diff --git a/data/data.yaml b/data/data.yaml index c463713..2305051 100644 --- a/data/data.yaml +++ b/data/data.yaml @@ -27,11 +27,16 @@ description: Mass screening of contigs for antimicrobial resistance or virulence genes. galaxy: - - title: ABRicate List 1.0.1 + - description: 'ABRicate List: List all of abricate''s available databases.' + title: ABRicate List 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fabricate%2Fabricate_list%2F1.0.1 - - title: ABRicate 1.0.1 + - description: 'ABRicate: Mass screening of contigs for antimicrobial and virulence + genes' + title: ABRicate 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fabricate%2Fabricate%2F1.0.1 - - title: ABRicate Summary 1.0.1 + - description: 'ABRicate Summary: Combine ABRicate results into a simple matrix + of gene presence/absence' + title: ABRicate Summary 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fabricate%2Fabricate_summary%2F1.0.1 homepage: https://github.com/tseemann/abricate id: abricate @@ -50,7 +55,8 @@ bunya: '' description: De novo genome sequence assembler using short reads. galaxy: - - title: ABySS 2.3.7+galaxy0 + - description: 'ABySS: de novo sequence assembler' + title: ABySS 2.3.7+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fabyss%2Fabyss-pe%2F2.3.7%2Bgalaxy0 homepage: https://github.com/bcgsc/abyss/ id: abyss @@ -134,7 +140,8 @@ and a package of molecular simulation programs which includes source code and demos.' galaxy: - - title: Generate MD topologies for small molecules 21.10+galaxy0 + - description: 'Generate MD topologies for small molecules: using acpype' + title: Generate MD topologies for small molecules 21.10+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fchemteam%2Fambertools_acpype%2Fambertools_acpype%2F21.10%2Bgalaxy0 homepage: http://ambermd.org/ id: amber @@ -164,7 +171,8 @@ itself. The suite can also be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB), with generalized Born solvent models. galaxy: - - title: MMPBSA/MMGBSA 21.10+galaxy0 + - description: 'MMPBSA/MMGBSA: tool for estimating ligand binding affinities' + title: MMPBSA/MMGBSA 21.10+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fchemteam%2Fmmpbsa_mmgbsa%2Fmmpbsa_mmgbsa%2F21.10%2Bgalaxy0 homepage: http://ambermd.org/#AmberTools id: ambertools @@ -252,13 +260,17 @@ bunya: '' description: '' galaxy: - - title: Export AnnData and loom files 0.10.3+galaxy0 + - description: 'Export AnnData and loom files: Interconvert AnnData and Loom formats' + title: Export AnnData and loom files 0.10.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fanndata_export%2Fanndata_export%2F0.10.3%2Bgalaxy0 - - title: Import Anndata and loom 0.10.3+galaxy0 + - description: 'Import Anndata and loom: from different format' + title: Import Anndata and loom 0.10.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fanndata_import%2Fanndata_import%2F0.10.3%2Bgalaxy0 - - title: Manipulate AnnData 0.10.3+galaxy0 + - description: 'Manipulate AnnData: object' + title: Manipulate AnnData 0.10.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fanndata_manipulate%2Fanndata_manipulate%2F0.10.3%2Bgalaxy0 - - title: Inspect AnnData 0.10.3+galaxy0 + - description: 'Inspect AnnData: object' + title: Inspect AnnData 0.10.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fanndata_inspect%2Fanndata_inspect%2F0.10.3%2Bgalaxy0 homepage: '' id: anndata @@ -280,7 +292,8 @@ be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. galaxy: - - title: annotateMyIDs 3.18.0+galaxy0 + - description: 'annotateMyIDs: annotate a generic set of identifiers' + title: annotateMyIDs 3.18.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fannotatemyids%2Fannotatemyids%2F3.18.0%2Bgalaxy0 homepage: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fannotatemyids%2Fannotatemyids%2F3.12.0%2Bgalaxy1 id: annotatemyids @@ -300,7 +313,9 @@ and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. galaxy: - - title: Antismash 6.1.1+galaxy1 + - description: 'Antismash: allows the genome-wide identification, annotation and + analysis of secondary metabolite biosynthesis gene clusters' + title: Antismash 6.1.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fantismash%2Fantismash%2F6.1.1%2Bgalaxy1 homepage: https://antismash.secondarymetabolites.org/#!/start id: antismash @@ -371,7 +386,8 @@ bunya: '' description: ARAGORN detects tRNA, mtRNA info about tmRNA, and tmRNA genes galaxy: - - title: tRNA and tmRNA 0.6 + - description: 'tRNA and tmRNA: prediction (Aragorn)' + title: tRNA and tmRNA 0.6 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftrna_prediction%2Faragorn_trna%2F0.6 homepage: http://www.ansikte.se/ARAGORN/ id: aragorn @@ -411,11 +427,14 @@ and truncations of genes (i.e., breakpoints in introns and intergenic regions). Arriba is the winner of the DREAM SMC-RNA Challenge. galaxy: - - title: Arriba 2.4.0+galaxy1 + - description: 'Arriba: detect gene fusions from STAR aligned RNA-Seq data' + title: Arriba 2.4.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Farriba%2Farriba%2F2.4.0%2Bgalaxy1 - - title: Arriba Get Filters 2.4.0+galaxy1 + - description: 'Arriba Get Filters: to history' + title: Arriba Get Filters 2.4.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Farriba_get_filters%2Farriba_get_filters%2F2.4.0%2Bgalaxy1 - - title: Arriba Draw Fusions 2.4.0+galaxy1 + - description: 'Arriba Draw Fusions: ' + title: Arriba Draw Fusions 2.4.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Farriba_draw_fusions%2Farriba_draw_fusions%2F2.4.0%2Bgalaxy1 homepage: https://github.com/suhrig/arriba/ id: arriba @@ -496,9 +515,11 @@ as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. galaxy: - - title: Augustus 3.4.0+galaxy1 + - description: 'Augustus: gene prediction for prokaryotic and eukaryotic genomes' + title: Augustus 3.4.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Faugustus%2Faugustus%2F3.4.0%2Bgalaxy1 - - title: Train Augustus 3.4.0+galaxy1 + - description: 'Train Augustus: ab-initio gene predictor' + title: Train Augustus 3.4.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Faugustus_training%2Faugustus_training%2F3.4.0%2Bgalaxy1 homepage: http://bioinf.uni-greifswald.de/augustus id: augustus @@ -541,13 +562,20 @@ docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use. galaxy: - - title: Prepare ligand 1.5.7+galaxy0 + - description: 'Prepare ligand: for docking with Autodock Vina' + title: Prepare ligand 1.5.7+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fautodock_vina_prepare_ligand%2Fprepare_ligand%2F1.5.7%2Bgalaxy0 - - title: Calculate the box parameters using RDKit 2021.03.5+galaxy0 + - description: 'Calculate the box parameters using RDKit: for an AutoDock Vina job + from a ligand or pocket input file (confounding box)' + title: Calculate the box parameters using RDKit 2021.03.5+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fautodock_vina_prepare_box%2Fprepare_box%2F2021.03.5%2Bgalaxy0 - - title: Prepare receptor 1.5.7+galaxy0 + - description: 'Prepare receptor: Tool to prepare receptor for docking with Autodock + Vina' + title: Prepare receptor 1.5.7+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fautodock_vina_prepare_receptor%2Fprepare_receptor%2F1.5.7%2Bgalaxy0 - - title: VINA Docking 1.2.3+galaxy0 + - description: 'VINA Docking: tool to perform protein-ligand docking with Autodock + Vina' + title: VINA Docking 1.2.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fautodock_vina%2Fdocking%2F1.2.3%2Bgalaxy0 homepage: http://vina.scripps.edu/ id: autodock_vina @@ -569,7 +597,8 @@ bunya: '' description: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids galaxy: - - title: Bakta 1.9.2+galaxy0 + - description: 'Bakta: Genome annotation via alignment-free sequence identification' + title: Bakta 1.9.