-hhu/Helixer
+  id: helixer
+  license: GPL-3.0
+  name: Helixer
+  nci-gadi: ''
+  nci-if89: ''
+  pawsey: ''
+  publications:
+  - title: 'Helixer: Cross-species gene annotation of large eukaryotic genomes using
+      deep learning'
+    url: https://doi.org/10.1093/bioinformatics/btaa1044
+  resources:
+  - title: .nan
+    url: .nan
+- biocontainers: ''
   biotools: hgv_david
   bunya: ''
   description: This tool provides functional annotation for a list of genes by connecting
@@ -9483,7 +9586,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: hgv_ldtools
+- biocontainers: ''
   biotools: hgv_ldtools
   bunya: ''
   description: This tool can be used to analyze the patterns of linkage disequilibrium
@@ -9528,7 +9631,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: hgv_linktogprofile
+- biocontainers: ''
   biotools: hgv_linktogprofile
   bunya: ''
   description: This tool creates a link to the g:GOSt tool (Gene Group Functional
@@ -9572,7 +9675,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: hicexplorer
+- biocontainers: ''
   biotools: hicexplorer
   bunya: ''
   description: "A web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C\
@@ -9592,6 +9695,196 @@
   - ChIP-seq
   - Epigenetics
   galaxy:
+  - description: 'hicValidateLocations: validate detected loops with protein peaks.'
+    title: hicValidateLocations 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicvalidatelocations%2Fhicexplorer_hicvalidatelocations%2F3.7.5%2Bgalaxy0
+  - description: 'hicTransform: transform a matrix to obs/exp, pearson and covariance
+      matrices'
+    title: hicTransform 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hictransform%2Fhicexplorer_hictransform%2F3.7.5%2Bgalaxy0
+  - description: 'hicSumMatrices: combine Hi-C matrices of the same size'
+    title: hicSumMatrices 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicsummatrices%2Fhicexplorer_hicsummatrices%2F3.7.5%2Bgalaxy0
+  - description: 'hicQuickQC: get a first quality estimate of Hi-C data'
+    title: hicQuickQC 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicquickqc%2Fhicexplorer_hicquickqc%2F3.7.5%2Bgalaxy0
+  - description: 'hicPlotViewpoint: plot interactions around a viewpoint'
+    title: hicPlotViewpoint 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicplotviewpoint%2Fhicexplorer_hicplotviewpoint%2F3.7.5%2Bgalaxy0
+  - description: 'hicPlotSVL: plots the relation of short vs long range contacts'
+    title: hicPlotSVL 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicplotsvl%2Fhicexplorer_hicplotsvl%2F3.7.5%2Bgalaxy0
+  - description: 'hicPlotAverageRegions: plot the average regions from hicAverageRegions'
+    title: hicPlotAverageRegions 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicplotaverageregions%2Fhicexplorer_hicplotaverageregions%2F3.7.5%2Bgalaxy0
+  - description: 'hicNormalize: normalizes a matrix to norm range or smallest read
+      count'
+    title: hicNormalize 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicnormalize%2Fhicexplorer_hicnormalize%2F3.7.5%2Bgalaxy0
+  - description: 'hicMergeLoops: merge detected loops of different resolutions.'
+    title: hicMergeLoops 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicmergeloops%2Fhicexplorer_hicmergeloops%2F3.7.5%2Bgalaxy0
+  - description: 'hicInterIntraTAD: computes the ratio of inter TAD-scores vs. intra
+      TADs'
+    title: hicInterIntraTAD 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicinterintratad%2Fhicexplorer_hicinterintratad%2F3.7.5%2Bgalaxy0
+  - description: 'hicInfo: get information about the content of a Hi-C matrix'
+    title: hicInfo 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicinfo%2Fhicexplorer_hicinfo%2F3.7.5%2Bgalaxy0
+  - description: 'hicHyperoptDetectLoops: optimizes parameters for hicDetectLoops'
+    title: hicHyperoptDetectLoops 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hichyperoptdetectloops%2Fhicexplorer_hichyperoptDetectLoops%2F3.7.5%2Bgalaxy0
+  - description: 'hicFindRestSite: identify restriction enzyme sites'
+    title: hicFindRestSite 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicfindrestrictionsites%2Fhicexplorer_hicfindrestrictionsites%2F3.7.5%2Bgalaxy0
+  - description: 'hicDifferentialTAD: searches for differential TADs'
+    title: hicDifferentialTAD 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicdifferentialtad%2Fhicexplorer_hicdifferentialtad%2F3.7.5%2Bgalaxy0
+  - description: 'hicDetectLoops: searches for enriched regions'
+    title: hicDetectLoops 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicdetectloops%2Fhicexplorer_hicdetectloops%2F3.7.5%2Bgalaxy0
+  - description: 'hicCorrelate: compute pairwise correlations between multiple Hi-C
+      contact matrices'
+    title: hicCorrelate 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hiccorrelate%2Fhicexplorer_hiccorrelate%2F3.7.5%2Bgalaxy0
+  - description: 'hicCorrectMatrix: run a Hi-C matrix correction algorithm'
+    title: hicCorrectMatrix 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hiccorrectmatrix%2Fhicexplorer_hiccorrectmatrix%2F3.7.5%2Bgalaxy0
+  - description: 'hicCompartmentalization: compute pairwise correlations between multiple
+      Hi-C contact matrices'
+    title: hicCompartmentalization 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hiccompartmentspolarization%2Fhicexplorer_hiccompartmentspolarization%2F3.7.5%2Bgalaxy0
+  - description: 'hicAverageRegions: sums Hi-C contacts around given reference points
+      and computes their average.'
+    title: hicAverageRegions 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicaverageregions%2Fhicexplorer_hicaverageregions%2F3.7.5%2Bgalaxy0
+  - description: 'hicAggregateContacts: allow plotting of aggregated Hi-C contacts
+      between regions specified in a file'
+    title: hicAggregateContacts 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicaggregatecontacts%2Fhicexplorer_hicaggregatecontacts%2F3.7.5%2Bgalaxy0
+  - description: 'hicAdjustMatrix: adjust the shape of a Hi-C matrix'
+    title: hicAdjustMatrix 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicadjustmatrix%2Fhicexplorer_hicadjustmatrix%2F3.7.5%2Bgalaxy0
+  - description: 'chicViewpointBackgroundModel: compute a background model for cHi-C
+      / HiChIP data'
+    title: chicViewpointBackgroundModel 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_chicviewpointbackgroundmodel%2Fhicexplorer_chicviewpointbackgroundmodel%2F3.7.5%2Bgalaxy0
+  - description: 'chicViewpoint: computes viewpoints with the given reference points
+      and a background model.'
+    title: chicViewpoint 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_chicviewpoint%2Fhicexplorer_chicviewpoint%2F3.7.5%2Bgalaxy0
+  - description: 'chicSignificantInteractions: computes viewpoints with the given
+      reference points and a background model'
+    title: chicSignificantInteractions 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_chicsignificantinteractions%2Fhicexplorer_chicsignificantinteractions%2F3.7.5%2Bgalaxy0
+  - description: 'chicPlotViewpoint: creates plots for viewpoints'
+    title: chicPlotViewpoint 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_chicplotviewpoint%2Fhicexplorer_chicplotviewpoint%2F3.7.5%2Bgalaxy0
+  - description: 'chicDifferentialTest: computes differential interactions of viewpoints'
+    title: chicDifferentialTest 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_chicdifferentialtest%2Fhicexplorer_chicdifferentialtest%2F3.7.5%2Bgalaxy0
+  - description: 'chicAggregateStatistic: computes with a target file the to be tested
+      regions for chicDifferentialTest'
+    title: chicAggregateStatistic 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_chicaggregatestatistic%2Fhicexplorer_chicaggregatestatistic%2F3.7.5%2Bgalaxy0
+  - description: 'scHicQualityControl: quality control for single-cell Hi-C interaction
+      matrices'
+    title: scHicQualityControl 4.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fschicexplorer_schicqualitycontrol%2Fschicexplorer_schicqualitycontrol%2F4.1
+  - description: 'scHicPlotClusterProfiles: plot single-cell Hi-C interaction matrices
+      cluster profiles'
+    title: scHicPlotClusterProfiles 4.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fschicexplorer_schicplotclusterprofiles%2Fschicexplorer_schicplotclusterprofiles%2F4.1
+  - description: 'scHicMergeToSCool: merge multiple cool files to one scool file'
+    title: scHicMergeToSCool 4.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fschicexplorer_schicmergetoscool%2Fschicexplorer_schicmergetoscool%2F4.1
+  - description: 'scHicMergeMatrixBins: change the resolution of the scHi-C matrices'
+    title: scHicMergeMatrixBins 4.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fschicexplorer_schicmergematrixbins%2Fschicexplorer_schicmergematrixbins%2F4.1
+  - description: 'scHicInfo: information about a single-cell scool matrix'
+    title: scHicInfo 4.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fschicexplorer_schicinfo%2Fschicexplorer_schicinfo%2F4.1
+  - description: 'scHicDemultiplex: demultiplexes Nagano 2017 raw fastq files'
+    title: scHicDemultiplex 4.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fschicexplorer_schicdemultiplex%2Fschicexplorer_schicdemultiplex%2F4.1
+  - description: 'scHicCreateBulkMatrix: creates the bulk matrix out of  single-cell
+      Hi-C interaction matrices'
+    title: scHicCreateBulkMatrix 4.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fschicexplorer_schiccreatebulkmatrix%2Fschicexplorer_schiccreatebulkmatrix%2F4.1
+  - description: 'scHicCorrectMatrices: correct with KR algorithm single-cell Hi-C
+      interaction matrices'
+    title: scHicCorrectMatrices 4.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fschicexplorer_schiccorrectmatrices%2Fschicexplorer_schiccorrectmatrices%2F4.1
+  - description: 'scHicConsensusMatrices: creates per cluster one average matrix'
+    title: scHicConsensusMatrices 4.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fschicexplorer_schicconsensusmatrices%2Fschicexplorer_schicconsensusmatrices%2F4.1
+  - description: 'scHicClusterSVL: clusters single-cell Hi-C interaction matrices
+      with svl dimension reduction'
+    title: scHicClusterSVL 4.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fschicexplorer_schicclustersvl%2Fschicexplorer_schicclustersvl%2F4.1
+  - description: 'scHicClusterMinHash: clusters single-cell Hi-C interaction matrices
+      with MinHash dimension reduction'
+    title: scHicClusterMinHash 4.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fschicexplorer_schicclusterminhash%2Fschicexplorer_schicclusterminhash%2F4.1
+  - description: 'scHicClusterCompartments: clusters single-cell Hi-C interaction
+      matrices with A/B compartments dimension reduction'
+    title: scHicClusterCompartments 4.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fschicexplorer_schicclustercompartments%2Fschicexplorer_schicclustercompartments%2F4.1
+  - description: 'scHicAdjustMatrix: clusters single-cell Hi-C interaction matrices
+      on the raw data'
+    title: scHicAdjustMatrix 4.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fschicexplorer_schicadjustmatrix%2Fschicexplorer_schicadjustmatrix%2F4.1
+  - description: 'hicTrainTADClassifier: train a TAD detection ML model'
+    title: hicTrainTADClassifier 3.7.2+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hictraintadclassifier%2Fhicexplorer_hictraintadclassifier%2F3.7.2%2Bgalaxy0
+  - description: 'hicPlotDistVsCounts: compute distance vs Hi-C counts plot per chromosome'
+    title: hicPlotDistVsCounts 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicplotdistvscounts%2Fhicexplorer_hicplotdistvscounts%2F3.7.5%2Bgalaxy0
+  - description: 'hicMergeDomains: Merges TAD domains'
+    title: hicMergeDomains 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicmergedomains%2Fhicexplorer_hicmergedomains%2F3.7.5%2Bgalaxy0
+  - description: 'hicConvertFormat: Convert between different file formats'
+    title: hicConvertFormat 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicconvertformat%2Fhicexplorer_hicconvertformat%2F3.7.5%2Bgalaxy0
+  - description: 'hicCompareMatrices: normalize and compare two Hi-C contact matrices'
+    title: hicCompareMatrices 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hiccomparematrices%2Fhicexplorer_hiccomparematrices%2F3.7.5%2Bgalaxy0
+  - description: 'chicExportData: exports data of hdf to txt based files'
+    title: chicExportData 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_chicexportdata%2Fhicexplorer_chicexportdata%2F3.7.5%2Bgalaxy0
+  - description: 'chicQualityControl: generates an estimate of the quality of each
+      viewpoint'
+    title: chicQualityControl 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_chicqualitycontrol%2Fhicexplorer_chicqualitycontrol%2F3.7.5%2Bgalaxy0
+  - description: 'hicTADClassifier: TAD detection based on ML models'
+    title: hicTADClassifier 3.7.2+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hictadclassifier%2Fhicexplorer_hictadclassifier%2F3.7.2%2Bgalaxy0
+  - description: 'scHicCluster: clusters single-cell Hi-C interaction matrices on
+      the raw data'
+    title: scHicCluster 4.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fschicexplorer_schiccluster%2Fschicexplorer_schiccluster%2F4.1
+  - description: 'scHicNormalize: normalize single-cell Hi-C interaction matrices
+      to the same read coverage'
+    title: scHicNormalize 4.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fschicexplorer_schicnormalize%2Fschicexplorer_schicnormalize%2F4.1
+  - description: 'scHicPlotConsensusMatrices: plot single-cell Hi-C interaction matrices
+      cluster consensus matrices'
+    title: scHicPlotConsensusMatrices 4.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fschicexplorer_schicplotconsensusmatrices%2Fschicexplorer_schicplotconsensusmatrices%2F4.1
+  - description: 'hicPlotTADs: plot Hi-C contact matrices heatmaps alongside other
+      data tracks'
+    title: hicPlotTADs 2.1.4.0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicplottads%2Fhicexplorer_hicplottads%2F2.1.4.0
+  - description: 'hicPlotMatrix: plot a Hi-C contact matrix heatmap'
+    title: hicPlotMatrix 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicplotmatrix%2Fhicexplorer_hicplotmatrix%2F3.7.5%2Bgalaxy0
+  - description: 'hicPCA: compute the principal components for A / B compartment analysis'
+    title: hicPCA 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicpca%2Fhicexplorer_hicpca%2F3.7.5%2Bgalaxy0
+  - description: 'hicMergeMatrixBins: merge adjacent bins from a Hi-C contact matrix
+      to reduce its resolution'
+    title: hicMergeMatrixBins 3.7.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicmergematrixbins%2Fhicexplorer_hicmergematrixbins%2F3.7.5%2Bgalaxy0
   - description: 'hicFindTADs: identify TAD boundaries by computing the degree of
       separation of each Hi-C matrix bin'
     title: hicFindTADs 3.7.5+galaxy0
@@ -9599,16 +9892,6 @@
   - description: 'hicBuildMatrix: create a contact matrix'
     title: hicBuildMatrix 3.7.5+galaxy0
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicbuildmatrix%2Fhicexplorer_hicbuildmatrix%2F3.7.5%2Bgalaxy0
-  - description: 'hicPCA: compute the principal components for A / B compartment analysis'
-    title: hicPCA 3.7.2+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicpca%2Fhicexplorer_hicpca%2F3.7.2%2Bgalaxy0
-  - description: 'hicPlotMatrix: plot a Hi-C contact matrix heatmap'
-    title: hicPlotMatrix 3.7.2+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicplotmatrix%2Fhicexplorer_hicplotmatrix%2F3.7.2%2Bgalaxy0
-  - description: 'hicMergeMatrixBins: merge adjacent bins from a Hi-C contact matrix
-      to reduce its resolution'
-    title: hicMergeMatrixBins 3.7.2+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicmergematrixbins%2Fhicexplorer_hicmergematrixbins%2F3.7.2%2Bgalaxy0
   homepage: https://hicexplorer.usegalaxy.eu
   id: hicexplorer
   license: ''
@@ -9623,7 +9906,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: hifiadapterfilt
+- biocontainers: ''
   biotools: hifiadapterfilt
   bunya: ''
   description: Remove CCS reads with remnant PacBio adapter sequences and convert
@@ -9661,7 +9944,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: hifiasm
+- biocontainers: ''
   biotools: hifiasm
   bunya:
   - 0.16.1-gcccore-10.3.0
@@ -9675,8 +9958,8 @@
   - Sequence assembly
   galaxy:
   - description: 'Hifiasm: haplotype-resolved de novo assembler for PacBio Hifi reads'
-    title: Hifiasm 0.19.8+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhifiasm%2Fhifiasm%2F0.19.8%2Bgalaxy1
+    title: Hifiasm 0.19.9+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhifiasm%2Fhifiasm%2F0.19.9%2Bgalaxy0
   homepage: https://github.com/chhylp123/hifiasm
   id: hifiasm
   license: MIT
@@ -9695,7 +9978,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: hifiasm-meta
+- biocontainers: ''
   biotools: hifiasm-meta
   bunya: ''
   description: Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved
@@ -9781,7 +10064,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: hmmer3
+- biocontainers: ''
   biotools: hmmer3
   bunya:
   - 3.3.2-gompi-2021a
@@ -9861,7 +10144,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: horovod
+- biocontainers: ''
   biotools: horovod
   bunya: ''
   description: Horovod is a distributed deep learning training framework for TensorFlow,
@@ -9916,7 +10199,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: htslib
+- biocontainers: htslib-test
   biotools: htslib
   bunya:
   - 1.12-gcc-10.3.0
@@ -9965,6 +10248,7 @@
   - '1.16'
   nci-if89:
   - 1.19.1
+  - '1.20'
   pawsey: ''
   publications:
   - title: 'HTSlib: C library for reading/writing high-Throughput sequencing data'
@@ -9972,7 +10256,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: humann
+- biocontainers: ''
   biotools: humann
   bunya:
   - 3.6-foss-2022a
@@ -10045,7 +10329,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: humann2
+- biocontainers: ''
   biotools: humann2
   bunya: ''
   description: "HUMAnN 2.0 is a pipeline for efficiently and accurately profiling\
@@ -10097,7 +10381,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: HybPiper
+- biocontainers: ''
   biotools: HybPiper
   bunya: ''
   description: 'Paralogs and off-target sequences improve phylogenetic resolution
@@ -10146,7 +10430,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: HyPhy
+- biocontainers: ''
   biotools: HyPhy
   bunya: ''
   description: Software package for the analysis of genetic sequences using techniques
@@ -10226,7 +10510,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ipa_hifi
+- biocontainers: ''
   biotools: ipa_hifi
   bunya: ''
   description: Improved Phased Assembler (IPA) is the official PacBio software for
@@ -10253,7 +10537,7 @@
   resources:
   - title: Install and testing at Pawsey
     url: https://github.com/AustralianBioCommons/ipa
-- biocontainers: infernal
+- biocontainers: ''
   biotools: infernal
   bunya: ''
   description: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence
@@ -10365,7 +10649,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: integron_finder
+- biocontainers: ''
   biotools: integron_finder
   bunya: ''
   description: A tool to detect Integron in DNA sequences.
@@ -10392,8 +10676,8 @@
   - Sequence analysis
   galaxy:
   - description: 'Integron Finder: is a program that detects integrons in DNA sequences'
-    title: Integron Finder 2.0.3+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fintegron_finder%2Fintegron_finder%2F2.0.3%2Bgalaxy0
+    title: Integron Finder 2.0.5+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fintegron_finder%2Fintegron_finder%2F2.0.5%2Bgalaxy0
   homepage: https://github.com/gem-pasteur/Integron_Finder
   id: integron_finder
   license: GPL-3.0
@@ -10411,7 +10695,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: intermine
+- biocontainers: ''
   biotools: intermine
   bunya: ''
   description: Open source data warehouse built specifically for the integration and
@@ -10452,7 +10736,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: interproscan_4
+- biocontainers: ''
   biotools: interproscan_4
   bunya:
   - 5.55-88.0-foss-2021a
@@ -10490,7 +10774,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ipyrad
+- biocontainers: ''
   biotools: ipyrad
   bunya:
   - 0.9.93
@@ -10524,7 +10808,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: iq-tree
+- biocontainers: ''
   biotools: iq-tree
   bunya:
   - 2.2.2.3--h2202e69_2
@@ -10543,8 +10827,8 @@
   galaxy:
   - description: 'IQ-TREE: Phylogenomic / evolutionary tree construction from multiple
       sequences'
-    title: IQ-TREE 2.3.3+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fiqtree%2Fiqtree%2F2.3.3%2Bgalaxy0
+    title: IQ-TREE 2.3.6+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fiqtree%2Fiqtree%2F2.3.6%2Bgalaxy0
   homepage: http://www.cibiv.at/software/iqtree/
   id: iq-tree
   license: ''
@@ -10559,7 +10843,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: isee
+- biocontainers: isee-galaxy
   biotools: isee
   bunya: ''
   description: Provides functions for creating an interactive Shiny-based graphical
@@ -10592,7 +10876,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: isescan
+- biocontainers: ''
   biotools: isescan
   bunya: ''
   description: Automated identification of insertion sequence elements in prokaryotic
@@ -10624,7 +10908,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: isoformswitchanalyzer
+- biocontainers: ''
   biotools: isoformswitchanalyzer
   bunya: ''
   description: Enables identification of isoform switches with predicted functional
@@ -10657,7 +10941,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: isoseq3
+- biocontainers: ''
   biotools: isoseq3
   bunya:
   - 4.0.0--h9ee0642_0
@@ -10687,7 +10971,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ivar
+- biocontainers: ''
   biotools: ivar
   bunya: ''
   description: 'Interpretation-oriented tool to manage the update and revision of
@@ -10706,6 +10990,9 @@
   - Evolutionary biology
   - Sequencing
   galaxy:
+  - description: 'ivar trim: Trim reads in aligned BAM'
+    title: ivar trim 1.4.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_trim%2Fivar_trim%2F1.4.3%2Bgalaxy0
   - description: 'ivar variants: Call variants from aligned BAM file'
     title: ivar variants 1.4.3+galaxy1
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_variants%2Fivar_variants%2F1.4.3%2Bgalaxy1
@@ -10723,9 +11010,6 @@
   - description: 'ivar removereads: Remove reads from trimmed BAM file'
     title: ivar removereads 1.4.3+galaxy0
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_removereads%2Fivar_removereads%2F1.4.3%2Bgalaxy0
-  - description: 'ivar trim: Trim reads in aligned BAM'
-    title: ivar trim 1.4.2+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_trim%2Fivar_trim%2F1.4.2%2Bgalaxy0
   homepage: https://github.com/CGR-UNIMORE/iVar
   id: ivar
   license: AGPL-3.0
@@ -10739,7 +11023,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: iwtomics
+- biocontainers: ''
   biotools: iwtomics
   bunya: ''
   description: Implementation of the Interval-Wise Testing (IWT) for omics data. This
@@ -10776,7 +11060,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: jags
+- biocontainers: ''
   biotools: jags
   bunya:
   - 4.3.0-foss-2021a
@@ -10799,7 +11083,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: jasmine-sv
+- biocontainers: ''
   biotools: jasmine-sv
   bunya: ''
   description: JASMINE (Jointly Accurate Sv Merging with Intersample Network Edges)
@@ -10999,7 +11283,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: juicer
+- biocontainers: ''
   biotools: juicer
   bunya:
   - '1.6'
@@ -11052,7 +11336,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: kallisto
+- biocontainers: ''
   biotools: kallisto
   bunya:
   - 0.48.0-gompi-2021a
@@ -11090,7 +11374,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: kat
+- biocontainers: ''
   biotools: kat
   bunya: ''
   description: Suite of tools that generate, analyse and compare k-mer spectra produced
@@ -11233,6 +11517,7 @@
   nci-gadi: ''
   nci-if89:
   - 3.2.1
+  - 3.2.4
   pawsey: ''
   publications:
   - title: 'KMC 2: Fast and resource-frugal k-mer counting'
@@ -11240,7 +11525,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: kofamscan
+- biocontainers: ''
   biotools: kofamscan
   bunya:
   - 1.3.0--hdfd78af_2
@@ -11333,7 +11618,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: kraken2
+- biocontainers: ''
   biotools: kraken2
   bunya:
   - 2.1.2-gompi-2021a
@@ -11359,8 +11644,8 @@
   - Metagenomics
   galaxy:
   - description: 'Kraken2: assign taxonomic labels to sequencing reads'
-    title: Kraken2 2.1.1+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkraken2%2Fkraken2%2F2.1.1%2Bgalaxy1
+    title: Kraken2 2.1.3+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkraken2%2Fkraken2%2F2.1.3%2Bgalaxy1
   homepage: https://ccb.jhu.edu/software/kraken2/
   id: kraken2
   license: MIT
@@ -11392,8 +11677,8 @@
   galaxy:
   - description: 'Krakentools: Combine multiple Kraken reports: into a combined report
       file'
-    title: 'Krakentools: Combine multiple Kraken reports 1.2+galaxy1'
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkrakentools_combine_kreports%2Fkrakentools_combine_kreports%2F1.2%2Bgalaxy1
+    title: 'Krakentools: Combine multiple Kraken reports 1.2+galaxy2'
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkrakentools_combine_kreports%2Fkrakentools_combine_kreports%2F1.2%2Bgalaxy2
   - description: 'Krakentools: calculates beta diversity (Bray-Curtis dissimilarity):
       from Kraken, Krona and Bracken files'
     title: 'Krakentools: calculates beta diversity (Bray-Curtis dissimilarity) 1.2+galaxy1'
@@ -11468,7 +11753,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: lama
+- biocontainers: ''
   biotools: lama
   bunya: ''
   description: 'Automated image analysis for developmental phenotyping of mouse embryos.
@@ -11500,6 +11785,7 @@
   - 0.9.100
   - 1.0.0
   - 1.0.1
+  - 1.0.2
   pawsey: ''
   publications:
   - title: 10.1101/2020.05.04.075853
@@ -11507,7 +11793,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: lastz
+- biocontainers: ''
   biotools: lastz
   bunya: ''
   description: A tool for (1) aligning two DNA sequences, and (2) inferring appropriate
@@ -11564,7 +11850,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: LFQ-Analyst
+- biocontainers: ''
   biotools: LFQ-Analyst
   bunya: ''
   description: "An Easy-To-Use Interactive Web Platform To Analyze and Visualize Label-Free\
@@ -11634,7 +11920,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: limma
+- biocontainers: bioconductor-limma
   biotools: limma
   bunya: ''
   description: Data analysis, linear models and differential expression for microarray
@@ -11670,7 +11956,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: links
+- biocontainers: ''
   biotools: links
   bunya: ''
   description: LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application
@@ -11708,7 +11994,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: lofreq
+- biocontainers: ''
   biotools: lofreq
   bunya: ''
   description: LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller
@@ -11753,7 +12039,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: longshot
+- biocontainers: ''
   biotools: longshot
   bunya: ''
   description: Longshot is a variant calling tool for diploid genomes using long error
@@ -11808,7 +12094,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ltr_retriever
+- biocontainers: ''
   biotools: ltr_retriever
   bunya: ''
   description: LTR_retriever is a highly accurate and sensitive program for identification
@@ -11858,7 +12144,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: macs
+- biocontainers: ''
   biotools: macs
   bunya:
   - 2.2.9.1
@@ -11961,7 +12247,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: MAFFT
+- biocontainers: ''
   biotools: MAFFT
   bunya:
   - 7.490-gcc-10.3.0-with-extensions
@@ -11981,12 +12267,12 @@
   - Sequence analysis
   galaxy:
   - description: 'MAFFT: Multiple alignment program for amino acid or nucleotide sequences'
-    title: MAFFT 7.520+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fmafft%2Frbc_mafft%2F7.520%2Bgalaxy0
+    title: MAFFT 7.526+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fmafft%2Frbc_mafft%2F7.526%2Bgalaxy0
   - description: 'MAFFT add: Align a sequence,alignment or fragments to an existing
       alignment.'