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbakta%2Fbakta%2F1.9.2%2Bgalaxy0 homepage: https://github.com/oschwengers/bakta id: bakta @@ -632,12 +661,15 @@ description: BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. galaxy: - - title: Split BAM into paired- and single-end 2.5.2+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbamtools_split_paired%2Fbamtools_split_paired%2F2.5.2%2Bgalaxy1 - - title: Filter BAM 2.5.2+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fbamtools_filter%2FbamFilter%2F2.5.2%2Bgalaxy1 - - title: Split BAM by read tag value 2.5.2+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbamtools_split_tag%2Fbamtools_split_tag%2F2.5.2%2Bgalaxy1 + - 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 + - description: 'Filter BAM: datasets on a variety of attributes' + title: Filter BAM 2.5.2+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fbamtools_filter%2FbamFilter%2F2.5.2%2Bgalaxy2 + - description: 'Split BAM into paired- and single-end: reads datasets' + title: Split BAM into paired- and single-end 2.5.2+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbamtools_split_paired%2Fbamtools_split_paired%2F2.5.2%2Bgalaxy2 homepage: https://github.com/pezmaster31/bamtools id: bamtools license: MIT @@ -660,7 +692,8 @@ bunya: '' description: Bamutil provides a serie of programs to work on SAM/BAM files. galaxy: - - title: BamUtil diff 1.0.15+galaxy1 + - description: 'BamUtil diff: two coordinate sorted SAM/BAM files' + title: BamUtil diff 1.0.15+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbamutil_diff%2Fbamutil_diff%2F1.0.15%2Bgalaxy1 homepage: http://genome.sph.umich.edu/wiki/BamUtil id: bamutil_diff @@ -683,9 +716,11 @@ made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. galaxy: - - title: Bandage Info 2022.09+galaxy2 + - description: 'Bandage Info: determine statistics of de novo assembly graphs' + title: Bandage Info 2022.09+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbandage%2Fbandage_info%2F2022.09%2Bgalaxy2 - - title: Bandage Image 2022.09+galaxy4 + - description: 'Bandage Image: visualize de novo assembly graphs' + title: Bandage Image 2022.09+galaxy4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbandage%2Fbandage_image%2F2022.09%2Bgalaxy4 homepage: https://rrwick.github.io/Bandage/ id: bandage @@ -723,7 +758,8 @@ bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). galaxy: - - title: barrnap 1.2.2 + - description: 'barrnap: Locate ribosomal RNA''s in a fasta file. (GFF output)' + title: barrnap 1.2.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbarrnap%2Fbarrnap%2F1.2.2 homepage: https://github.com/tseemann/barrnap id: barrnap @@ -763,7 +799,8 @@ than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. galaxy: - - title: 'BBTools: BBduk 39.06+galaxy0' + - description: 'BBTools: BBduk: decontamination using kmers' + title: 'BBTools: BBduk 39.06+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbbtools_bbduk%2Fbbtools_bbduk%2F39.06%2Bgalaxy0 homepage: https://jgi.doe.gov/data-and-tools/bbtools/ id: bbmap @@ -790,11 +827,14 @@ by rebasing some analysis results against the parent features which were originally analysed. galaxy: - - title: Rebase GFF3 features 1.2 + - description: 'Rebase GFF3 features: against parent features' + title: Rebase GFF3 features 1.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgff3_rebase%2Fgff3.rebase%2F1.2 - - title: Table to GFF3 1.2 + - description: 'Table to GFF3: ' + title: Table to GFF3 1.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftbl2gff3%2Ftbl2gff3%2F1.2 - - title: BlastXML to gapped GFF3 1.1 + - description: 'BlastXML to gapped GFF3: ' + title: BlastXML to gapped GFF3 1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fblastxml_to_gapped_gff3%2Fblastxml_to_gapped_gff3%2F1.1 homepage: https://toolshed.g2.bx.psu.edu/view/iuc/gff3_rebase id: bcbiogff @@ -818,65 +858,111 @@ Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. galaxy: - - title: bcftools annotate 1.15.1+galaxy3 + - 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 - - title: bcftools call 1.15.1+galaxy3 + - 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 - - title: bcftools cnv 1.15.1+galaxy3 + - 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 - - title: bcftools concat 1.15.1+galaxy3 + - 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 consensus 1.15.1+galaxy3 + - 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 - - title: bcftools convert from vcf 1.15.1+galaxy3 + - 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 convert to vcf 1.15.1+galaxy3 + - 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 - - title: bcftools csq 1.15.1+galaxy3 + - 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 - - title: bcftools filter 1.15.1+galaxy3 + - 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 - - title: bcftools gtcheck 1.15.1+galaxy3 + - 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 isec 1.15.1+galaxy3 + - 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 - - title: bcftools merge 1.15.1+galaxy3 + - 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 - - title: bcftools mpileup 1.15.1+galaxy3 + - 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 - - title: bcftools norm 1.15.1+galaxy3 + - 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 - - title: bcftools counts 1.15.1+galaxy3 + - 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 - - title: bcftools dosage 1.15.1+galaxy3 + - 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 fill-AN-AC 1.15.1+galaxy3 + - 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 - - title: bcftools fill-tags 1.15.1+galaxy3 + - 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 fixploidy 1.15.1+galaxy3 + - 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 impute-info 1.15.1+galaxy3 + - 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 - - title: bcftools mendelian 1.15.1+galaxy3 + - 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 missing2ref 1.15.1+galaxy3 + - 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 - - title: bcftools setGT 1.15.1+galaxy3 + - 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 - - title: bcftools tag2tag 1.15.1+galaxy3 + - 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 - - title: bcftools query 1.15.1+galaxy3 + - 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 - - title: bcftools List Samples 1.15.1+galaxy3 + - 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 - - title: bcftools reheader 1.15.1+galaxy3 + - 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 - - title: bcftools roh 1.15.1+galaxy3 + - 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 - - title: bcftools stats 1.15.1+galaxy3 + - 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 - - title: bcftools view 1.15.1+galaxy3 + - 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 homepage: http://www.htslib.org/ id: bcftools @@ -1045,7 +1131,8 @@ description: Convert a BED format file of the proteins from a proteomics search database into a tabular format for the Multiomics Visualization Platform (MVP). galaxy: - - title: bed to protein map 0.2.0 + - description: 'bed to protein map: genomic location of proteins for MVP' + title: bed to protein map 0.2.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fbed_to_protein_map%2Fbed_to_protein_map%2F0.2.0 homepage: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/bed_to_protein_map/bed_to_protein_map/0.2.0 id: bed_to_protein_map @@ -1063,7 +1150,8 @@ bunya: '' description: '' galaxy: - - title: BED-to-GFF 2.0.0 + - description: 'BED-to-GFF: converter' + title: BED-to-GFF 2.0.0 url: https://usegalaxy.org.au/root?tool_id=bed2gff1 homepage: '' id: bed2gff1 @@ -1083,83 +1171,142 @@ description: BEDTools is an extensive suite of utilities for comparing genomic features in BED format. galaxy: - - title: bedtools GroupByBed 2.30.0 + - 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 - - title: bedtools ComplementBed 2.30.0+galaxy1 + - 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 - - title: bedtools MergeBED 2.30.0 + - 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 - - title: bedtools WindowBed 2.30.0 + - 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 - - title: bedtools SpacingBed 2.30.0 + - 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 - - title: bedtools getfasta 2.30.0+galaxy1 + - 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 - - title: bedtools RandomBed 2.30.0+galaxy1 + - 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 - - title: bedtools MultiCovBed 2.30.0 + - 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 - - title: bedtools ReldistBed 2.30.0 + - 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 - - title: bedtools SlopBed 2.30.0+galaxy1 + - 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 - - title: bedtools ExpandBed 2.30.0 + - 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 Compute both the depth and breadth of coverage 2.30.0+galaxy1 + - 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 - - title: bedtools ShuffleBed 2.30.0+galaxy1 + - 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 - - title: bedtools SortBED 2.30.0+galaxy2 + - 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 AnnotateBed 2.30.0 + - 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 - - title: bedtools MapBed 2.30.0.3 + - description: 'bedtools MapBed: apply a function to a column for each overlapping + 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 BED to BAM 2.30.0+galaxy1 + - 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 MaskFastaBed 2.30.0 + - 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 - - title: bedtools NucBed 2.30.0 + - 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 BED to IGV 2.30.0 + - 