-    title: MAFFT add 7.520+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fmafft%2Frbc_mafft_add%2F7.520%2Bgalaxy0
+    title: MAFFT add 7.526+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fmafft%2Frbc_mafft_add%2F7.526%2Bgalaxy0
   homepage: http://mafft.cbrc.jp/alignment/server/index.html
   id: mafft
   license: BSD-Source-Code
@@ -12014,7 +12300,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: mageck
+- biocontainers: ''
   biotools: mageck
   bunya: ''
   description: Computational tool to identify important genes from the recent genome-scale
@@ -12098,7 +12384,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: maldi_quant
+- biocontainers: ''
   biotools: maldi_quant
   bunya: ''
   description: MALDIquant is a complete analysis pipeline for matrix-assisted laser
@@ -12226,7 +12512,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: masurca
+- biocontainers: ''
   biotools: masurca
   bunya: ''
   description: "Whole genome assembly software. It combines the efficiency of the\
@@ -12259,7 +12545,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: matchms
+- biocontainers: ''
   biotools: matchms
   bunya: ''
   description: Tool to import, process, clean, and compare mass spectrometry data.
@@ -12285,46 +12571,46 @@
   edam-topics:
   - Metabolomics
   galaxy:
-  - description: 'matchms convert: convert between mass spectral library formats (.mgf/.msp/.json)
-      using matchms'
-    title: matchms convert 0.20.0+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_convert%2Fmatchms_convert%2F0.20.0%2Bgalaxy0
-  - description: 'matchms filtering: filter and normalize mass spectrometry data'
-    title: matchms filtering 0.20.0+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_filtering%2Fmatchms_filtering%2F0.20.0%2Bgalaxy0
+  - description: 'recetox-xMSannotator: annotate peak intensity table including scores
+      and confidence levels'
+    title: recetox-xMSannotator 0.10.0+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frecetox_xmsannotator_advanced%2Frecetox_xmsannotator_advanced%2F0.10.0%2Bgalaxy1
+  - description: 'matchms split library: split a large library into subsets'
+    title: matchms split library 0.27.0+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_split%2Fmatchms_split%2F0.27.0%2Bgalaxy0
+  - description: 'matchms networking: create similarity network graph from matchms
+      similarity scores'
+    title: matchms networking 0.27.0+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_networking%2Fmatchms_networking%2F0.27.0%2Bgalaxy0
+  - description: 'matchms metadata export: extract all metadata from mass spectra
+      file to tabular format'
+    title: matchms metadata export 0.27.0+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_metadata_export%2Fmatchms_metadata_export%2F0.27.0%2Bgalaxy0
   - description: 'matchms fingerprint similarity: calculate similarity between molecular
       fingerprints calculated from structural spectrum metadata descriptors'
-    title: matchms fingerprint similarity 0.20.0+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_fingerprint_similarity%2Fmatchms_fingerprint_similarity%2F0.20.0%2Bgalaxy0
+    title: matchms fingerprint similarity 0.27.0+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_fingerprint_similarity%2Fmatchms_fingerprint_similarity%2F0.27.0%2Bgalaxy0
+  - description: 'matchms filtering: filter and normalize mass spectrometry data'
+    title: matchms filtering 0.27.0+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_filtering%2Fmatchms_filtering%2F0.27.0%2Bgalaxy0
+  - description: 'matchms convert: convert between mass spectral library formats (.mgf/.msp/.json)
+      using matchms'
+    title: matchms convert 0.27.0+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_convert%2Fmatchms_convert%2F0.27.0%2Bgalaxy0
   - description: 'matchms scores formatter: reformat scores object of matchms to long
       format table'
-    title: matchms scores formatter 0.20.0+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_formatter%2Fmatchms_formatter%2F0.20.0%2Bgalaxy0
-  - description: 'matchms metadata export : extract all metadata from mass spectra
-      file to tabular format'
-    title: matchms metadata export  0.20.0+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_metadata_export%2Fmatchms_metadata_export%2F0.20.0%2Bgalaxy0
+    title: matchms scores formatter 0.27.0+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_formatter%2Fmatchms_formatter%2F0.27.0%2Bgalaxy0
   - description: 'matchms metadata match: matchms metadata match calculation for numeric
       fields based on tolerance'
-    title: matchms metadata match 0.20.0+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_metadata_match%2Fmatchms_metadata_match%2F0.20.0%2Bgalaxy0
-  - description: 'matchms networking: create similarity network graph from matchms
-      similarity scores'
-    title: matchms networking 0.20.0+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_networking%2Fmatchms_networking%2F0.20.0%2Bgalaxy0
+    title: matchms metadata match 0.27.0+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_metadata_match%2Fmatchms_metadata_match%2F0.27.0%2Bgalaxy0
   - description: 'matchms similarity: calculate the similarity score and matched peaks'
     title: matchms similarity 0.20.0+galaxy0
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_similarity%2Fmatchms_similarity%2F0.20.0%2Bgalaxy0
   - description: 'matchms spectral similarity: matchms spectral similarity calculation'
-    title: matchms spectral similarity 0.20.0+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_spectral_similarity%2Fmatchms_spectral_similarity%2F0.20.0%2Bgalaxy0
-  - description: 'matchms split library: split a large library into subsets'
-    title: matchms split library 0.20.0+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_split%2Fmatchms_split%2F0.20.0%2Bgalaxy0
-  - description: 'recetox-xMSannotator: annotate peak intensity table including scores
-      and confidence levels'
-    title: recetox-xMSannotator 0.10.0+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frecetox_xmsannotator_advanced%2Frecetox_xmsannotator_advanced%2F0.10.0%2Bgalaxy0
+    title: matchms spectral similarity 0.27.0+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmatchms_spectral_similarity%2Fmatchms_spectral_similarity%2F0.27.0%2Bgalaxy0
   homepage: https://github.com/matchms/matchms
   id: matchms
   license: Apache-2.0
@@ -12336,7 +12622,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: matplotlib
+- biocontainers: ''
   biotools: matplotlib
   bunya:
   - 3.4.2-foss-2021a
@@ -12362,7 +12648,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: maxbin
+- biocontainers: ''
   biotools: maxbin
   bunya: ''
   description: Software for binning assembled metagenomic sequences based on an Expectation-Maximization
@@ -12487,7 +12773,30 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: mdanalysis
+- biocontainers: ''
+  biotools: ''
+  bunya: ''
+  description: ''
+  edam-inputs: ''
+  edam-operations: ''
+  edam-outputs: ''
+  edam-topics: ''
+  galaxy:
+  - description: 'MCQUANT: a module for single-cell data extraction'
+    title: MCQUANT 1.5.3+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fperssond%2Fquantification%2Fquantification%2F1.5.3%2Bgalaxy1
+  homepage: ''
+  id: mcquant
+  license: ''
+  name: MCQUANT
+  nci-gadi: ''
+  nci-if89: ''
+  pawsey: ''
+  publications: ''
+  resources:
+  - title: .nan
+    url: .nan
+- biocontainers: ''
   biotools: mdanalysis
   bunya: ''
   description: MDAnalysis is an object-oriented python toolkit to analyze molecular
@@ -12545,7 +12854,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: medaka
+- biocontainers: ''
   biotools: medaka
   bunya:
   - 1.9.1
@@ -12586,7 +12895,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: megahit
+- biocontainers: ''
   biotools: megahit
   bunya:
   - 1.2.9-gcccore-10.3.0
@@ -12604,6 +12913,10 @@
   - Ecology
   - Sequence assembly
   galaxy:
+  - description: 'megahit contig2fastg: for converting MEGAHIT''s contigs (.fa) to
+      assembly graphs (.fastg)'
+    title: megahit contig2fastg 1.1.3+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmegahit_contig2fastg%2Fmegahit_contig2fastg%2F1.1.3%2Bgalaxy1
   - description: 'MEGAHIT: for metagenomics assembly'
     title: MEGAHIT 1.2.9+galaxy1
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmegahit%2Fmegahit%2F1.2.9%2Bgalaxy1
@@ -12644,7 +12957,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: merqury
+- biocontainers: ''
   biotools: merqury
   bunya: ''
   description: 'Reference-free quality, completeness, and phasing assessment for genome
@@ -12691,7 +13004,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: meryl
+- biocontainers: ''
   biotools: meryl
   bunya: ''
   description: Meryl is a tool for counting and working with sets of k-mers that was
@@ -12731,7 +13044,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: MetaBAT_2
+- biocontainers: ''
   biotools: MetaBAT_2
   bunya: ''
   description: an adaptive binning algorithm for robust and efficient genome reconstruction
@@ -12770,7 +13083,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: MetaDEGalaxy
+- biocontainers: ''
   biotools: MetaDEGalaxy
   bunya: ''
   description: 'Galaxy workflow for differential abundance analysis of 16s metagenomic
@@ -12841,7 +13154,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: MetaEuk
+- biocontainers: ''
   biotools: MetaEuk
   bunya:
   - 5-gcc-10.3.0
@@ -12878,7 +13191,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: metaphlan
+- biocontainers: ''
   biotools: metaphlan
   bunya: ''
   description: Computational tool for profiling the composition of microbial communities
@@ -12893,11 +13206,11 @@
   - Phylogenomics
   galaxy:
   - description: 'MetaPhlAn: to profile the composition of microbial communities'
-    title: MetaPhlAn 4.0.6+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmetaphlan%2Fmetaphlan%2F4.0.6%2Bgalaxy3
+    title: MetaPhlAn 4.1.1+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmetaphlan%2Fmetaphlan%2F4.1.1%2Bgalaxy1
   - description: 'Merge: MetaPhlAn abundance tables'
-    title: Merge 4.0.6+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmerge_metaphlan_tables%2Fmerge_metaphlan_tables%2F4.0.6%2Bgalaxy3
+    title: Merge 4.1.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmerge_metaphlan_tables%2Fmerge_metaphlan_tables%2F4.1.1%2Bgalaxy0
   - description: 'MetaPhlAn2: to profile the composition of microbial communities'
     title: MetaPhlAn2 2.6.0.1
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmetaphlan2%2Fmetaphlan2%2F2.6.0.1
@@ -12918,7 +13231,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: metaQuantome
+- biocontainers: ''
   biotools: metaQuantome
   bunya: ''
   description: metaQuantome software suite analyzes the state of a microbiome by leveraging
@@ -13007,7 +13320,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: metaspades
+- biocontainers: ''
   biotools: metaspades
   bunya: ''
   description: Genome assembler for metagenomics datasets.
@@ -13065,7 +13378,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: metawrap
+- biocontainers: ''
   biotools: metawrap
   bunya: ''
   description: 'MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that
@@ -13103,7 +13416,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: methyldackel
+- biocontainers: ''
   biotools: methyldackel
   bunya: ''
   description: A (mostly) universal methylation extractor for BS-seq experiments.
@@ -13159,7 +13472,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: MIGRATE
+- biocontainers: ''
   biotools: MIGRATE
   bunya: ''
   description: Estimates effective population sizes,past migration rates between n
@@ -13192,7 +13505,7 @@
   resources:
   - title: Install and testing on Gadi (NCI)
     url: https://github.com/AustralianBioCommons/migrate
-- biocontainers: mikado
+- biocontainers: ''
   biotools: mikado
   bunya:
   - 2.2.4--py39h70b41aa_0
@@ -13334,7 +13647,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: miniasm
+- biocontainers: ''
   biotools: miniasm
   bunya: ''
   description: Miniasm is a very fast OLC-based de novo assembler for noisy long reads.
@@ -13423,8 +13736,8 @@
   galaxy:
   - description: 'Map with minimap2: A fast pairwise aligner for genomic and spliced
       nucleotide sequences'
-    title: Map with minimap2 2.26+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fminimap2%2Fminimap2%2F2.26%2Bgalaxy0
+    title: Map with minimap2 2.28+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fminimap2%2Fminimap2%2F2.28%2Bgalaxy0
   homepage: https://github.com/lh3/minimap2
   id: minimap2
   license: MIT
@@ -13442,7 +13755,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: miniprot
+- biocontainers: ''
   biotools: miniprot
   bunya: ''
   description: Miniprot aligns a protein sequence against a genome with affine gap
@@ -13522,7 +13835,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: mirdeep2
+- biocontainers: ''
   biotools: mirdeep2
   bunya: ''
   description: miRDeep2 discovers active known or novel miRNAs from deep sequencing
@@ -13580,7 +13893,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: mitohifi
+- biocontainers: ''
   biotools: mitohifi
   bunya: ''
   description: Find, circularise and annotate mitogenome from PacBio assemblies
@@ -13613,7 +13926,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: mitos
+- biocontainers: ''
   biotools: mitos
   bunya: ''
   description: De novo metazoan mitochondrial genome annotation.
@@ -13688,7 +14001,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: MMseqs2
+- biocontainers: ''
   biotools: MMseqs2
   bunya: ''
   description: "MMseqs2 (Many-against-Many sequence searching) is a software suite\
@@ -13748,7 +14061,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: mob-suite
+- biocontainers: ''
   biotools: mob-suite
   bunya: ''
   description: 'Universal whole-sequence-based plasmid typing and its utility to prediction
@@ -13797,7 +14110,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: moff
+- biocontainers: ''
   biotools: moff
   bunya: ''
   description: A modest Feature Finder to extract features in MS1 Data.
@@ -13851,7 +14164,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: morpheus
+- biocontainers: ''
   biotools: morpheus
   bunya: ''
   description: A proteomics search algorithm specifically designed for high-resolution
@@ -13865,8 +14178,8 @@
   galaxy:
   - description: 'Morpheus: database search algorithm for high-resolution tandem mass
       spectra'
-    title: Morpheus 2.255.0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmorpheus%2Fmorpheus%2F2.255.0
+    title: Morpheus 288+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmorpheus%2Fmorpheus%2F288%2Bgalaxy0
   homepage: https://cwenger.github.io/Morpheus/
   id: morpheus
   license: MIT
@@ -13910,7 +14223,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: mothur
+- biocontainers: ''
   biotools: mothur
   bunya: ''
   description: Open-source, platform-independent, community-supported software for
@@ -14362,7 +14675,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: mousemine
+- biocontainers: ''
   biotools: mousemine
   bunya: ''
   description: Data warehouse for accessing mouse data from Mouse Genome Informatics
@@ -14393,7 +14706,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: mrbayes
+- biocontainers: ''
   biotools: mrbayes
   bunya:
   - 3.2.7a-foss-2022a
@@ -14426,7 +14739,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: MRtrix3
+- biocontainers: ''
   biotools: MRtrix3
   bunya:
   - 3.0.3-foss-2021a
@@ -14464,7 +14777,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: msconvert
+- biocontainers: ''
   biotools: msconvert
   bunya: ''
   description: msConvert is a command-line utility for converting between various
@@ -14497,8 +14810,8 @@
   - Proteomics experiment
   galaxy:
   - description: 'msconvert: Convert and/or filter mass spectrometry files'
-    title: msconvert 3.0.20287.2
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmsconvert%2Fmsconvert%2F3.0.20287.2
+    title: msconvert 3.0.20287.4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmsconvert%2Fmsconvert%2F3.0.20287.4
   homepage: http://proteowizard.sourceforge.net/tools.shtml
   id: msconvert
   license: Apache-2.0
@@ -14512,7 +14825,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: msmetaenhancer
+- biocontainers: ''
   biotools: msmetaenhancer
   bunya: ''
   description: Tool for mass spectra metadata annotation.
@@ -14563,8 +14876,8 @@
   - Data submission, annotation and curation
   galaxy:
   - description: 'MSMetaEnhancer: annotate MS data'
-    title: MSMetaEnhancer 0.3.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmsmetaenhancer%2Fmsmetaenhancer%2F0.3.0%2Bgalaxy1
+    title: MSMetaEnhancer 0.4.0+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Fmsmetaenhancer%2Fmsmetaenhancer%2F0.4.0%2Bgalaxy1
   homepage: https://github.com/RECETOX/MSMetaEnhancer
   id: msmetaenhancer
   license: MIT
@@ -14578,7 +14891,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: msstats
+- biocontainers: bioconductor-msstats
   biotools: msstats
   bunya: ''
   description: Statistical tool for quantitative mass spectrometry-based proteomics.
@@ -14621,7 +14934,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: msstatstmt
+- biocontainers: ''
   biotools: msstatstmt
   bunya: ''
   description: Tools for detecting differentially abundant peptides and proteins in
@@ -14776,7 +15089,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: popmusic
+- biocontainers: ''
   biotools: popmusic
   bunya: ''
   description: "MuSiC is a suite of programs that evaluate the biophysical effects\
@@ -14865,7 +15178,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: mztosqlite
+- biocontainers: ''
   biotools: mztosqlite
   bunya: ''
   description: Convert proteomics data files into a SQLite database
@@ -14918,7 +15231,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: Nanocompore
+- biocontainers: ''
   biotools: Nanocompore
   bunya:
   - 1.0.4--pyhdfd78af_0
@@ -14995,7 +15308,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: nanoplot
+- biocontainers: ''
   biotools: nanoplot
   bunya: ''
   description: NanoPlot is a tool with various visualizations of sequencing data in
@@ -15015,8 +15328,8 @@
   galaxy:
   - description: 'NanoPlot: Plotting suite for Oxford Nanopore sequencing data and
       alignments'
-    title: NanoPlot 1.42.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fnanoplot%2Fnanoplot%2F1.42.0%2Bgalaxy1
+    title: NanoPlot 1.43.0+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fnanoplot%2Fnanoplot%2F1.43.0%2Bgalaxy0
   homepage: https://github.com/wdecoster/NanoPlot
   id: nanoplot
   license: GPL-3.0
@@ -15131,7 +15444,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ncbi_datasets
+- biocontainers: ncbi-datasets-cli
   biotools: ncbi_datasets
   bunya: ''
   description: NCBI Datasets is a new resource that lets you easily gather data from
@@ -15161,7 +15474,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ncbi_resources
+- biocontainers: ''
   biotools: ncbi_resources
   bunya: ''
   description: The National Center for Biotechnology Information (NCBI) provides analysis
@@ -15246,7 +15559,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: nccmp
+- biocontainers: ''
   biotools: nccmp
   bunya: ''
   description: nccmp compares two NetCDF files bitwise, semantically or with a user
@@ -15293,7 +15606,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: nco
+- biocontainers: ''
   biotools: nco
   bunya: ''
   description: The NCO toolkit manipulates and analyzes data stored in netCDF-accessible
@@ -15317,7 +15630,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ncview
+- biocontainers: ''
   biotools: ncview
   bunya: ''
   description: Ncview is a netCDF visual browser.
@@ -15339,7 +15652,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: netcdf
+- biocontainers: ''
   biotools: netcdf
   bunya:
   - 4.8.0-gompi-2021a
@@ -15376,7 +15689,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: newick_utilities
+- biocontainers: ''
   biotools: newick_utilities
   bunya: ''
   description: The Newick Utilities are a set of command-line tools for processing
@@ -15410,7 +15723,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: nextclade
+- biocontainers: ''
   biotools: nextclade
   bunya: ''
   description: Nextclade is an open-source project for viral genome alignment, mutation
@@ -15440,7 +15753,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: nextflow
+- biocontainers: ''
   biotools: nextflow
   bunya:
   - 22.10.1
@@ -15473,7 +15786,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: NextPolish
+- biocontainers: ''
   biotools: NextPolish
   bunya:
   - 1.4.1--py311he4a0461_1
@@ -15513,7 +15826,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: NextPolish
+- biocontainers: ''
   biotools: NextPolish
   bunya:
   - 0.1.0--hd03093a_0
@@ -15608,7 +15921,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ninja
+- biocontainers: ''
   biotools: ninja
   bunya:
   - 1.10.2-gcccore-10.3.0
@@ -15699,6 +16012,29 @@
   resources:
   - title: .nan
     url: .nan
+- biocontainers: ''
+  biotools: ''
+  bunya: ''
+  description: ''
+  edam-inputs: ''
+  edam-operations: ''
+  edam-outputs: ''
+  edam-topics: ''
+  galaxy:
+  - description: 'Nucleotide subsequence search: providing regions in BED format'
+    title: Nucleotide subsequence search 0.2
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ffind_subsequences%2Fbg_find_subsequences%2F0.2
+  homepage: ''
+  id: bg_find_subsequences
+  license: ''
+  name: Nucleotide subsequence search
+  nci-gadi: ''
+  nci-if89: ''
+  pawsey: ''
+  publications: ''
+  resources:
+  - title: .nan
+    url: .nan
 - biocontainers: obitools
   biotools: obitools
   bunya: ''
@@ -15895,6 +16231,10 @@
   - Proteomics
   - Metabolomics
   galaxy:
+  - description: 'TargetedFileConverter: Converts different transition files for targeted
+      proteomics / metabolomics analysis'
+    title: TargetedFileConverter 3.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_targetedfileconverter%2FTargetedFileConverter%2F3.1%2Bgalaxy0
   - description: 'XTandemAdapter: Annotates MS/MS spectra using X! Tandem.'
     title: XTandemAdapter 2.8+galaxy0
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_xtandemadapter%2FXTandemAdapter%2F2.8%2Bgalaxy0
@@ -15904,10 +16244,6 @@
   - description: 'TextExporter: Exports various XML formats to a text file.'
     title: TextExporter 2.8+galaxy0
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_textexporter%2FTextExporter%2F2.8%2Bgalaxy0
-  - description: 'TargetedFileConverter: Converts different transition files for targeted
-      proteomics / metabolomics analysis.'
-    title: TargetedFileConverter 2.8+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_targetedfileconverter%2FTargetedFileConverter%2F2.8%2Bgalaxy0
   - description: 'ProteinQuantifier: Compute peptide and protein abundances'
     title: ProteinQuantifier 2.8+galaxy0
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_proteinquantifier%2FProteinQuantifier%2F2.8%2Bgalaxy0
@@ -16062,7 +16398,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: OrthoFinder
+- biocontainers: ''
   biotools: OrthoFinder
   bunya: ''
   description: OrthoFinder is a fast, accurate and comprehensive platform for comparative
@@ -16163,7 +16499,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: pangolin
+- biocontainers: ''
   biotools: pangolin
   bunya: ''
   description: Pangolin is a deep-learning based method for predicting splice site
@@ -16230,7 +16566,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: paraview
+- biocontainers: ''
   biotools: paraview
   bunya: ''
   description: "ParaView is an open-source, multi-platform data analysis and visualization\
@@ -16291,7 +16627,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: parsnp
+- biocontainers: ''
   biotools: parsnp
   bunya:
   - 1.7.4--hdcf5f25_2
@@ -16319,7 +16655,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: pathview
+- biocontainers: bioconductor-pathview
   biotools: pathview
   bunya: ''
   description: Tool set for pathway based data integration and visualization that
@@ -16355,7 +16691,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: pavian
+- biocontainers: ''
   biotools: pavian
   bunya: ''
   description: Web application for exploring metagenomics classification results,
@@ -16389,7 +16725,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: pblat
+- biocontainers: ''
   biotools: pblat
   bunya: ''
   description: Multithread blat algorithm speeding up aligning sequences to genomes.
@@ -16418,7 +16754,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: seqcode
+- biocontainers: ''
   biotools: seqcode
   bunya: ''
   description: Productive visualization of high-throughput sequencing data using the
@@ -16454,7 +16790,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: pear
+- biocontainers: ''
   biotools: pear
   bunya:
   - 0.9.6--h9d449c0_10
@@ -16469,8 +16805,8 @@
   - Sequence assembly
   galaxy:
   - description: 'Pear: Paired-End read merger'
-    title: Pear 0.9.6.2
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpear%2Fiuc_pear%2F0.9.6.2
+    title: Pear 0.9.6.3
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpear%2Fiuc_pear%2F0.9.6.3
   homepage: http://sco.h-its.org/exelixis/web/software/pear/
   id: pear
   license: CC-BY-NC-1.0
@@ -16507,7 +16843,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: peptideshaker
+- biocontainers: ''
   biotools: peptideshaker
   bunya: ''
   description: PeptideShaker is a search engine independent platform for interpretation
@@ -16679,7 +17015,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: pfamscan
+- biocontainers: ''
   biotools: pfamscan
   bunya: ''
   description: This tool is used to search a FASTA sequence against a library of Pfam
@@ -16705,7 +17041,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: pharokka
+- biocontainers: ''
   biotools: pharokka
   bunya: ''
   description: Pharokka is a rapid standardised annotation tool for bacteriophage
@@ -16785,7 +17121,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: phyloseq
+- biocontainers: bioconductor-phyloseq
   biotools: phyloseq
   bunya: ''
   description: Provides a set of classes and tools to facilitate the import, storage,
@@ -16867,7 +17203,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: picard_tools
+- biocontainers: picard
   biotools: picard_tools
   bunya:
   - 2.25.1-java-11
@@ -17004,7 +17340,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: picrust
+- biocontainers: ''
   biotools: picrust
   bunya: ''
   description: PICRUSt (Phylogenetic Investigation of Communities by Reconstruction
@@ -17060,7 +17396,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: picrust2
+- biocontainers: ''
   biotools: picrust2
   bunya: ''
   description: PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction
@@ -17079,29 +17415,29 @@
   - Phylogenetics
   - Metagenomic sequencing
   galaxy:
-  - description: 'PICRUSt2 Add descriptions: column to a function abundance table'
-    title: PICRUSt2 Add descriptions 2.5.1+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust2_add_descriptions%2Fpicrust2_add_descriptions%2F2.5.1%2Bgalaxy0
-  - description: 'PICRUSt2 Hidden state prediction (HSP): to predict gene family abundances'
-    title: PICRUSt2 Hidden state prediction (HSP) 2.5.1+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust2_hsp%2Fpicrust2_hsp%2F2.5.1%2Bgalaxy0
+  - description: 'PICRUSt2 Generation of shuffled predictions: for a specified number
+      of replicates'
+    title: PICRUSt2 Generation of shuffled predictions 2.5.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust2_shuffle_predictions%2Fpicrust2_shuffle_predictions%2F2.5.3%2Bgalaxy0
+  - description: 'PICRUSt2 Sequence placement: into reference tree'
+    title: PICRUSt2 Sequence placement 2.5.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust2_place_seqs%2Fpicrust2_place_seqs%2F2.5.3%2Bgalaxy0
+  - description: 'PICRUSt2 Pathway abundance inference: '
+    title: PICRUSt2 Pathway abundance inference 2.5.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust2_pathway_pipeline%2Fpicrust2_pathway_pipeline%2F2.5.3%2Bgalaxy0
   - description: 'PICRUSt2 Metagenome prediction: to generate per-sample metagenome
       functional profiles based on the predicted functions for each study sequence'
-    title: PICRUSt2 Metagenome prediction 2.5.1+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust2_metagenome_pipeline%2Fpicrust2_metagenome_pipeline%2F2.5.1%2Bgalaxy0
-  - description: 'PICRUSt2 Pathway abundance inference: '
-    title: PICRUSt2 Pathway abundance inference 2.5.1+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust2_pathway_pipeline%2Fpicrust2_pathway_pipeline%2F2.5.1%2Bgalaxy0
+    title: PICRUSt2 Metagenome prediction 2.5.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust2_metagenome_pipeline%2Fpicrust2_metagenome_pipeline%2F2.5.3%2Bgalaxy0
+  - description: 'PICRUSt2 Hidden state prediction (HSP): to predict gene family abundances'
+    title: PICRUSt2 Hidden state prediction (HSP) 2.5.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust2_hsp%2Fpicrust2_hsp%2F2.5.3%2Bgalaxy0
+  - description: 'PICRUSt2 Add descriptions: column to a function abundance table'
+    title: PICRUSt2 Add descriptions 2.5.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust2_add_descriptions%2Fpicrust2_add_descriptions%2F2.5.3%2Bgalaxy0
   - description: 'PICRUSt2 Full pipeline: '
-    title: PICRUSt2 Full pipeline 2.5.1+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust2_pipeline%2Fpicrust2_pipeline%2F2.5.1%2Bgalaxy0
-  - description: 'PICRUSt2 Sequence placement: into reference tree'
-    title: PICRUSt2 Sequence placement 2.5.1+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust2_place_seqs%2Fpicrust2_place_seqs%2F2.5.1%2Bgalaxy0
-  - description: 'PICRUSt2 Generation of shuffled predictions: for a specified number
-      of replicates'
-    title: PICRUSt2 Generation of shuffled predictions 2.5.1+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust2_shuffle_predictions%2Fpicrust2_shuffle_predictions%2F2.5.1%2Bgalaxy0
+    title: PICRUSt2 Full pipeline 2.5.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust2_pipeline%2Fpicrust2_pipeline%2F2.5.3%2Bgalaxy0
   homepage: https://github.com/picrust/picrust2
   id: picrust2
   license: GPL-3.0
@@ -17191,7 +17527,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: PIPE-T
+- biocontainers: ''
   biotools: PIPE-T
   bunya: ''
   description: 'PIPE-T is a Galaxy Workflow for processing and analyzing miR expression
@@ -17234,7 +17570,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: plasflow
+- biocontainers: ''
   biotools: plasflow
   bunya: ''
   description: PlasFlow is a set of scripts used for prediction of plasmid sequences
@@ -17256,7 +17592,41 @@
   nci-gadi: ''
   nci-if89: ''
   pawsey: ''
-  publications: ''
+  publications: ''
+  resources:
+  - title: .nan
+    url: .nan
+- biocontainers: ''
+  biotools: PlasmidFinder
+  bunya: ''
+  description: PlasmidFinder is a tool for the identification and typing of Plasmid
+    Replicons in Whole-Genome Sequencing (WGS).