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 ClosestBed 2.30.0 + - 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 - - title: bedtools SubtractBed 2.30.0 + - 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 - - title: bedtools TagBed 2.30.0 + - 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 - - title: bedtools Genome Coverage 2.30.0 + - 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 - - title: bedtools OverlapBed 2.30.0 + - 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 Multiple Intersect 2.30.0 + - 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 - - title: bedtools BEDPE to BAM 2.30.0+galaxy1 + - 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 - - title: bedtools MakeWindowsBed 2.30.0 + - 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 - - title: bedtools JaccardBed 2.30.0 + - 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 - - title: bedtools LinksBed 2.30.0 + - 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 - - title: bedtools Intersect intervals 2.30.0+galaxy1 + - 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 - - title: bedtools BED12 to BED6 2.30.0 + - 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 - - title: bedtools BAM to BED 2.30.0+galaxy2 + - 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 - - title: bedtools FisherBed 2.30.0+galaxy1 + - 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 - - title: bedtools Merge BedGraph files 2.30.0 + - 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 - - title: bedtools ClusterBed 2.30.0 + - 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 - - title: bedtools FlankBed 2.30.0+galaxy1 + - 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 Convert from BAM to FastQ 2.27.1 + - 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 - - title: Annotate DESeq2/DEXSeq output tables 1.1.0 + - description: 'Annotate DESeq2/DEXSeq output tables: Append annotation from GTF + to differential expression tool outputs' + title: Annotate DESeq2/DEXSeq output tables 1.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdeg_annotate%2Fdeg_annotate%2F1.1.0 homepage: https://github.com/arq5x/bedtools2 id: bedtools @@ -1190,7 +1337,8 @@ The pipeline can be downloaded as a vragrant virtual machine (https://app.vagrantup.com/bellerophon/boxes/bellerophon). This is recommended, as it avoids backwards compatibility problems with TransRate' galaxy: - - title: Filter and merge 1.0+galaxy1 + - description: 'Filter and merge: chimeric reads from Arima Genomics' + title: Filter and merge 1.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbellerophon%2Fbellerophon%2F1.0%2Bgalaxy1 homepage: https://github.com/JesseKerkvliet/Bellerophon id: bellerophon @@ -1214,7 +1362,9 @@ bunya: '' description: Trim, circularise, orient and filter long read bacterial genome assemblies galaxy: - - title: Berokka 0.2.3 + - description: 'Berokka: Trim, circularise, orient and filter long read bacterial + genome assemblies' + title: Berokka 0.2.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fberokka%2Fberokka%2F0.2.3 homepage: https://github.com/tseemann/berokka id: berokka @@ -1232,9 +1382,11 @@ bunya: '' description: '' galaxy: - - title: Convert image format 6.7.0+galaxy2 + - 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 - - title: Show image info 5.7.1 + - 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 homepage: '' id: bftools @@ -1284,13 +1436,18 @@ description: Bio3D is an R package containing utilities for the analysis of protein structure, sequence and trajectory data. galaxy: - - title: PCA 2.3.4 + - description: 'PCA: - principal component analysis using Bio3D' + title: PCA 2.3.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fchemteam%2Fbio3d_pca%2Fbio3d_pca%2F2.3.4 - - title: PCA visualization 2.3.4 + - description: 'PCA visualization: - generate trajectories of principal components + of atomic motion' + title: PCA visualization 2.3.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fchemteam%2Fbio3d_pca_visualize%2Fbio3d_pca_visualize%2F2.3.4 - - title: RMSD Analysis 2.3.4 + - description: 'RMSD Analysis: using Bio3D' + title: RMSD Analysis 2.3.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fchemteam%2Fbio3d_rmsd%2Fbio3d_rmsd%2F2.3.4 - - title: RMSF Analysis 2.3.4 + - description: 'RMSF Analysis: using Bio3D' + title: RMSF Analysis 2.3.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fchemteam%2Fbio3d_rmsf%2Fbio3d_rmsf%2F2.3.4 homepage: http://thegrantlab.org/bio3d/ id: bio3d @@ -1410,10 +1567,12 @@ but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods. galaxy: - - title: Convert 2.1.15+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbiom_convert%2Fbiom_convert%2F2.1.15%2Bgalaxy0 - - title: Add metadata 2.1.15+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbiom_add_metadata%2Fbiom_add_metadata%2F2.1.15%2Bgalaxy0 + - description: 'Convert: between BIOM table formats' + title: Convert 2.1.15+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbiom_convert%2Fbiom_convert%2F2.1.15%2Bgalaxy1 + - description: 'Add metadata: to a BIOM table' + title: Add metadata 2.1.15+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbiom_add_metadata%2Fbiom_add_metadata%2F2.1.15%2Bgalaxy1 homepage: http://bioconductor.org/packages/release/bioc/html/biomformat.html id: biom-format license: GPL-2.0 @@ -1433,7 +1592,8 @@ bunya: '' description: '' galaxy: - - title: Bionano Hybrid Scaffold 3.7.0+galaxy3 + - description: 'Bionano Hybrid Scaffold: automates the scaffolding process' + title: Bionano Hybrid Scaffold 3.7.0+galaxy3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fbionano_scaffold%2Fbionano_scaffold%2F3.7.0%2Bgalaxy3 homepage: '' id: bionano_solve @@ -1477,11 +1637,16 @@ description: Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. galaxy: - - title: Translate BED transcripts 0.1.0 + - description: 'Translate BED transcripts: cDNA in 3frames or CDS' + title: Translate BED transcripts 0.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Ftranslate_bed%2Ftranslate_bed%2F0.1.0 - - title: Get open reading frames (ORFs) or coding sequences (CDSs) 0.2.3 + - description: 'Get open reading frames (ORFs) or coding sequences (CDSs): e.g. + to get peptides from ESTs' + title: Get open reading frames (ORFs) or coding sequences (CDSs) 0.2.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fpeterjc%2Fget_orfs_or_cdss%2Fget_orfs_or_cdss%2F0.2.3 - - title: Kraken taxonomic report 0.0.3 + - description: 'Kraken taxonomic report: view report of classification for multiple + samples' + title: Kraken taxonomic report 0.0.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkraken_taxonomy_report%2Fkraken_taxonomy_report%2F0.0.3 homepage: http://biopython.org/ id: biopython @@ -1507,7 +1672,8 @@ description: BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. galaxy: - - title: BioTransformer 3.0_20230403+galaxy1 + - 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 homepage: https://biotransformer.ca id: biotransformer @@ -1591,37 +1757,62 @@ The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. galaxy: - - title: NCBI BLAST+ segmasker 2.14.1+galaxy1 + - description: 'NCBI BLAST+ segmasker: low-complexity regions in protein sequences' + title: NCBI BLAST+ segmasker 2.14.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_segmasker_wrapper%2F2.14.1%2Bgalaxy1 - - title: NCBI BLAST+ convert2blastmask 2.14.1+galaxy1 + - description: 'NCBI BLAST+ convert2blastmask: Convert masking information in lower-case + masked FASTA input to file formats suitable for makeblastdb' + title: NCBI BLAST+ convert2blastmask 2.14.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_convert2blastmask_wrapper%2F2.14.1%2Bgalaxy1 - - title: NCBI BLAST+ makeblastdb 2.14.1+galaxy1 + - description: 'NCBI BLAST+ makeblastdb: Make BLAST database' + title: NCBI BLAST+ makeblastdb 2.14.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_makeblastdb%2F2.14.1%2Bgalaxy1 - - title: NCBI BLAST+ blastn 2.14.1+galaxy1 + - description: 'NCBI BLAST+ blastn: Search nucleotide database with nucleotide query + sequence(s)' + title: NCBI BLAST+ blastn 2.14.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_blastn_wrapper%2F2.14.1%2Bgalaxy1 - - title: NCBI BLAST+ tblastx 2.14.1+galaxy1 + - description: 'NCBI BLAST+ tblastx: Search translated nucleotide database with + translated nucleotide query sequence(s)' + title: NCBI BLAST+ tblastx 2.14.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_tblastx_wrapper%2F2.14.1%2Bgalaxy1 - - title: NCBI BLAST+ tblastn 2.14.1+galaxy1 + - description: 'NCBI BLAST+ tblastn: Search translated nucleotide database with + protein query sequence(s)' + title: NCBI BLAST+ tblastn 2.14.