+  edam-inputs: []
+  edam-operations:
+  - Genome assembly
+  - Scaffolding
+  - Multilocus sequence typing
+  edam-outputs: []
+  edam-topics:
+  - Whole genome sequencing
+  - Sequence assembly
+  - Mapping
+  - Probes and primers
+  galaxy:
+  - description: 'PlasmidFinder: Plasmid identification in bacteria.'
+    title: PlasmidFinder 2.1.6+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fplasmidfinder%2Fplasmidfinder%2F2.1.6%2Bgalaxy1
+  homepage: https://cge.cbs.dtu.dk/services/PlasmidFinder/
+  id: plasmidfinder
+  license: ''
+  name: PlasmidFinder
+  nci-gadi: ''
+  nci-if89: ''
+  pawsey: ''
+  publications:
+  - title: 'PlasmidFinder and In Silico pMLST: Identification and Typing of Plasmid
+      Replicons in Whole-Genome Sequencing (WGS)'
+    url: https://doi.org/10.1007/978-1-4939-9877-7_20
   resources:
   - title: .nan
     url: .nan
@@ -17289,7 +17659,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: pnetcdf
+- biocontainers: ''
   biotools: pnetcdf
   bunya: ''
   description: 'PnetCDF: A Parallel I/O Library for NetCDF File Access'
@@ -17426,7 +17796,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: clstutils
+- biocontainers: bioconductor-clstutils
   biotools: clstutils
   bunya:
   - 1.1.alpha19
@@ -17475,7 +17845,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: pretextview
+- biocontainers: ''
   biotools: pretextview
   bunya: ''
   description: Pretext is an OpenGL-powered pretext contact map viewer.
@@ -17500,7 +17870,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: gmv
+- biocontainers: ''
   biotools: gmv
   bunya:
   - 2.6.3-gcccore-10.3.0
@@ -17535,7 +17905,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: profia
+- biocontainers: ''
   biotools: profia
   bunya: ''
   description: Flow Injection Analysis coupled to High-Resolution Mass Spectrometry
@@ -17643,7 +18013,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: purge_dups
+- biocontainers: ''
   biotools: purge_dups
   bunya: ''
   description: 'Identifying and removing haplotypic duplication in primary genome
@@ -17703,7 +18073,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: pycoqc
+- biocontainers: ''
   biotools: pycoqc
   bunya:
   - 2.5.2-foss-2021a
@@ -17733,7 +18103,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: pygenometracks
+- biocontainers: ''
   biotools: pygenometracks
   bunya: ''
   description: 'reproducible plots for multivariate genomic data sets.
@@ -17803,7 +18173,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: pysam
+- biocontainers: ''
   biotools: pysam
   bunya:
   - 0.16.0.1-gcc-10.3.0
@@ -17831,7 +18201,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: pytorch
+- biocontainers: ''
   biotools: pytorch
   bunya: ''
   description: PyTorch is an optimized tensor library for deep learning using GPUs
@@ -17859,7 +18229,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: qiime2
+- biocontainers: ''
   biotools: qiime2
   bunya:
   - '2022.8'
@@ -18484,15 +18854,15 @@
   edam-topics:
   - Data quality management
   galaxy:
-  - description: 'QualiMap BamQC: '
-    title: QualiMap BamQC 2.2.2d+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fqualimap_bamqc%2Fqualimap_bamqc%2F2.2.2d%2Bgalaxy3
   - description: 'QualiMap Multi-Sample BamQC: '
-    title: QualiMap Multi-Sample BamQC 2.2.2d
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fqualimap_multi_bamqc%2Fqualimap_multi_bamqc%2F2.2.2d
+    title: QualiMap Multi-Sample BamQC 2.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fqualimap_multi_bamqc%2Fqualimap_multi_bamqc%2F2.3%2Bgalaxy0
+  - description: 'QualiMap BamQC: '
+    title: QualiMap BamQC 2.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fqualimap_bamqc%2Fqualimap_bamqc%2F2.3%2Bgalaxy0
   - description: 'QualiMap Counts QC: '
-    title: QualiMap Counts QC 2.2.2d
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fqualimap_counts%2Fqualimap_counts%2F2.2.2d
+    title: QualiMap Counts QC 2.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fqualimap_counts%2Fqualimap_counts%2F2.3%2Bgalaxy0
   - description: 'QualiMap RNA-Seq QC: '
     title: QualiMap RNA-Seq QC 2.2.2d+galaxy1
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fqualimap_rnaseq%2Fqualimap_rnaseq%2F2.2.2d%2Bgalaxy1
@@ -18509,7 +18879,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: quasitools
+- biocontainers: ''
   biotools: quasitools
   bunya: ''
   description: 'A Collection of Tools for Viral Quasispecies Analysis | Abstract Summary
@@ -18585,7 +18955,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: quast
+- biocontainers: ''
   biotools: quast
   bunya:
   - 5.0.2-foss-2021a
@@ -18618,7 +18988,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: Query_Tabular
+- biocontainers: ''
   biotools: Query_Tabular
   bunya: ''
   description: Query Tabular is a Galaxy-based tool which manipulates tabular files.  Query
@@ -18644,8 +19014,8 @@
   - Workflows
   galaxy:
   - description: 'Query Tabular: using sqlite sql'
-    title: Query Tabular 3.3.1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fquery_tabular%2Fquery_tabular%2F3.3.1
+    title: Query Tabular 3.3.2
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fquery_tabular%2Fquery_tabular%2F3.3.2
   homepage: https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular
   id: query_tabular
   license: CC-BY-4.0
@@ -18659,7 +19029,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: r
+- biocontainers: ''
   biotools: r
   bunya:
   - 4.1.0-foss-2021a
@@ -18703,26 +19073,26 @@
   edam-outputs: ''
   edam-topics: ''
   galaxy:
+  - description: 'Lineage computation using StemID: generates lineage from prior clustering'
+    title: Lineage computation using StemID 3.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fraceid_trajectory%2Fraceid_trajectory%2F3.1
   - description: 'Initial processing using RaceID: performs filtering, normalisation,
       and confounder removal to generate a normalised and filtered count matrix of
       single-cell RNA data'
-    title: Initial processing using RaceID 0.2.3+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fraceid_filtnormconf%2Fraceid_filtnormconf%2F0.2.3%2Bgalaxy3
+    title: Initial processing using RaceID 3.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fraceid_filtnormconf%2Fraceid_filtnormconf%2F3.1
   - description: 'Clustering using RaceID: performs clustering, outlier detection,
       dimensional reduction'
-    title: Clustering using RaceID 0.2.3+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fraceid_clustering%2Fraceid_clustering%2F0.2.3%2Bgalaxy3
-  - description: 'Cluster Inspection using RaceID: examines gene expression within
-      clusters'
-    title: Cluster Inspection using RaceID 0.2.3+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fraceid_inspectclusters%2Fraceid_inspectclusters%2F0.2.3%2Bgalaxy3
+    title: Clustering using RaceID 3.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fraceid_clustering%2Fraceid_clustering%2F3.1
   - description: 'Lineage Branch Analysis using StemID: inspects branches of a lineage
       tree'
-    title: Lineage Branch Analysis using StemID 0.2.3+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fraceid_inspecttrajectory%2Fraceid_inspecttrajectory%2F0.2.3%2Bgalaxy3
-  - description: 'Lineage computation using StemID: generates lineage from prior clustering'
-    title: Lineage computation using StemID 0.2.3+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fraceid_trajectory%2Fraceid_trajectory%2F0.2.3%2Bgalaxy3
+    title: Lineage Branch Analysis using StemID 3.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fraceid_inspecttrajectory%2Fraceid_inspecttrajectory%2F3.1
+  - description: 'Cluster Inspection using RaceID: examines gene expression within
+      clusters'
+    title: Cluster Inspection using RaceID 3.1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fraceid_inspectclusters%2Fraceid_inspectclusters%2F3.1
   homepage: ''
   id: r-raceid
   license: ''
@@ -18734,7 +19104,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: Racon
+- biocontainers: ''
   biotools: Racon
   bunya: ''
   description: 'Consensus module for raw de novo DNA assembly of long uncorrected
@@ -18776,7 +19146,90 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ramclustr
+- biocontainers: ''
+  biotools: ragtag
+  bunya: ''
+  description: RagTag is a collection of software tools for scaffolding and improving
+    modern genome assemblies.
+  edam-inputs: []
+  edam-operations:
+  - Genome assembly
+  edam-outputs: []
+  edam-topics:
+  - Sequence assembly
+  galaxy:
+  - description: 'RagTag: reference-guided scaffolding of draft genomes'
+    title: RagTag 2.1.0+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fragtag%2Fragtag%2F2.1.0%2Bgalaxy1
+  homepage: https://github.com/malonge/RagTag
+  id: ragtag
+  license: MIT
+  name: ragtag
+  nci-gadi: ''
+  nci-if89: ''
+  pawsey: ''
+  publications:
+  - title: 'RaGOO: Fast and accurate reference-guided scaffolding of draft genomes'
+    url: https://doi.org/10.1186/s13059-019-1829-6
+  resources:
+  - title: .nan
+    url: .nan
+- biocontainers: ''
+  biotools: RaGOO
+  bunya: ''
+  description: 'fast and accurate reference-guided scaffolding of draft genomes.
+
+
+    Fast Reference-Guided Scaffolding of Genome Assembly Contigs.
+
+
+    Index of /shares/schatzlab/www-data/ragoo.
+
+
+    A tool to order and orient genome assembly contigs via Minimap2 alignments to
+    a reference genome.
+
+
+    Alonge, Michael, et al. "RaGOO: fast and accurate reference-guided scaffolding
+    of draft genomes." Genome biology 20.1 (2019): 1-17.
+
+
+    Contigs and reference fasta files may now be gzipped.
+
+
+    RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes
+    via minimap2 alignments to a closely related reference genome. The focus of this
+    tool is on practicality and therefore has the following features:'
+  edam-inputs: []
+  edam-operations:
+  - Genome assembly
+  - Sequence trimming
+  - Scaffolding
+  - Genome alignment
+  edam-outputs: []
+  edam-topics:
+  - Sequence assembly
+  - Sequencing
+  - Plant biology
+  - Cell biology
+  galaxy:
+  - description: 'RaGOO: Order and assign scaffolds'
+    title: RaGOO 1.0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdereeper%2Fragoo%2Fragoo%2F1.0
+  homepage: https://github.com/malonge/RaGOO
+  id: ragoo
+  license: MIT
+  name: RaGOO
+  nci-gadi: ''
+  nci-if89: ''
+  pawsey: ''
+  publications:
+  - title: 'RaGOO: Fast and accurate reference-guided scaffolding of draft genomes'
+    url: https://doi.org/10.1186/S13059-019-1829-6
+  resources:
+  - title: .nan
+    url: .nan
+- biocontainers: ''
   biotools: ramclustr
   bunya: ''
   description: A feature clustering algorithm for non-targeted mass spectrometric
@@ -18810,12 +19263,12 @@
   galaxy:
   - description: 'RAMClustR define experiment: Definition of experimental design used
       for record keeping and writing spectra data.'