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_tblastn_wrapper%2F2.14.1%2Bgalaxy1 - - title: BLAST XML to tabular 2.14.1+galaxy1 + - description: 'BLAST XML to tabular: Convert BLAST XML output to tabular' + title: BLAST XML to tabular 2.14.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fblastxml_to_tabular%2F2.14.1%2Bgalaxy1 - - title: NCBI get species taxids 2.14.1+galaxy1 + - description: 'NCBI get species taxids: ' + title: NCBI get species taxids 2.14.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fget_species_taxids%2F2.14.1%2Bgalaxy1 - - title: NCBI BLAST+ rpstblastn 2.14.1+galaxy1 + - description: 'NCBI BLAST+ rpstblastn: Search protein domain database (PSSMs) with + translated nucleotide query sequence(s)' + title: NCBI BLAST+ rpstblastn 2.14.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_rpstblastn_wrapper%2F2.14.1%2Bgalaxy1 - - title: NCBI BLAST+ blastdbcmd entry(s) 2.14.1+galaxy1 + - description: 'NCBI BLAST+ blastdbcmd entry(s): Extract sequence(s) from BLAST + database' + title: NCBI BLAST+ blastdbcmd entry(s) 2.14.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_blastdbcmd_wrapper%2F2.14.1%2Bgalaxy1 - - title: NCBI BLAST+ blastx 2.14.1+galaxy1 + - description: 'NCBI BLAST+ blastx: Search protein database with translated nucleotide + query sequence(s)' + title: NCBI BLAST+ blastx 2.14.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_blastx_wrapper%2F2.14.1%2Bgalaxy1 - - title: NCBI BLAST+ dustmasker 2.14.1+galaxy1 + - description: 'NCBI BLAST+ dustmasker: masks low complexity regions' + title: NCBI BLAST+ dustmasker 2.14.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_dustmasker_wrapper%2F2.14.1%2Bgalaxy1 - - title: NCBI BLAST+ makeprofiledb 2.14.1+galaxy1 + - description: 'NCBI BLAST+ makeprofiledb: Make profile database' + title: NCBI BLAST+ makeprofiledb 2.14.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_makeprofiledb%2F2.14.1%2Bgalaxy1 - - title: NCBI BLAST+ blastp 2.14.1+galaxy1 + - description: 'NCBI BLAST+ blastp: Search protein database with protein query sequence(s)' + title: NCBI BLAST+ blastp 2.14.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_blastp_wrapper%2F2.14.1%2Bgalaxy1 - - title: NCBI BLAST+ rpsblast 2.14.1+galaxy1 + - description: 'NCBI BLAST+ rpsblast: Search protein domain database (PSSMs) with + protein query sequence(s)' + title: NCBI BLAST+ rpsblast 2.14.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_rpsblast_wrapper%2F2.14.1%2Bgalaxy1 - - title: NCBI BLAST+ database info 2.14.1+galaxy1 + - description: 'NCBI BLAST+ database info: Show BLAST database information from + blastdbcmd' + title: NCBI BLAST+ database info 2.14.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_blastdbcmd_info%2F2.14.1%2Bgalaxy1 homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi id: blast+ @@ -1695,7 +1886,9 @@ bunya: '' description: detect blocks of overlapping reads using a gaussian-distribution approach galaxy: - - title: blockbuster 0.1.2 + - description: 'blockbuster: detects blocks of overlapping reads using a gaussian-distribution + approach' + title: blockbuster 0.1.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fblockbuster%2Fblockbuster%2F0.1.2 homepage: http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html id: Blockbuster @@ -1715,7 +1908,9 @@ bunya: '' description: '' galaxy: - - title: BlockClust 1.1.1 + - description: 'BlockClust: efficient clustering and classification of non-coding + RNAs from short read RNA-seq profiles' + title: BlockClust 1.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fblockclust%2Fblockclust%2F1.1.1 homepage: '' id: BlockClust @@ -1776,9 +1971,11 @@ - 1.3.1-gcc-11.3.0 description: Bowtie is an ultrafast, memory-efficient short read aligner. galaxy: - - title: Bowtie2 2.5.0+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fbowtie2%2Fbowtie2%2F2.5.0%2Bgalaxy0 - - title: Map with Bowtie for Illumina 1.2.0 + - description: 'Bowtie2: - map reads against reference genome' + title: Bowtie2 2.5.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fbowtie2%2Fbowtie2%2F2.5.3%2Bgalaxy0 + - description: 'Map with Bowtie for Illumina: ' + title: Map with Bowtie for Illumina 1.2.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fbowtie_wrappers%2Fbowtie_wrapper%2F1.2.0 homepage: http://bowtie-bio.sourceforge.net/index.shtml id: bowtie @@ -1848,7 +2045,8 @@ bunya: '' description: '' galaxy: - - title: Genbank to GFF3 1.1 + - description: 'Genbank to GFF3: converter' + title: Genbank to GFF3 1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbp_genbank2gff3%2Fbp_genbank2gff3%2F1.1 homepage: '' id: bp_genbank2gff3 @@ -1883,7 +2081,8 @@ description: Pipeline for unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS. galaxy: - - title: BRAKER3 3.0.6+galaxy2 + - description: 'BRAKER3: genome annotation' + title: BRAKER3 3.0.6+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgenouest%2Fbraker3%2Fbraker3%2F3.0.6%2Bgalaxy2 homepage: http://bioinf.uni-greifswald.de/bioinf/braker/index.html id: braker @@ -1927,7 +2126,8 @@ bunya: '' description: Runs Breseq software on a set of fastq files. galaxy: - - title: breseq 0.35.5+0 + - description: 'breseq: find mutations in haploid microbial genomes' + title: breseq 0.35.5+0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbreseq%2Fbreseq%2F0.35.5%2B0 homepage: http://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing id: breseq @@ -1998,7 +2198,8 @@ set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. galaxy: - - title: Busco 5.5.0+galaxy0 + - description: 'Busco: assess genome assembly and annotation completeness' + title: Busco 5.5.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbusco%2Fbusco%2F5.5.0%2Bgalaxy0 homepage: https://busco.ezlab.org/ id: busco @@ -2055,9 +2256,12 @@ description: Fast, accurate, memory-efficient aligner for short and long sequencing reads galaxy: - - title: Map with BWA 0.7.17.5 + - description: 'Map with BWA: - map short reads (< 100 bp) against reference genome' + title: Map with BWA 0.7.17.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fbwa%2Fbwa%2F0.7.17.5 - - title: Map with BWA-MEM 0.7.17.2 + - description: 'Map with BWA-MEM: - map medium and long reads (> 100 bp) against + reference genome' + title: Map with BWA-MEM 0.7.17.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fbwa%2Fbwa_mem%2F0.7.17.2 homepage: http://bio-bwa.sourceforge.net id: bwa @@ -2113,7 +2317,8 @@ bunya: '' description: '' galaxy: - - title: bwameth 0.2.6+galaxy0 + - description: 'bwameth: Fast and accurate aligner of BS-Seq reads.' + title: bwameth 0.2.6+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbwameth%2Fbwameth%2F0.2.6%2Bgalaxy0 homepage: '' id: BWA-meth @@ -2147,31 +2352,45 @@ description: Tools for manipulating biological data, particularly multiple sequence alignments. galaxy: - - title: Base Coverage 1.0.0 + - description: 'Base Coverage: of all intervals' + title: Base Coverage 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fbasecoverage%2Fgops_basecoverage_1%2F1.0.0 - - title: Cluster 1.0.0 + - description: 'Cluster: the intervals of a dataset' + title: Cluster 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcluster%2Fgops_cluster_1%2F1.0.0 - - title: Complement 1.0.0 + - description: 'Complement: intervals of a dataset' + title: Complement 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcomplement%2Fgops_complement_1%2F1.0.0 - - title: Concatenate 1.0.1 + - description: 'Concatenate: two BED files' + title: Concatenate 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fconcat%2Fgops_concat_1%2F1.0.1 - - title: Coverage 1.0.0 + - description: 'Coverage: of a set of intervals on second set of intervals' + title: Coverage 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcoverage%2Fgops_coverage_1%2F1.0.0 - - title: Fetch closest non-overlapping feature 4.0.1 + - description: 'Fetch closest non-overlapping feature: for every interval' + title: Fetch closest non-overlapping feature 4.