-    title: RAMClustR define experiment 1.0.2+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Framclustr_define_experiment%2Framclustr_define_experiment%2F1.0.2%2Bgalaxy0
+    title: RAMClustR define experiment 1.0.2+galaxy2
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Framclustr_define_experiment%2Framclustr_define_experiment%2F1.0.2%2Bgalaxy2
   - description: 'RAMClustR: A feature clustering algorithm for non-targeted mass
       spectrometric metabolomics data.'
-    title: RAMClustR 1.3.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Framclustr%2Framclustr%2F1.3.0%2Bgalaxy1
+    title: RAMClustR 1.3.0+galaxy7
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Framclustr%2Framclustr%2F1.3.0%2Bgalaxy7
   homepage: https://github.com/cbroeckl/RAMClustR
   id: ramclustr
   license: GPL-2.0
@@ -18830,7 +19283,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ratatosk
+- biocontainers: ''
   biotools: ratatosk
   bunya:
   - 0.7.6.3--h43eeafb_2
@@ -18865,7 +19318,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: raven
+- biocontainers: ''
   biotools: raven
   bunya: ''
   description: 'a de novo genome assembler for long reads.
@@ -18899,7 +19352,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: rawtools
+- biocontainers: ''
   biotools: rawtools
   bunya: ''
   description: A standalone tool for extracting data directly from raw files generated
@@ -18969,7 +19422,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: RDKit
+- biocontainers: ''
   biotools: RDKit
   bunya: ''
   description: RDKit is an Open-Source Cheminformatics Software. Fast, Efficient Fragment-Based
@@ -19028,7 +19481,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: recon
+- biocontainers: ''
   biotools: recon
   bunya: ''
   description: Tool for calculating the probability of nucleosome formation along
@@ -19059,7 +19512,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: recetox-aplcms
+- biocontainers: ''
   biotools: recetox-aplcms
   bunya: ''
   description: recetox-aplcms is a tool for peak detection in mass spectrometry data.
@@ -19089,37 +19542,37 @@
   edam-topics:
   - Metabolomics
   galaxy:
-  - description: 'recetox-aplcms - align features: align peaks across samples'
-    title: recetox-aplcms - align features 0.12.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frecetox_aplcms_align_features%2Frecetox_aplcms_align_features%2F0.12.0%2Bgalaxy1
+  - description: 'recetox-aplcms - remove noise: filter noise and detect peaks in
+      high resolution mass spectrometry (HRMS) profile data'
+    title: recetox-aplcms - remove noise 0.13.2+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frecetox_aplcms_remove_noise%2Frecetox_aplcms_remove_noise%2F0.13.2%2Bgalaxy0
+  - description: 'recetox-aplcms - merge known table: join knowledge from aligned
+      features and known table.'
+    title: recetox-aplcms - merge known table 0.13.2+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frecetox_aplcms_merge_known_table%2Frecetox_aplcms_merge_known_table%2F0.13.2%2Bgalaxy0
+  - description: 'recetox-aplcms - generate feature table: generate feature table
+      from noise-removed HRMS profile data'
+    title: recetox-aplcms - generate feature table 0.13.2+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frecetox_aplcms_generate_feature_table%2Frecetox_aplcms_generate_feature_table%2F0.13.2%2Bgalaxy0
+  - description: 'recetox-aplcms - correct time: correct retention time across samples
+      for peak alignment'
+    title: recetox-aplcms - correct time 0.13.2+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frecetox_aplcms_correct_time%2Frecetox_aplcms_correct_time%2F0.13.2%2Bgalaxy0
   - description: 'recetox-aplcms - compute clusters: compute clusters of mz and rt
       across samples and assign cluster IDs to individual features'
-    title: recetox-aplcms - compute clusters 0.12.0+galaxy2
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frecetox_aplcms_compute_clusters%2Frecetox_aplcms_compute_clusters%2F0.12.0%2Bgalaxy2
+    title: recetox-aplcms - compute clusters 0.13.2+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frecetox_aplcms_compute_clusters%2Frecetox_aplcms_compute_clusters%2F0.13.2%2Bgalaxy0
+  - description: 'recetox-aplcms - align features: align peaks across samples'
+    title: recetox-aplcms - align features 0.13.2+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frecetox_aplcms_align_features%2Frecetox_aplcms_align_features%2F0.13.2%2Bgalaxy0
   - description: 'recetox-aplcms - compute template: compute retention time correction
       template feature table'
-    title: recetox-aplcms - compute template 0.12.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frecetox_aplcms_compute_template%2Frecetox_aplcms_compute_template%2F0.12.0%2Bgalaxy1
-  - description: 'recetox-aplcms - correct time: correct retention time across samples
-      for peak alignment'
-    title: recetox-aplcms - correct time 0.12.0+galaxy2
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frecetox_aplcms_correct_time%2Frecetox_aplcms_correct_time%2F0.12.0%2Bgalaxy2
-  - description: 'recetox-aplcms - generate feature table: generate feature table
-      from noise-removed HRMS profile data'
-    title: recetox-aplcms - generate feature table 0.12.0+galaxy2
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frecetox_aplcms_generate_feature_table%2Frecetox_aplcms_generate_feature_table%2F0.12.0%2Bgalaxy2
-  - description: 'recetox-aplcms - merge known table: join knowledge from aligned
-      features and known table.'
-    title: recetox-aplcms - merge known table 0.12.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frecetox_aplcms_merge_known_table%2Frecetox_aplcms_merge_known_table%2F0.12.0%2Bgalaxy1
+    title: recetox-aplcms - compute template 0.13.2+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frecetox_aplcms_compute_template%2Frecetox_aplcms_compute_template%2F0.13.2%2Bgalaxy0
   - description: 'recetox-aplcms - recover weaker signals: recover weaker signals
       from raw data using an aligned feature table'
-    title: recetox-aplcms - recover weaker signals 0.12.0+galaxy2
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frecetox_aplcms_recover_weaker_signals%2Frecetox_aplcms_recover_weaker_signals%2F0.12.0%2Bgalaxy2
-  - description: 'recetox-aplcms - remove noise: filter noise and detect peaks in
-      high resolution mass spectrometry (HRMS) profile data'
-    title: recetox-aplcms - remove noise 0.12.0+galaxy2
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frecetox_aplcms_remove_noise%2Frecetox_aplcms_remove_noise%2F0.12.0%2Bgalaxy2
+    title: recetox-aplcms - recover weaker signals 0.13.2+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frecetox_aplcms_recover_weaker_signals%2Frecetox_aplcms_recover_weaker_signals%2F0.13.2%2Bgalaxy0
   homepage: https://github.com/RECETOX/recetox-aplcms
   id: recetox-aplcms
   license: GPL-2.0
@@ -19131,7 +19584,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: red
+- biocontainers: ''
   biotools: red
   bunya: ''
   description: This is a program to detect and visualize RNA editing events at genomic
@@ -19183,7 +19636,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: repeatmasker
+- biocontainers: ''
   biotools: repeatmasker
   bunya:
   - 4.1.5--pl5321hdfd78af_0
@@ -19217,7 +19670,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: RepeatModeler2
+- biocontainers: ''
   biotools: RepeatModeler2
   bunya:
   - 2.0.4--pl5321hdfd78af_0
@@ -19258,7 +19711,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: RepeatScout
+- biocontainers: ''
   biotools: RepeatScout
   bunya: ''
   description: RepeatScout is a tool to discover repetitive substrings in DNA.
@@ -19306,7 +19759,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: rjags
+- biocontainers: ''
   biotools: rjags
   bunya:
   - 4-10-foss-2021a-r-4.1.0
@@ -19332,7 +19785,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: rmassbank
+- biocontainers: ''
   biotools: rmassbank
   bunya: ''
   description: Workflow to process tandem MS files and build MassBank records. Functions
@@ -19354,8 +19807,8 @@
   - Metabolomics
   galaxy:
   - description: 'RMassBank: '
-    title: RMassBank 3.0.0+galaxy2
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frmassbank%2Frmassbank%2F3.0.0%2Bgalaxy2
+    title: RMassBank 3.0.0+galaxy3
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frecetox%2Frmassbank%2Frmassbank%2F3.0.0%2Bgalaxy3
   homepage: http://bioconductor.org/packages/release/bioc/html/RMassBank.html
   id: rmassbank
   license: Artistic-2.0
@@ -19391,7 +19844,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: rmblast
+- biocontainers: ''
   biotools: rmblast
   bunya: ''
   description: RMBlast is a RepeatMasker compatible version of the standard NCBI blastn
@@ -19446,6 +19899,37 @@
   resources:
   - title: .nan
     url: .nan
+- biocontainers: ''
+  biotools: rnaQUAST
+  bunya: ''
+  description: Quality assessment tool for de novo transcriptome assemblies.
+  edam-inputs: []
+  edam-operations:
+  - De-novo assembly
+  - Transcriptome assembly
+  - Sequence assembly validation
+  edam-outputs: []
+  edam-topics:
+  - Sequence assembly
+  - Transcriptomics
+  - RNA-seq
+  galaxy:
+  - description: 'rnaQUAST: A quality assessment tool for De Novo transcriptome assemblies'
+    title: rnaQUAST 2.2.3+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Frnaquast%2Frna_quast%2F2.2.3%2Bgalaxy0
+  homepage: http://cab.spbu.ru/software/rnaquast/
+  id: rnaquast
+  license: Unlicense
+  name: rnaQUAST
+  nci-gadi: ''
+  nci-if89: ''
+  pawsey: ''
+  publications:
+  - title: 'RnaQUAST: A quality assessment tool for de novo transcriptome assemblies'
+    url: https://doi.org/10.1093/bioinformatics/btw218
+  resources:
+  - title: .nan
+    url: .nan
 - biocontainers: roary
   biotools: roary
   bunya: ''
@@ -19463,8 +19947,8 @@
   galaxy:
   - description: 'Roary: the pangenome pipeline - Quickly generate a core gene alignment
       from gff3 files'
-    title: Roary 3.13.0+galaxy2
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Froary%2Froary%2F3.13.0%2Bgalaxy2
+    title: Roary 3.13.0+galaxy3
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Froary%2Froary%2F3.13.0%2Bgalaxy3
   homepage: https://sanger-pathogens.github.io/Roary/
   id: roary
   license: ''
@@ -19607,7 +20091,8 @@
   license: ''
   name: rseqc
   nci-gadi: ''
-  nci-if89: ''
+  nci-if89:
+  - 5.0.1
   pawsey: ''
   publications:
   - title: 'RSeQC: Quality control of RNA-seq experiments'
@@ -19617,7 +20102,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: rstudio
+- biocontainers: ''
   biotools: rstudio
   bunya: ''
   description: Integrated development environment (IDE) for the R programming language.
@@ -19647,7 +20132,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: rtg_core
+- biocontainers: ''
   biotools: rtg_core
   bunya: ''
   description: 'RTG Core: Software for alignment and analysis of next-gen sequencing
@@ -19699,7 +20184,30 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: sailfish
+- biocontainers: ''
+  biotools: ''
+  bunya: ''
+  description: ''
+  edam-inputs: ''
+  edam-operations: ''
+  edam-outputs: ''
+  edam-topics: ''
+  galaxy:
+  - description: 's3segmenter: single cell (nuclei and cytoplasm) label masks.'
+    title: s3segmenter 1.3.12+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fperssond%2Fs3segmenter%2Fs3segmenter%2F1.3.12%2Bgalaxy0
+  homepage: ''
+  id: s3segmenter
+  license: ''
+  name: s3segmenter
+  nci-gadi: ''
+  nci-if89: ''
+  pawsey: ''
+  publications: ''
+  resources:
+  - title: .nan
+    url: .nan
+- biocontainers: ''
   biotools: sailfish
   bunya: ''
   description: A software tool that implements a novel, is an alignment-free algorithm
@@ -19732,7 +20240,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: salmon
+- biocontainers: ''
   biotools: salmon
   bunya:
   - 1.4.0-gompi-2021a
@@ -19801,7 +20309,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: SALSA
+- biocontainers: ''
   biotools: SALSA
   bunya:
   - '2.3'
@@ -19822,10 +20330,7 @@
   - Sequence assembly
   - DNA binding sites
   - Mapping
-  galaxy:
-  - description: 'SALSA: scaffold long read assemblies with Hi-C'
-    title: SALSA 2.3+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsalsa%2Fsalsa%2F2.3%2Bgalaxy3
+  galaxy: ''
   homepage: https://github.com/machinegun/SALSA
   id: salsa
   license: MIT
@@ -19908,7 +20413,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: sambamba
+- biocontainers: ''
   biotools: sambamba
   bunya: ''
   description: This tool is a high performance modern robust and fast tool (and library),
@@ -20005,6 +20510,12 @@
   - Sequencing
   - Rare diseases
   galaxy:
+  - description: 'Samtools markdup: marks duplicate alignments'
+    title: Samtools markdup 1.15.1+galaxy2
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsamtools_markdup%2Fsamtools_markdup%2F1.15.1%2Bgalaxy2
+  - description: 'Samtools coverage: computes the depth at each position or region'
+    title: Samtools coverage 1.15.1+galaxy2
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsamtools_coverage%2Fsamtools_coverage%2F1.15.1%2Bgalaxy2
   - description: 'Samtools split: BAM dataset on readgroups'
     title: Samtools split 1.15.1+galaxy2
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsamtools_split%2Fsamtools_split%2F1.15.1%2Bgalaxy2
@@ -20063,6 +20574,10 @@
   - description: 'Samtools depth: compute the depth at each position or region'
     title: Samtools depth 1.15.1+galaxy2
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsamtools_depth%2Fsamtools_depth%2F1.15.1%2Bgalaxy2
+  - description: 'Samtools fixmate: fill mate coordinates, ISIZE and mate related
+      flags'
+    title: Samtools fixmate 1.15.1+galaxy2
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsamtools_fixmate%2Fsamtools_fixmate%2F1.15.1%2Bgalaxy2
   - description: 'samtools BAM to CRAM: convert BAM alignments to CRAM format'
     title: samtools BAM to CRAM 1.15.1+galaxy2
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsamtools_bam_to_cram%2Fsamtools_bam_to_cram%2F1.15.1%2Bgalaxy2
@@ -20090,7 +20605,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: scanpy
+- biocontainers: ''
   biotools: scanpy
   bunya: ''
   description: Scalable toolkit for analyzing single-cell gene expression data. It
@@ -20106,27 +20621,27 @@
   - Cell biology
   - Genetics
   galaxy:
-  - description: 'Remove confounders: with scanpy'
-    title: Remove confounders 1.9.6+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_remove_confounders%2Fscanpy_remove_confounders%2F1.9.6%2Bgalaxy3
+  - description: 'Filter: with scanpy'
+    title: Filter 1.9.6+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_filter%2Fscanpy_filter%2F1.9.6%2Bgalaxy4
   - description: 'Plot: with scanpy'
-    title: Plot 1.9.6+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_plot%2Fscanpy_plot%2F1.9.6%2Bgalaxy3
-  - description: 'Inspect and manipulate: with scanpy'
-    title: Inspect and manipulate 1.9.6+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_inspect%2Fscanpy_inspect%2F1.9.6%2Bgalaxy3
+    title: Plot 1.9.6+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_plot%2Fscanpy_plot%2F1.9.6%2Bgalaxy4
   - description: 'Cluster, infer trajectories and embed: with scanpy'
-    title: Cluster, infer trajectories and embed 1.9.6+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_cluster_reduce_dimension%2Fscanpy_cluster_reduce_dimension%2F1.9.6%2Bgalaxy3
-  - description: 'Filter: with scanpy'
-    title: Filter 1.9.6+galaxy2
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_filter%2Fscanpy_filter%2F1.9.6%2Bgalaxy2
+    title: Cluster, infer trajectories and embed 1.9.6+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_cluster_reduce_dimension%2Fscanpy_cluster_reduce_dimension%2F1.9.6%2Bgalaxy4
+  - description: 'Remove confounders: with scanpy'
+    title: Remove confounders 1.9.6+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_remove_confounders%2Fscanpy_remove_confounders%2F1.9.6%2Bgalaxy4
+  - description: 'Normalize: and impute with scanpy'
+    title: Normalize 1.9.6+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_normalize%2Fscanpy_normalize%2F1.9.6%2Bgalaxy4
+  - description: 'Inspect and manipulate: with scanpy'
+    title: Inspect and manipulate 1.9.6+galaxy4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_inspect%2Fscanpy_inspect%2F1.9.6%2Bgalaxy4
   - description: 'AnnData Operations: modifies metadata and flags genes'
     title: AnnData Operations 1.8.1+galaxy93
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fanndata_ops%2Fanndata_ops%2F1.8.1%2Bgalaxy93
-  - description: 'Normalize: and impute with scanpy'
-    title: Normalize 1.9.6+galaxy3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_normalize%2Fscanpy_normalize%2F1.9.6%2Bgalaxy3
   - description: 'Scanpy FilterGenes: based on counts and numbers of cells expressed'
     title: Scanpy FilterGenes 1.9.3+galaxy0
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_filter_genes%2Fscanpy_filter_genes%2F1.9.3%2Bgalaxy0
@@ -20224,7 +20739,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: scater
+- biocontainers: ''
   biotools: scater
   bunya: ''
   description: Pre-processing, quality control, normalization and visualization of
@@ -20295,7 +20810,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: scikit-image
+- biocontainers: ''
   biotools: scikit-image
   bunya: ''
   description: Scikit-image contains image processing algorithms for SciPy, including
@@ -20312,24 +20827,24 @@
   - Software engineering
   - Literature and language
   galaxy:
+  - description: 'Filter 2-D image: with scipy'
+    title: Filter 2-D image 1.12.0+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2F2d_simple_filter%2Fip_filter_standard%2F1.12.0%2Bgalaxy1
+  - description: 'Filter label map by rules: '
+    title: Filter label map by rules 0.0.1-4
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2F2d_filter_segmentation_by_features%2Fip_2d_filter_segmentation_by_features%2F0.0.1-4
+  - description: 'Threshold image: with scikit-image'
+    title: Threshold image 0.18.1+galaxy3
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2F2d_auto_threshold%2Fip_threshold%2F0.18.1%2Bgalaxy3
   - description: 'Extract image features: with scikit-image'
     title: Extract image features 0.18.1+galaxy0
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2F2d_feature_extraction%2Fip_2d_feature_extraction%2F0.18.1%2Bgalaxy0
   - description: 'Count objects in label map: '
     title: Count objects in label map 0.0.5-2
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2Fcount_objects%2Fip_count_objects%2F0.0.5-2
-  - description: 'Threshold image: with scikit-image'
-    title: Threshold image 0.18.1+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2F2d_auto_threshold%2Fip_threshold%2F0.18.1%2Bgalaxy1
-  - description: 'Filter label map by rules: '
-    title: Filter label map by rules 0.0.1-2
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2F2d_filter_segmentation_by_features%2Fip_2d_filter_segmentation_by_features%2F0.0.1-2
   - description: 'Perform histogram equalization: with scikit-image'
-    title: Perform histogram equalization 0.0.1-2
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2F2d_histogram_equalization%2Fip_histogram_equalization%2F0.0.1-2
-  - description: 'Filter 2D image: with scikit-image'
-    title: Filter 2D image 0.0.3-3
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2F2d_simple_filter%2Fip_filter_standard%2F0.0.3-3
+    title: Perform histogram equalization 0.18.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2F2d_histogram_equalization%2Fip_histogram_equalization%2F0.18.1%2Bgalaxy0
   - description: 'Convert binary image to label map: '
     title: Convert binary image to label map 0.5+galaxy0
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2Fbinary2labelimage%2Fip_binary_to_labelimage%2F0.5%2Bgalaxy0
@@ -20537,7 +21052,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: seqkit
+- biocontainers: ''
   biotools: seqkit
   bunya: ''
   description: FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide
@@ -20689,7 +21204,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: seurat
+- biocontainers: ''
   biotools: seurat
   bunya: ''
   description: Seurat is an R package designed for QC, analysis, and exploration of
@@ -20706,6 +21221,54 @@
   - description: 'Seurat: - toolkit for exploration of single-cell RNA-seq data'
     title: Seurat 4.3.0.1+galaxy1
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseurat%2Fseurat%2F4.3.0.1%2Bgalaxy1
+  - description: 'Seurat ScaleData: scale and center genes'
+    title: Seurat ScaleData 4.0.4+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_scale_data%2Fseurat_scale_data%2F4.0.4%2Bgalaxy0
+  - description: 'Seurat RunTSNE: run t-SNE dimensionality reduction'
+    title: Seurat RunTSNE 4.0.4+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_run_tsne%2Fseurat_run_tsne%2F4.0.4%2Bgalaxy0
+  - description: 'Seurat RunPCA: run a PCA dimensionality reduction'
+    title: Seurat RunPCA 4.0.4+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_run_pca%2Fseurat_run_pca%2F4.0.4%2Bgalaxy0
+  - description: 'Seurat Read10x: Loads Tabular or 10x data into a serialized seurat
+      R object'
+    title: Seurat Read10x 4.0.4+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_read10x%2Fseurat_read10x%2F4.0.4%2Bgalaxy0
+  - description: 'Plot: with Seurat'
+    title: Plot 4.0.4+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_plot%2Fseurat_plot%2F4.0.4%2Bgalaxy0
+  - description: 'Seurat FindVariableGenes: identify variable genes'
+    title: Seurat FindVariableGenes 4.0.4+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_find_variable_genes%2Fseurat_find_variable_genes%2F4.0.4%2Bgalaxy0
+  - description: 'Seurat FindNeighbours: constructs a Shared Nearest Neighbor (SNN)
+      Graph'
+    title: Seurat FindNeighbours 4.0.4+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_find_neighbours%2Fseurat_find_neighbours%2F4.0.4%2Bgalaxy0
+  - description: 'Seurat FindMarkers: find markers (differentially expressed genes)'
+    title: Seurat FindMarkers 4.0.4+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_find_markers%2Fseurat_find_markers%2F4.0.4%2Bgalaxy0
+  - description: 'Seurat FilterCells: filter cells in a Seurat object'
+    title: Seurat FilterCells 4.0.4+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_filter_cells%2Fseurat_filter_cells%2F4.0.4%2Bgalaxy0
+  - description: 'Seurat Export2CellBrowser: produces files for UCSC CellBrowser import.'
+    title: Seurat Export2CellBrowser 4.0.4+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_export_cellbrowser%2Fseurat_export_cellbrowser%2F4.0.4%2Bgalaxy0
+  - description: 'Seurat CreateSeuratObject: create a Seurat object'
+    title: Seurat CreateSeuratObject 2.3.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_create_seurat_object%2Fseurat_create_seurat_object%2F2.3.1%2Bgalaxy0
+  - description: 'Seurat Plot dimension reduction: graphs the output of a dimensional
+      reduction technique (PCA by default). Cells are colored by their identity class.'
+    title: Seurat Plot dimension reduction 4.0.4+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_dim_plot%2Fseurat_dim_plot%2F4.0.4%2Bgalaxy0
+  - description: 'Seurat FindClusters: find clusters of cells'
+    title: Seurat FindClusters 4.0.4+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_find_clusters%2Fseurat_find_clusters%2F4.0.4%2Bgalaxy0
+  - description: 'Seurat NormaliseData: normalise data'
+    title: Seurat NormaliseData 4.0.4+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_normalise_data%2Fseurat_normalise_data%2F4.0.4%2Bgalaxy0
+  - description: 'Seurat UMAP: dimensionality reduction'
+    title: Seurat UMAP 4.0.4+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_run_umap%2Fseurat_run_umap%2F4.0.4%2Bgalaxy0
   homepage: https://satijalab.org/seurat/
   id: seurat
   license: MIT
@@ -20719,7 +21282,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: shasta
+- biocontainers: ''
   biotools: shasta
   bunya: ''
   description: De novo assembly from Oxford Nanopore reads.
@@ -20793,7 +21356,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: sicer
+- biocontainers: ''
   biotools: sicer
   bunya: ''
   description: A clustering approach for identification of enriched domains from histone
@@ -20824,7 +21387,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: simtext
+- biocontainers: ''
   biotools: simtext
   bunya: ''
   description: 'A text mining framework for interactive analysis and visualization
@@ -20893,7 +21456,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: SISTR
+- biocontainers: ''
   biotools: SISTR
   bunya: ''
   description: The Salmonella In Silico Typing Resource (SISTR) is an open-source
@@ -20972,7 +21535,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: slow5tools
+- biocontainers: ''
   biotools: slow5tools
   bunya: ''
   description: 'Slow5tools is a simple toolkit for converting (FAST5 <-> SLOW5), compressing,
@@ -21032,7 +21595,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: Smudgeplots
+- biocontainers: ''
   biotools: Smudgeplots
   bunya: ''
   description: 'Reference-free profiling of polyploid genomes | Inference of ploidy
@@ -21137,7 +21700,50 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: SNAPPy
+- biocontainers: ''
+  biotools: snapatac
+  bunya: ''
+  description: SnapATAC (Single Nucleus Analysis Pipeline for ATAC-seq) is a fast,
+    accurate and comprehensive method for analyzing single cell ATAC-seq datasets.
+  edam-inputs: []
+  edam-operations:
+  - Essential dynamics
+  - Dimensionality reduction
+  - Gene expression profiling
+  edam-outputs: []
+  edam-topics:
+  - Epigenomics
+  - Cell biology
+  - Chromosome conformation capture
+  - Mapping
+  - Sequencing
+  galaxy:
+  - description: 'SnapATAC2 Preprocessing: and integration'
+    title: SnapATAC2 Preprocessing 2.6.4+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnapatac2_preprocessing%2Fsnapatac2_preprocessing%2F2.6.4%2Bgalaxy1
+  - description: 'SnapATAC2 peaks and motif: analysis'
+    title: SnapATAC2 peaks and motif 2.6.4+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnapatac2_peaks_and_motif%2Fsnapatac2_peaks_and_motif%2F2.6.4%2Bgalaxy1
+  - description: 'SnapATAC2 Clustering: and dimension reduction'
+    title: SnapATAC2 Clustering 2.6.4+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnapatac2_clustering%2Fsnapatac2_clustering%2F2.6.4%2Bgalaxy1
+  - description: 'SnapATAC2 Plotting: '
+    title: SnapATAC2 Plotting 2.6.4+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnapatac2_plotting%2Fsnapatac2_plotting%2F2.6.4%2Bgalaxy1
+  homepage: https://github.com/r3fang/SnapATAC
+  id: snapatac
+  license: GPL-3.0
+  name: SnapATAC
+  nci-gadi: ''
+  nci-if89: ''
+  pawsey: ''
+  publications:
+  - title: Comprehensive analysis of single cell ATAC-seq data with SnapATAC
+    url: https://doi.org/10.1038/S41467-021-21583-9
+  resources:
+  - title: .nan
+    url: .nan
+- biocontainers: ''
   biotools: SNAPPy
   bunya:
   - 1.1.8-gcccore-10.3.0
@@ -21208,6 +21814,8 @@
   nci-gadi: ''
   nci-if89:
   - 2.0.2
+  - 2.3.3
+  - '2.4'
   pawsey: ''
   publications:
   - title: Accurate detection of complex structural variations using single-molecule
@@ -21416,7 +22024,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: snpsift
+- biocontainers: ''
   biotools: snpsift
   bunya: ''
   description: Toolbox that allows you to filter and manipulate annotated vcf files.