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fflanking_features%2Fflanking_features_1%2F4.0.1 - - title: Get flanks 1.0.0 + - description: 'Get flanks: returns flanking region/s for every gene' + title: Get flanks 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fget_flanks%2Fget_flanks1%2F1.0.0 - - title: Join 1.0.0 + - description: 'Join: the intervals of two datasets side-by-side' + title: Join 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fjoin%2Fgops_join_1%2F1.0.0 - - title: Merge 1.0.0 + - description: 'Merge: the overlapping intervals of a dataset' + title: Merge 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fmerge%2Fgops_merge_1%2F1.0.0 - - title: Subtract 1.0.0 + - description: 'Subtract: the intervals of two datasets' + title: Subtract 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsubtract%2Fgops_subtract_1%2F1.0.0 - - title: Subtract Whole Dataset 0.1 + - description: 'Subtract Whole Dataset: from another dataset' + title: Subtract Whole Dataset 0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsubtract_query%2Fsubtract_query1%2F0.1 - - title: Wiggle-to-Interval 1.0.1 + - description: 'Wiggle-to-Interval: converter' + title: Wiggle-to-Interval 1.0.1 url: https://usegalaxy.org.au/root?tool_id=wiggle2simple1 - - title: Aggregate datapoints 1.1.4 + - description: 'Aggregate datapoints: Appends the average, min, max of datapoints + per interval' + title: Aggregate datapoints 1.1.4 url: https://usegalaxy.org.au/root?tool_id=aggregate_scores_in_intervals2 homepage: https://github.com/bxlab/bx-python id: bx-python @@ -2199,7 +2418,8 @@ solid statistical evaluations and interpretable visualizations on the integration results galaxy: - - title: Copernicus Climate Data Store 0.1.0 + - 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 id: c3s @@ -2221,9 +2441,12 @@ bunya: '' description: Cactus is a reference-free whole-genome multiple alignment program. galaxy: - - title: Cactus 2.7.1+galaxy0 + - description: 'Cactus: whole-genome multiple sequence alignment' + title: Cactus 2.7.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxy-australia%2Fcactus_cactus%2Fcactus_cactus%2F2.7.1%2Bgalaxy0 - - title: 'Cactus: export 2.7.1+galaxy0' + - description: 'Cactus: export: whole-genome multiple sequence alignment to other + formats' + title: 'Cactus: export 2.7.1+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxy-australia%2Fcactus_export%2Fcactus_export%2F2.7.1%2Bgalaxy0 homepage: https://github.com/ComparativeGenomicsToolkit/cactus id: cactus @@ -2256,9 +2479,13 @@ isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments. galaxy: - - title: CAMERA.annotate 2.2.4 + - description: 'CAMERA.annotate: CAMERA annotate function. Returns annotation results + (isotope peaks, adducts and fragments) and a diffreport if more than one condition.' + title: CAMERA.annotate 2.2.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Flecorguille%2Fcamera_annotate%2Fabims_CAMERA_annotateDiffreport%2F2.2.4 - - title: CAMERA.combinexsAnnos 2.2.2 + - description: 'CAMERA.combinexsAnnos: Wrapper function for the combinexsAnnos CAMERA + function. Returns a dataframe with recalculated annotations.' + title: CAMERA.combinexsAnnos 2.2.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fmmonsoor%2Fcamera_combinexsannos%2Fabims_CAMERA_combinexsAnnos%2F2.2.2 homepage: http://bioconductor.org/packages/release/bioc/html/CAMERA.html id: camera @@ -2282,7 +2509,9 @@ description: De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. galaxy: - - title: Canu assembler 2.2+galaxy0 + - description: 'Canu assembler: Assembler optimized for long error-prone reads such + as PacBio, Oxford Nanopore' + title: Canu assembler 2.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcanu%2Fcanu%2F2.2%2Bgalaxy0 homepage: https://github.com/marbl/canu id: canu @@ -2308,7 +2537,8 @@ bunya: '' description: Web-based contig assembly. galaxy: - - title: cap3 2.0.0 + - description: 'cap3: Sequence Assembly tool' + title: cap3 2.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fartbio%2Fcap3%2Fcap3%2F2.0.0 homepage: http://biosrv.cab.unina.it/webcap3/ id: cap3 @@ -2333,23 +2563,34 @@ imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification. galaxy: - - title: MSI classification 2.10.0.0 + - 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 - - title: MSI combine 2.10.0.0 + - 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 - - title: MSI data exporter 2.10.0.0 + - 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 filtering 2.10.0.0 + - 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 - - title: MSI mz images 2.10.0.0 + - 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 - - title: MSI preprocessing 2.10.0.1 + - 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 - - title: MSI Qualitycontrol 2.10.0.0 + - 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 segmentation 2.10.0.0 + - 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 - - title: MSI plot spectra 2.10.0.0 + - 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 homepage: http://bioconductor.org/packages/release/bioc/html/Cardinal.html id: cardinal @@ -2376,9 +2617,12 @@ classification of the entire contig / MAG based on classification of the individual ORFs. galaxy: - - title: CAT bins 5.0.3.1 + - 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 summarise 5.2.3+galaxy0 + - description: 'CAT summarise: the number of contigs or bins assigned to each taxonomic + name' + title: CAT summarise 5.2.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcat_summarise%2Fcat_summarise%2F5.2.3%2Bgalaxy0 homepage: https://github.com/dutilh/CAT id: cat_bins @@ -2419,9 +2663,11 @@ - 4.8.1-gcc-11.3.0 (D) description: Cluster a nucleotide dataset into representative sequences. galaxy: - - title: CD-HIT-EST 1.3 + - description: 'CD-HIT-EST: Cluster a nucleotide dataset into representative sequences' + title: CD-HIT-EST 1.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbebatut%2Fcdhit%2Fcd_hit_est%2F1.3 - - title: CD-HIT PROTEIN 1.3 + - description: 'CD-HIT PROTEIN: Cluster a protein dataset into representative sequences' + title: CD-HIT PROTEIN 1.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbebatut%2Fcdhit%2Fcd_hit_protein%2F1.3 homepage: https://github.com/weizhongli/cdhit id: cd-hit @@ -2490,51 +2736,74 @@ description: Tool for quantifying data from biological images, particularly in high-throughput experiments. galaxy: - - title: TrackObjects 3.1.9+galaxy1 + - description: 'TrackObjects: with CellProfiler' + title: TrackObjects 3.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_track_objects%2Fcp_track_objects%2F3.1.9%2Bgalaxy1 - - title: SaveImages 3.1.9+galaxy2 + - description: 'SaveImages: with CellProfiler' + title: SaveImages 3.1.9+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_save_images%2Fcp_save_images%2F3.1.9%2Bgalaxy2 - - title: RelateObjects 3.1.9+galaxy1 + - description: 'RelateObjects: with CellProfiler' + title: RelateObjects 3.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_relate_objects%2Fcp_relate_objects%2F3.1.9%2Bgalaxy1 - - title: MeasureObjectSizeShape 3.1.9+galaxy1 + - description: 'MeasureObjectSizeShape: with CellProfiler' + title: MeasureObjectSizeShape 3.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_measure_object_size_shape%2Fcp_measure_object_size_shape%2F3.1.9%2Bgalaxy1 - - title: MeasureGranularity 3.1.9+galaxy1 + - description: 'MeasureGranularity: with CellProfiler' + title: MeasureGranularity 3.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_measure_granularity%2Fcp_measure_granularity%2F3.1.9%2Bgalaxy1 - - title: EnhanceOrSuppressFeatures 3.1.9+galaxy1 + - description: 'EnhanceOrSuppressFeatures: with CellProfiler' + title: EnhanceOrSuppressFeatures 3.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_enhance_or_suppress_features%2Fcp_enhance_or_suppress_features%2F3.1.9%2Bgalaxy1 - - title: DisplayDataOnImage 3.1.9+galaxy1 + - description: 'DisplayDataOnImage: with CellProfiler' + title: DisplayDataOnImage 3.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_display_data_on_image%2Fcp_display_data_on_image%2F3.1.9%2Bgalaxy1 - - title: Run CellProfiler pipeline 3.1.9+galaxy1 + - description: 'Run CellProfiler pipeline: with CellProfiler 3' + title: Run CellProfiler pipeline 3.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_cellprofiler%2Fcp_cellprofiler%2F3.1.9%2Bgalaxy1 - - title: ColorToGray 3.1.9+galaxy1 + - description: 'ColorToGray: with CellProfiler' + title: ColorToGray 3.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_color_to_gray%2Fcp_color_to_gray%2F3.1.9%2Bgalaxy1 - - title: Starting Modules 3.1.9+galaxy2 + - description: 'Starting Modules: Load images and metadata' + title: Starting Modules 3.1.9+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_common%2Fcp_common%2F3.1.9%2Bgalaxy2 - - title: ConvertObjectsToImage 3.1.9+galaxy1 + - description: 'ConvertObjectsToImage: with CellProfiler' + title: ConvertObjectsToImage 3.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_convert_objects_to_image%2Fcp_convert_objects_to_image%2F3.1.9%2Bgalaxy1 - - title: ExportToSpreadsheet 3.1.9+galaxy2 + - description: 'ExportToSpreadsheet: with CellProfiler' + title: ExportToSpreadsheet 3.1.9+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_export_to_spreadsheet%2Fcp_export_to_spreadsheet%2F3.1.9%2Bgalaxy2 - - title: GrayToColor 3.1.9+galaxy1 + - description: 'GrayToColor: with CellProfiler' + title: GrayToColor 3.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_gray_to_color%2Fcp_gray_to_color%2F3.1.9%2Bgalaxy1 - - title: IdentifyPrimaryObjects 3.1.9+galaxy2 + - description: 'IdentifyPrimaryObjects: with CellProfiler' + title: IdentifyPrimaryObjects 3.1.9+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_identify_primary_objects%2Fcp_identify_primary_objects%2F3.1.9%2Bgalaxy2 - - title: ImageMath 3.1.9+galaxy1 + - description: 'ImageMath: with CellProfiler' + title: ImageMath 3.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_image_math%2Fcp_image_math%2F3.1.9%2Bgalaxy1 - - title: MaskImage 3.1.9+galaxy1 + - description: 'MaskImage: with CellProfiler' + title: MaskImage 3.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_mask_image%2Fcp_mask_image%2F3.1.9%2Bgalaxy1 - - title: MeasureImageAreaOccupied 3.1.9+galaxy1 + - description: 'MeasureImageAreaOccupied: with CellProfiler' + title: MeasureImageAreaOccupied 3.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_measure_image_area_occupied%2Fcp_measure_image_area_occupied%2F3.1.9%2Bgalaxy1 - - title: MeasureImageIntensity 3.1.9+galaxy1 + - description: 'MeasureImageIntensity: with CellProfiler' + title: MeasureImageIntensity 3.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_measure_image_intensity%2Fcp_measure_image_intensity%2F3.1.9%2Bgalaxy1 - - title: MeasureImageQuality 3.1.9+galaxy1 + - description: 'MeasureImageQuality: with CellProfiler' + title: MeasureImageQuality 3.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_measure_image_quality%2Fcp_measure_image_quality%2F3.1.9%2Bgalaxy1 - - title: MeasureObjectIntensity 3.1.9+galaxy1 + - description: 'MeasureObjectIntensity: with CellProfiler' + title: MeasureObjectIntensity 3.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_measure_object_intensity%2Fcp_measure_object_intensity%2F3.1.9%2Bgalaxy1 - - title: MeasureTexture 3.1.9+galaxy1 + - description: 'MeasureTexture: with CellProfiler' + title: MeasureTexture 3.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_measure_texture%2Fcp_measure_texture%2F3.1.9%2Bgalaxy1 - - title: OverlayOutlines 3.1.9+galaxy1 + - description: 'OverlayOutlines: with CellProfiler' + title: OverlayOutlines 3.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_overlay_outlines%2Fcp_overlay_outlines%2F3.1.9%2Bgalaxy1 - - title: Tile 3.1.9+galaxy0 + - description: 'Tile: with CellProfiler' + title: Tile 3.1.9+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcp_tile%2Fcp_tile%2F3.1.9%2Bgalaxy0 homepage: https://cellprofiler.org/ id: CellProfiler @@ -2578,7 +2847,8 @@ for single-cell transcriptomics datasets, such as those coming from the Human Cell Atlas. galaxy: - - title: Interactive CellXgene Environment 0.16.2 + - description: 'Interactive CellXgene Environment: ' + title: Interactive CellXgene Environment 0.16.2 url: https://usegalaxy.org.au/root?tool_id=interactive_tool_cellxgene homepage: https://github.com/chanzuckerberg/cellxgene id: cellxgene @@ -2636,6 +2906,7 @@ - Phylogenetics - Taxonomy - Metagenomics + - Data quality management - biocontainers: checkm bunya: - '2015_01_16' @@ -2661,6 +2932,7 @@ - Phylogenetics - Taxonomy - Metagenomics + - Data quality management - biocontainers: checkm bunya: '' description: CheckM provides a set of tools for assessing the quality of genomes @@ -2685,15 +2957,20 @@ - Phylogenetics - Taxonomy - Metagenomics + - Data quality management - biocontainers: chembl bunya: '' description: Database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. galaxy: - - title: Search ChEMBL database 0.10.1+galaxy4 + - description: 'Search ChEMBL database: for compounds which are similar to a SMILES + string' + title: Search ChEMBL database 0.10.1+galaxy4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fchembl%2Fchembl%2F0.10.1%2Bgalaxy4 - - title: ChEMBL structure pipeline 1.0.0+galaxy0 + - description: 'ChEMBL structure pipeline: for curation and standardizing of molecular + structures' + title: ChEMBL structure pipeline 1.0.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fchembl%2Fchembl_structure_pipeline%2F1.0.0%2Bgalaxy0 homepage: https://www.ebi.ac.uk/chembldb/ id: chembl @@ -2728,13 +3005,18 @@ an evaluation copy of the most recent version of chemfp, or you can download an earlier version for no cost under the MIT license' galaxy: - - title: Molecule to fingerprint 1.6.1+galaxy0 + - description: 'Molecule to fingerprint: conversion to several different fingerprint + formats' + title: Molecule to fingerprint 1.6.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fchemfp%2Fctb_chemfp_mol2fps%2F1.6.1%2Bgalaxy0 - - title: SDF to Fingerprint 1.6.1+0 + - description: 'SDF to Fingerprint: - extract fingerprints from sdf file metadata' + title: SDF to Fingerprint 1.6.1+0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fchemfp%2Fctb_sdf2fps%2F1.6.1%2B0 - - title: Taylor-Butina clustering 1.6.1+0 + - description: 'Taylor-Butina clustering: of molecular fingerprints' + title: Taylor-Butina clustering 1.6.1+0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fchemfp%2Fctb_chemfp_butina_clustering%2F1.6.1%2B0 - - title: NxN clustering 1.6.1+0 + - description: 'NxN clustering: of molecular fingerprints' + title: NxN clustering 1.6.1+0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fchemfp%2Fctb_chemfp_nxn_clustering%2F1.6.1%2B0 homepage: http://www.chemfp.com/ id: chemfp @@ -2767,11 +3049,14 @@ covering assembly of a compound library, hole filling, protein-ligand docking, and construction of a quantitative structure-activity relationship (QSAR) model. galaxy: - - title: Online data 0.2 + - description: 'Online data: fetching ...' + title: Online data 0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fchemical_data_sources%2Fctb_online_data_fetch%2F0.2 - - title: PubChem Download 1.0.0 + - description: 'PubChem Download: as canonical SMILES' + title: PubChem Download 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fchemical_data_sources%2Fctb_pubchem_download_as_smiles%2F1.0.0 - - title: PubChem Assay Downloader 1.0.0 + - description: 'PubChem Assay Downloader: as canonical SMILES' + title: PubChem Assay Downloader 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fchemical_data_sources%2Fctb_pubchem_download_assays%2F1.0.0 homepage: https://cheminformatics.usegalaxy.eu/ id: chemicaltoolbox @@ -2800,7 +3085,8 @@ to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. galaxy: - - title: ChIPseeker 1.28.3+galaxy0 + - description: 'ChIPseeker: for ChIP peak annotation and visualization' + title: ChIPseeker 1.28.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fchipseeker%2Fchipseeker%2F1.28.3%2Bgalaxy0 homepage: http://bioconductor.org/packages/release/bioc/html/ChIPseeker.html id: chipseeker @@ -2824,7 +3110,8 @@ description: An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons (dotplot). galaxy: - - title: Chromeister 1.5.a+galaxy1 + - description: 'Chromeister: ultra-fast pairwise genome comparisons' + title: Chromeister 1.5.a+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fchromeister%2Fchromeister%2F1.5.a%2Bgalaxy1 homepage: https://github.com/estebanpw/chromeister id: chromeister @@ -2861,7 +3148,8 @@ bunya: '' description: '' galaxy: - - title: CIRCexplorer 1.1.9.0 + - description: 'CIRCexplorer: ' + title: CIRCexplorer 1.1.9.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcircexplorer%2Fcircexplorer%2F1.1.9.0 homepage: https://github.com/YangLab/CIRCexplorer id: circexplorer @@ -2895,29 +3183,49 @@ description: Circos is tool for visualizing data in a circular format. It was developed for genomic data but can work for many other kinds of data as well. galaxy: - - title: 'Circos: Interval to Circos Text Labels 0.69.8+galaxy8' + - description: 'Circos: Interval to Circos Text Labels: reformats interval files + to prepare for Circos text labels' + title: 'Circos: Interval to Circos Text Labels 0.69.8+galaxy8' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcircos%2Fcircos_interval_to_text%2F0.69.8%2Bgalaxy8 - - title: 'Circos: Alignments to links 0.69.8+galaxy8' + - description: 'Circos: Alignments to links: reformats alignment files to prepare + for Circos' + title: 'Circos: Alignments to links 0.69.8+galaxy8' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcircos%2Fcircos_aln_to_links%2F0.69.8%2Bgalaxy8 - - title: 'Circos: Stack bigWigs as Histogram 0.69.8+galaxy8' + - description: 'Circos: Stack bigWigs as Histogram: reformats for use in Circos + stacked histogram plots' + title: 'Circos: Stack bigWigs as Histogram 0.69.8+galaxy8' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcircos%2Fcircos_wiggle_to_stacked%2F0.69.8%2Bgalaxy8 - - title: 'Circos: Table viewer 0.69.8+galaxy8' + - description: 'Circos: Table viewer: easily creates circos plots from tabular data' + title: 'Circos: Table viewer 0.69.8+galaxy8' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcircos%2Fcircos_tableviewer%2F0.69.8%2Bgalaxy8 - - title: GC Skew 0.69.8+galaxy8 + - description: 'GC Skew: calculates skew over genomic sequences' + title: GC Skew 0.69.8+galaxy8 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcircos%2Fcircos_gc_skew%2F0.69.8%2Bgalaxy8 - - title: 'Circos: Interval to Tiles 0.69.8+galaxy8' + - description: 'Circos: Interval to Tiles: reformats interval files to prepare for + Circos tile plots' + title: 'Circos: Interval to Tiles 0.69.8+galaxy8' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcircos%2Fcircos_interval_to_tile%2F0.69.8%2Bgalaxy8 - - title: 'Circos: bigWig to Scatter 0.69.8+galaxy8' + - description: 'Circos: bigWig to Scatter: reformats bigWig files to prepare for + Circos 2d scatter/line/histogram plots' + title: 'Circos: bigWig to Scatter 0.69.8+galaxy8' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcircos%2Fcircos_wiggle_to_scatter%2F0.69.8%2Bgalaxy8 - - title: 'Circos: Resample 1/2D data 0.69.8+galaxy8' + - description: 'Circos: Resample 1/2D data: reduce numbers of points in a dataset + before plotting' + title: 'Circos: Resample 1/2D data 0.69.8+galaxy8' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcircos%2Fcircos_resample%2F0.69.8%2Bgalaxy8 - - title: 'Circos: Link Density Track 0.69.8+galaxy8' + - description: 'Circos: Link Density Track: reduce links to a density plot' + title: 'Circos: Link Density Track 0.69.8+galaxy8' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcircos%2Fcircos_binlinks%2F0.69.8%2Bgalaxy8 - - title: Circos 0.69.8+galaxy8 + - description: 'Circos: visualizes data in a circular layout' + title: Circos 0.69.8+galaxy8 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcircos%2Fcircos%2F0.69.8%2Bgalaxy8 - - title: 'Circos: Bundle Links 0.69.8+galaxy8' + - description: 'Circos: Bundle Links: reduce numbers of links in datasets before + plotting' + title: 'Circos: Bundle Links 0.69.8+galaxy8' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcircos%2Fcircos_bundlelinks%2F0.69.8%2Bgalaxy8 - - title: Circos Builder 0.9-RC2 + - description: 'Circos Builder: creates circos plots from standard bioinformatics + datatypes.' + title: Circos Builder 0.9-RC2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcircos%2Fcircgraph%2F0.9-RC2 homepage: http://circos.ca/ id: circos @@ -2940,7 +3248,8 @@ bunya: '' description: '' galaxy: - - title: CLIFinder 0.5.1 + - description: 'CLIFinder: Find chimerics transcripts containing LINEs sequences' + title: CLIFinder 0.5.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fclifinder%2Fclifinder%2FCLIFinder%2F0.5.1 homepage: '' id: clifinder @@ -2957,7 +3266,8 @@ bunya: '' description: '' galaxy: - - title: climate stripes 1.0.1 + - description: 'climate stripes: from timeseries' + title: climate stripes 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fclimate%2Fclimate_stripes%2Fclimate_stripes%2F1.0.1 homepage: '' id: climate_stripes @@ -2995,7 +3305,9 @@ clustermap.js is an interactive, reusable d3 chart designed to visualise homology between multiple gene clusters.' galaxy: - - title: clinker 0.0.23+galaxy0 + - description: 'clinker: Automatic creation of publication-ready gene cluster comparison + figures' + title: clinker 0.0.23+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fthanhlv%2Fclinker%2Fclinker%2F0.0.23%2Bgalaxy0 homepage: http://github.com/gamcil/clinker id: clinker @@ -3018,7 +3330,8 @@ bunya: '' description: '' galaxy: - - title: ClipKIT. Alignment trimming software for phylogenetics. 0.1.0 + - description: 'ClipKIT. Alignment trimming software for phylogenetics.: ' + title: ClipKIT. Alignment trimming software for phylogenetics. 0.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fpadge%2Fclipkit%2Fclipkit%2F0.1.0 homepage: '' id: clipkit @@ -3061,7 +3374,8 @@ description: Multiple sequence alignment software. Old deprecated versions. Even older versions were CLUSTAL and CLUSTAL V (ClustalV). galaxy: - - title: ClustalW 2.1+galaxy1 + - description: 'ClustalW: multiple sequence alignment program for DNA or proteins' + title: ClustalW 2.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fclustalw%2Fclustalw%2F2.1%2Bgalaxy1 homepage: http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/ id: clustalw @@ -3157,7 +3471,9 @@ bunya: '' description: '' galaxy: - - title: Combine MetaPhlAn2 and HUMAnN2 outputs 0.2.0 + - description: 'Combine MetaPhlAn2 and HUMAnN2 outputs: to relate genus/species + abundances and gene families/pathways abundances' + title: Combine MetaPhlAn2 and HUMAnN2 outputs 0.2.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbebatut%2Fcombine_metaphlan2_humann2%2Fcombine_metaphlan2_humann2%2F0.2.0 homepage: '' id: combine_metaphlan2_humann2 @@ -3174,7 +3490,8 @@ bunya: '' description: '' galaxy: - - title: Compose text parameter value 0.1.1 + - description: 'Compose text parameter value: from parameters' + title: Compose text parameter value 0.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcompose_text_param%2Fcompose_text_param%2F0.1.1 homepage: '' id: compose_text_param @@ -3237,7 +3554,8 @@ bunya: '' description: '' galaxy: - - title: Count 1.0.3 + - description: 'Count: occurrences of each record' + title: Count 1.0.3 url: https://usegalaxy.org.au/root?tool_id=Count1 homepage: '' id: Count1 @@ -3259,7 +3577,8 @@ \ outputs the probabilities p (0 \u2264 p \u2264 1), which measure the likelihood\ \ of protein coding." galaxy: - - title: CPAT 3.0.5+galaxy0 + - 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 homepage: http://lilab.research.bcm.edu/cpat/ id: cpat @@ -3319,7 +3638,9 @@ bunya: '' description: '' galaxy: - - title: CTSM/FATES-EMERALD 2.0.1 + - description: 'CTSM/FATES-EMERALD: Functionally Assembled Terrestrial Ecosystem + Simulator' + title: CTSM/FATES-EMERALD 2.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fclimate%2Fctsm_fates%2Fctsm_fates%2F2.0.1 homepage: https://github.com/NordicESMhub/ctsm/tree/fates_emerald_api id: ctsm_fates @@ -3383,15 +3704,22 @@ parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. galaxy: - - title: Cuffcompare 2.2.1.2 + - description: 'Cuffcompare: compare assembled transcripts to a reference annotation + and track Cufflinks transcripts across multiple experiments' + title: Cuffcompare 2.2.1.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcuffcompare%2Fcuffcompare%2F2.2.1.2 - - title: Cufflinks 2.2.1.3 + - description: 'Cufflinks: transcript assembly and FPKM (RPKM) estimates for RNA-Seq + data' + title: Cufflinks 2.2.1.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcufflinks%2Fcufflinks%2F2.2.1.3 - - title: Cuffmerge 2.2.1.3 + - description: 'Cuffmerge: merge together several Cufflinks assemblies' + title: Cuffmerge 2.2.1.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcuffmerge%2Fcuffmerge%2F2.2.1.3 - - title: Cuffnorm 2.2.1.3 + - description: 'Cuffnorm: Create normalized expression levels' + title: Cuffnorm 2.2.1.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcuffnorm%2Fcuffnorm%2F2.2.1.3 - - title: Cuffquant 2.2.1.1 + - description: 'Cuffquant: Precompute gene expression levels' + title: Cuffquant 2.2.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcuffquant%2Fcuffquant%2F2.2.1.1 homepage: http://cole-trapnell-lab.github.io/cufflinks id: cufflinks @@ -3425,7 +3753,8 @@ of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations. galaxy: - - title: cummeRbund 2.16.0+galaxy1 + - description: 'cummeRbund: visualize Cuffdiff output' + title: cummeRbund 2.16.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcummerbund%2FcummeRbund%2F2.16.0%2Bgalaxy1 homepage: http://bioconductor.org/packages/release/bioc/html/cummeRbund.html id: cummeRbund @@ -3447,7 +3776,9 @@ description: Generate customized protein sequence database from RNA-Seq data for proteomics search. galaxy: - - title: CustomProDB 1.22.0 + - description: 'CustomProDB: Generate protein FASTAs from exosome or transcriptome + data' + title: CustomProDB 1.22.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fcustom_pro_db%2Fcustom_pro_db%2F1.22.0 homepage: http://bioconductor.org/packages/release/bioc/html/customProDB.html id: customprodb @@ -3488,7 +3819,8 @@ description: Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. galaxy: - - title: Cutadapt 4.6+galaxy1 + - description: 'Cutadapt: Remove adapter sequences from FASTQ/FASTA' + title: Cutadapt 4.6+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Flparsons%2Fcutadapt%2Fcutadapt%2F4.6%2Bgalaxy1 homepage: https://pypi.org/project/cutadapt/ id: cutadapt @@ -3523,7 +3855,8 @@ yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis galaxy: - - title: cuteSV 1.0.8+galaxy0 + - description: 'cuteSV: detects long-read-based SVs' + title: cuteSV 1.0.