@@ -21467,7 +22075,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: soapdenovo2
+- biocontainers: ''
   biotools: soapdenovo2
   bunya: ''
   description: SOAPdenovo2 is a next generation sequencing reads de novo assembler.
@@ -21652,7 +22260,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: srf
+- biocontainers: ''
   biotools: srf
   bunya: ''
   description: Spectral Repeat Finder (SRF) is a program to find repeats through an
@@ -21700,7 +22308,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: sra-tools
+- biocontainers: ''
   biotools: sra-tools
   bunya:
   - 3.0.3-gompi-2022a
@@ -21717,14 +22325,14 @@
   - Sequencing
   galaxy:
   - description: 'Download and Extract Reads in BAM: format from NCBI SRA'
-    title: Download and Extract Reads in BAM 3.1.1+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Fsam_dump%2F3.1.1%2Bgalaxy0
+    title: Download and Extract Reads in BAM 3.1.1+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Fsam_dump%2F3.1.1%2Bgalaxy1
   - description: 'Faster Download and Extract Reads in FASTQ: format from NCBI SRA'
-    title: Faster Download and Extract Reads in FASTQ 3.1.1+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffasterq_dump%2F3.1.1%2Bgalaxy0
+    title: Faster Download and Extract Reads in FASTQ 3.1.1+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffasterq_dump%2F3.1.1%2Bgalaxy1
   - description: 'Download and Extract Reads in FASTQ: format from NCBI SRA'
-    title: Download and Extract Reads in FASTQ 3.1.1+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffastq_dump%2F3.1.1%2Bgalaxy0
+    title: Download and Extract Reads in FASTQ 3.1.1+galaxy1
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffastq_dump%2F3.1.1%2Bgalaxy1
   homepage: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc
   id: sra-tools
   license: ''
@@ -21760,7 +22368,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ssw
+- biocontainers: ''
   biotools: ssw
   bunya:
   - 1.1-gcccore-10.3.0
@@ -21951,7 +22559,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: staramr
+- biocontainers: ''
   biotools: staramr
   bunya: ''
   description: staramr (*AMR) scans bacterial genome contigs against the ResFinder,
@@ -21984,7 +22592,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: star-fusion
+- biocontainers: ''
   biotools: star-fusion
   bunya: ''
   description: STAR-Fusion, a method that is both fast and accurate in identifying
@@ -22011,7 +22619,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: stringtie
+- biocontainers: ''
   biotools: stringtie
   bunya:
   - 2.1.7-gcc-10.3.0
@@ -22084,7 +22692,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: super-focus
+- biocontainers: ''
   biotools: super-focus
   bunya: ''
   description: An agile homology-based approach using a reduced SEED database to report
@@ -22113,7 +22721,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: suppa
+- biocontainers: ''
   biotools: suppa
   bunya:
   - 2.3--py_2
@@ -22142,7 +22750,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: svim-asm
+- biocontainers: ''
   biotools: svim-asm
   bunya: ''
   description: 'Structural variant detection from haploid and diploid genome assemblies.
@@ -22182,7 +22790,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: SyRI
+- biocontainers: ''
   biotools: SyRI
   bunya: ''
   description: 'SyRI is tool for finding genomic rearrangements and local sequence
@@ -22229,7 +22837,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: targetfinder.org
+- biocontainers: ''
   biotools: targetfinder.org
   bunya: ''
   description: Targetfinder.org provides a web based resource that allows users to
@@ -22287,7 +22895,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: tbl2asn
+- biocontainers: ''
   biotools: tbl2asn
   bunya:
   - 20220427-linux64
@@ -22323,7 +22931,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: tb-profiler
+- biocontainers: ''
   biotools: tb-profiler
   bunya: ''
   description: A tool for drug resistance prediction from _M. tuberculosis_ genomic
@@ -22355,7 +22963,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: combat-tb_workbench
+- biocontainers: ''
   biotools: combat-tb_workbench
   bunya: ''
   description: The COMBAT-TB Workbench is an IRIDA based, module workbench for M.
@@ -22387,7 +22995,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: tensorflow
+- biocontainers: ''
   biotools: tensorflow
   bunya: ''
   description: 'Prediction of cognitive impairment via deep learning trained with
@@ -22433,7 +23041,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: TEsorter
+- biocontainers: ''
   biotools: TEsorter
   bunya: ''
   description: 'lineage-level classification of transposable elements using conserved
@@ -22515,6 +23123,9 @@
   - description: 'Create text file: with recurring lines'
     title: Create text file 9.3+galaxy1
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_text_file_with_recurring_lines%2F9.3%2Bgalaxy1
+  - description: 'Advanced Cut: columns from a table (cut)'
+    title: Advanced Cut 9.3+galaxy2
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_cut_tool%2F9.3%2Bgalaxy2
   - description: 'Concatenate datasets: tail-to-head (cat)'
     title: Concatenate datasets 9.3+galaxy1
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_cat%2F9.3%2Bgalaxy1
@@ -22527,9 +23138,6 @@
   - description: 'Search in textfiles: (grep)'
     title: Search in textfiles 9.3+galaxy1
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_grep_tool%2F9.3%2Bgalaxy1
-  - description: 'Advanced Cut: columns from a table (cut)'
-    title: Advanced Cut 9.3+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_cut_tool%2F9.3%2Bgalaxy1
   - description: 'Sort: data in ascending or descending order'
     title: Sort 9.3+galaxy1
     url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_sort_header_tool%2F9.3%2Bgalaxy1
@@ -22568,7 +23176,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ThermoRawFileParser
+- biocontainers: ''
   biotools: ThermoRawFileParser
   bunya: ''
   description: Open-source, crossplatform tool that converts Thermo RAW files into
@@ -22684,7 +23292,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: totalview
+- biocontainers: ''
   biotools: totalview
   bunya: ''
   description: TotalView is a debugger for High Performance Computing applications.
@@ -22707,7 +23315,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: TransDecoder
+- biocontainers: ''
   biotools: TransDecoder
   bunya:
   - 5.5.0--pl5321hdfd78af_5
@@ -22743,7 +23351,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: transit
+- biocontainers: ''
   biotools: transit
   bunya: ''
   description: A tool for the analysis of Tn-Seq data. It provides an easy to use
@@ -22786,7 +23394,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: TPP_SPC
+- biocontainers: ''
   biotools: TPP_SPC
   bunya: ''
   description: Institute for Systems Biology "Trans-Proteomic Pipeline"
@@ -22879,7 +23487,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: trf
+- biocontainers: ''
   biotools: trf
   bunya: ''
   description: Tandem Repeats Finder. Find tandem repeats in DNA sequences without
@@ -22932,7 +23540,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: trimal
+- biocontainers: ''
   biotools: trimal
   bunya: ''
   description: Tool for the automated removal of spurious sequences or poorly aligned
@@ -22972,7 +23580,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: trim_galore
+- biocontainers: ''
   biotools: trim_galore
   bunya: ''
   description: A wrapper tool around Cutadapt and FastQC to consistently apply quality
@@ -23056,7 +23664,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: trinity
+- biocontainers: ''
   biotools: trinity
   bunya:
   - 2.9.1-foss-2021a
@@ -23137,7 +23745,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: trinotate
+- biocontainers: ''
   biotools: trinotate
   bunya:
   - 3.2.2--pl5321hdfd78af_1
@@ -23169,7 +23777,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: trnascan-se
+- biocontainers: ''
   biotools: trnascan-se
   bunya: ''
   description: A program for improved detection of transfer RNA genes in genomic sequence.
@@ -23202,7 +23810,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: trycycler
+- biocontainers: ''
   biotools: trycycler
   bunya: ''
   description: 'Trycycler: consensus long-read assemblies for bacterial genomes'
@@ -23252,7 +23860,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: UCSC_Genome_Browser_Utilities
+- biocontainers: ''
   biotools: UCSC_Genome_Browser_Utilities
   bunya: ''
   description: Utilities for handling sequences and assemblies from the UCSC Genome
@@ -23293,7 +23901,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: umi-tools
+- biocontainers: ''
   biotools: umi-tools
   bunya: ''
   description: Tools for handling Unique Molecular Identifiers in NGS data sets.
@@ -23359,8 +23967,8 @@
   - Sequence assembly
   galaxy:
   - description: 'Create assemblies with Unicycler: pipeline for bacterial genomes'
-    title: Create assemblies with Unicycler 0.5.0+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Funicycler%2Funicycler%2F0.5.0%2Bgalaxy1
+    title: Create assemblies with Unicycler 0.5.1+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Funicycler%2Funicycler%2F0.5.1%2Bgalaxy0
   homepage: https://github.com/rrwick/Unicycler
   id: unicycler
   license: GPL-3.0
@@ -23375,7 +23983,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: unipept
+- biocontainers: ''
   biotools: unipept
   bunya: ''
   description: Metaproteomics data analysis with a focus on interactive data visualizations.
@@ -23415,7 +24023,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: uniprot
+- biocontainers: ''
   biotools: uniprot
   bunya: ''
   description: 'The universal protein knowledgebase in 2021.
@@ -23481,7 +24089,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: uniprot
+- biocontainers: ''
   biotools: uniprot
   bunya: ''
   description: 'The universal protein knowledgebase in 2021.
@@ -23504,8 +24112,8 @@
   - Proteomics experiment
   galaxy:
   - description: 'UniProt: ID mapping and retrieval'
-    title: UniProt 0.4
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Funiprot_rest_interface%2Funiprot%2F0.4
+    title: UniProt 0.6
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Funiprot_rest_interface%2Funiprot%2F0.6
   homepage: https://www.uniprot.org/
   id: uniprot_rest_interface
   license: CC-BY-4.0
@@ -23573,7 +24181,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: vep
+- biocontainers: ''
   biotools: vep
   bunya:
   - 107-gcc-11.3.0
@@ -23647,7 +24255,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: vcflib
+- biocontainers: ''
   biotools: vcflib
   bunya:
   - 1.0.3-foss-2021a-r-4.1.0
@@ -23753,7 +24361,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: vcftools
+- biocontainers: perl-vcftools-vcf
   biotools: vcftools
   bunya:
   - 0.1.16-gcc-10.3.0
@@ -23961,7 +24569,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: whatshap
+- biocontainers: ''
   biotools: whatshap
   bunya: ''
   description: Software for phasing genomic variants using DNA sequencing reads, also
@@ -23982,6 +24590,7 @@
   nci-gadi: ''
   nci-if89:
   - '1.7'
+  - '2.3'
   pawsey: ''
   publications:
   - title: 'WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing
@@ -23992,7 +24601,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: windowmasker
+- biocontainers: ''
   biotools: windowmasker
   bunya: ''
   description: windowmasker identifies and masks highly repetitive DNA sequences in
@@ -24023,7 +24632,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: winnowmap
+- biocontainers: ''
   biotools: winnowmap
   bunya: ''
   description: Winnowmap is a long-read mapping algorithm optimized for mapping ONT
@@ -24053,7 +24662,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: workflow4metabolomics
+- biocontainers: ''
   biotools: workflow4metabolomics
   bunya: ''
   description: First fully open-source and collaborative online platform for computational
@@ -24165,7 +24774,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: wormbase
+- biocontainers: ''
   biotools: wormbase
   bunya: ''
   description: Caenorhabditis elegans genome database. International consortium of
@@ -24230,7 +24839,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: xcms
+- biocontainers: ''
   biotools: xcms
   bunya: ''
   description: Framework for processing and visualization of chromatographically separated
@@ -24266,6 +24875,14 @@
   - Data visualisation
   - Metabolomics
   galaxy:
+  - description: 'xcms plot raw: Plot raw data filtered by m/z range and retention
+      time (RT) range'
+    title: xcms plot raw 4.0.0+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fworkflow4metabolomics%2Fxcms_plot_raw%2Fxcms_plot_raw%2F4.0.0%2Bgalaxy0
+  - description: 'xcms plot eic: Plot the extracted ion chromatogram (EIC) from mzML
+      file'
+    title: xcms plot eic 4.0.0+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fworkflow4metabolomics%2Fxcms_plot_eic%2Fxcms_plot_eic%2F4.0.0%2Bgalaxy0
   - description: 'xcms get a sampleMetadata file: which need to be filled with extra
       information'
     title: xcms get a sampleMetadata file 3.4.4.0
@@ -24364,7 +24981,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: xtandem
+- biocontainers: tandem
   biotools: xtandem
   bunya: ''
   description: Matches tandem mass spectra with peptide sequences.
@@ -24415,7 +25032,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: yahs
+- biocontainers: ''
   biotools: yahs
   bunya: ''
   description: YaHS is scaffolding tool using Hi-C data. It relies on a new algorithm
@@ -24432,8 +25049,8 @@
   - DNA binding sites
   galaxy:
   - description: 'YAHS: yet another HI-C scaffolding tool'
-    title: YAHS 1.2a.2+galaxy1
-    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fyahs%2Fyahs%2F1.2a.2%2Bgalaxy1
+    title: YAHS 1.2a.2+galaxy2
+    url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fyahs%2Fyahs%2F1.2a.2%2Bgalaxy2
   homepage: https://github.com/c-zhou/yahs
   id: yahs
   license: MIT
@@ -24448,7 +25065,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: YeastMine
+- biocontainers: ''
   biotools: YeastMine
   bunya: ''
   description: Search and retrieve S. cerevisiae data, populated by SGD and powered
@@ -24492,7 +25109,7 @@
   resources:
   - title: .nan
     url: .nan
-- biocontainers: ZebrafishMine
+- biocontainers: ''
   biotools: ZebrafishMine
   bunya: ''
   description: "ZebrafishMine is powered by the InterMIne data warehouse system, and\