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcutesv%2Fcutesv%2F1.0.8%2Bgalaxy0 homepage: https://github.com/tjiangHIT/cuteSV id: cutesv @@ -3577,25 +3910,38 @@ classification is available via a native implementation of the RDP naive Bayesian classifier. galaxy: - - title: 'dada2: assignTaxonomy and addSpecies 1.28+galaxy0' + - 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: dada 1.28+galaxy0' + - description: 'dada2: dada: Remove sequencing errors' + title: 'dada2: dada 1.28+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_dada%2Fdada2_dada%2F1.28%2Bgalaxy0 - - title: 'dada2: filterAndTrim 1.28+galaxy0' + - description: 'dada2: filterAndTrim: Filter and trim short read data' + title: 'dada2: filterAndTrim 1.28+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_filterandtrim%2Fdada2_filterAndTrim%2F1.28%2Bgalaxy0 - - title: 'dada2: learnErrors 1.28+galaxy0' + - description: 'dada2: learnErrors: Learn Error rates' + title: 'dada2: learnErrors 1.28+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_learnerrors%2Fdada2_learnErrors%2F1.28%2Bgalaxy0 - - title: 'dada2: makeSequenceTable 1.28+galaxy0' + - description: 'dada2: makeSequenceTable: construct a sequence table (analogous + to OTU table)' + title: 'dada2: makeSequenceTable 1.28+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_makesequencetable%2Fdada2_makeSequenceTable%2F1.28%2Bgalaxy0 - - title: 'dada2: mergePairs 1.28+galaxy0' + - description: 'dada2: mergePairs: Merge denoised forward and reverse reads' + title: 'dada2: mergePairs 1.28+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_mergepairs%2Fdada2_mergePairs%2F1.28%2Bgalaxy0 - - title: 'dada2: plotComplexity 1.28+galaxy0' + - description: 'dada2: plotComplexity: Plot sequence complexity profile' + title: 'dada2: plotComplexity 1.28+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_plotcomplexity%2Fdada2_plotComplexity%2F1.28%2Bgalaxy0 - - title: 'dada2: plotQualityProfile 1.28+galaxy0' + - description: 'dada2: plotQualityProfile: plot a visual summary of the quality + scores' + title: 'dada2: plotQualityProfile 1.28+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_plotqualityprofile%2Fdada2_plotQualityProfile%2F1.28%2Bgalaxy0 - - title: 'dada2: removeBimeraDenovo 1.28+galaxy0' + - description: 'dada2: removeBimeraDenovo: Remove bimeras from collections of unique + sequences' + title: 'dada2: removeBimeraDenovo 1.28+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_removebimeradenovo%2Fdada2_removeBimeraDenovo%2F1.28%2Bgalaxy0 - - title: 'dada2: sequence counts 1.28+galaxy0' + - description: 'dada2: sequence counts: ' + title: 'dada2: sequence counts 1.28+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_seqcounts%2Fdada2_seqCounts%2F1.28%2Bgalaxy0 homepage: https://bioconductor.org/packages/release/bioc/html/dada2.html id: dada2 @@ -3634,7 +3980,8 @@ bunya: '' description: '' galaxy: - - title: Datamash 1.8+galaxy0 + - description: 'Datamash: (operations on tabular data)' + title: Datamash 1.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdatamash_ops%2Fdatamash_ops%2F1.8%2Bgalaxy0 homepage: '' id: datamash @@ -3651,7 +3998,8 @@ bunya: '' description: '' galaxy: - - title: Protein Database Downloader 0.3.4 + - description: 'Protein Database Downloader: ' + title: Protein Database Downloader 0.3.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fdbbuilder%2Fdbbuilder%2F0.3.4 homepage: '' id: dbbuilder @@ -3719,39 +4067,70 @@ description: User-friendly tools for the normalization and visualization of deep-sequencing data. galaxy: - - title: bamCompare 3.5.4+galaxy0 + - description: 'bamCompare: normalizes and compares two BAM or CRAM files to obtain + the ratio, log2ratio or difference between them' + title: bamCompare 3.5.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdeeptools_bam_compare%2Fdeeptools_bam_compare%2F3.5.4%2Bgalaxy0 - - title: bamCoverage 3.5.4+galaxy0 + - description: 'bamCoverage: generates a coverage bigWig file from a given BAM or + CRAM file' + title: bamCoverage 3.5.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdeeptools_bam_coverage%2Fdeeptools_bam_coverage%2F3.5.4%2Bgalaxy0 - - title: bamPEFragmentSize 3.5.4+galaxy0 + - description: 'bamPEFragmentSize: Estimate the predominant cDNA fragment length + from paired-end sequenced BAM/CRAM files' + title: bamPEFragmentSize 3.5.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdeeptools_bam_pe_fragmentsize%2Fdeeptools_bam_pe_fragmentsize%2F3.5.4%2Bgalaxy0 - - title: bigwigCompare 3.5.4+galaxy0 + - description: 'bigwigCompare: normalizes and compares two bigWig files to obtain + the ratio, log2ratio or difference between them' + title: bigwigCompare 3.5.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdeeptools_bigwig_compare%2Fdeeptools_bigwig_compare%2F3.5.4%2Bgalaxy0 - - title: computeGCBias 3.5.4+galaxy0 + - description: 'computeGCBias: Determine the GC bias of your sequenced reads' + title: computeGCBias 3.5.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdeeptools_compute_gc_bias%2Fdeeptools_compute_gc_bias%2F3.5.4%2Bgalaxy0 - - title: computeMatrix 3.5.4+galaxy0 + - description: 'computeMatrix: prepares data for plotting a heatmap or a profile + of given regions' + title: computeMatrix 3.5.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdeeptools_compute_matrix%2Fdeeptools_compute_matrix%2F3.5.4%2Bgalaxy0 - - title: computeMatrixOperations 3.5.4+galaxy0 + - description: 'computeMatrixOperations: Modify or combine the output of computeMatrix + in a variety of ways.' + title: computeMatrixOperations 3.5.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdeeptools_compute_matrix_operations%2Fdeeptools_compute_matrix_operations%2F3.5.4%2Bgalaxy0 - - title: correctGCBias 3.5.4+galaxy0 + - description: 'correctGCBias: uses the output from computeGCBias to generate GC-corrected + BAM/CRAM files' + title: correctGCBias 3.5.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdeeptools_correct_gc_bias%2Fdeeptools_correct_gc_bias%2F3.5.4%2Bgalaxy0 - - title: multiBamSummary 3.5.4+galaxy0 + - description: 'multiBamSummary: calculates average read coverages for a list of + two or more BAM/CRAM files' + title: multiBamSummary 3.5.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdeeptools_multi_bam_summary%2Fdeeptools_multi_bam_summary%2F3.5.4%2Bgalaxy0 - - title: multiBigwigSummary 3.5.4+galaxy0 + - description: 'multiBigwigSummary: calculates average scores for a list of two + or more bigwig files' + title: multiBigwigSummary 3.5.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdeeptools_multi_bigwig_summary%2Fdeeptools_multi_bigwig_summary%2F3.5.4%2Bgalaxy0 - - title: plotCorrelation 3.5.4+galaxy0 + - description: 'plotCorrelation: Create a heatmap or scatterplot of correlation + scores between different samples' + title: plotCorrelation 3.5.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdeeptools_plot_correlation%2Fdeeptools_plot_correlation%2F3.5.4%2Bgalaxy0 - - title: plotCoverage 3.5.4+galaxy0 + - description: 'plotCoverage: assesses the sequencing depth of BAM/CRAM files' + title: plotCoverage 3.5.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdeeptools_plot_coverage%2Fdeeptools_plot_coverage%2F3.5.4%2Bgalaxy0 - - title: plotEnrichment 3.5.4+galaxy0 + - description: 'plotEnrichment: plots read/fragment coverage over sets of regions' + title: plotEnrichment 3.5.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdeeptools_plot_enrichment%2Fdeeptools_plot_enrichment%2F3.5.4%2Bgalaxy0 - - title: plotFingerprint 3.5.4+galaxy0 + - description: 'plotFingerprint: plots profiles of BAM files; useful for assessing + ChIP signal strength' + title: plotFingerprint 3.5.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdeeptools_plot_fingerprint%2Fdeeptools_plot_fingerprint%2F3.5.4%2Bgalaxy0 - - title: plotHeatmap 3.5.4+galaxy0 + - description: 'plotHeatmap: creates a heatmap for score distributions across genomic + regions' + title: plotHeatmap 3.5.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdeeptools_plot_heatmap%2Fdeeptools_plot_heatmap%2F3.5.4%2Bgalaxy0 - - title: plotPCA 3.5.4+galaxy0 + - description: 'plotPCA: Generate principal component analysis (PCA) plots from + multiBamSummary or multiBigwigSummary output' + title: plotPCA 3.5.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdeeptools_plot_pca%2Fdeeptools_plot_pca%2F3.5.4%2Bgalaxy0 - - title: plotProfile 3.5.4+galaxy0 + - description: 'plotProfile: creates a profile plot for score distributions across + genomic regions' + title: plotProfile 3.5.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdeeptools_plot_profile%2Fdeeptools_plot_profile%2F3.5.4%2Bgalaxy0 homepage: https://deeptools.readthedocs.io/en/latest/ id: deeptools @@ -3821,7 +4200,8 @@ bunya: '' description: '' galaxy: - - title: Describe samples 2.15.1+galaxy0 + - description: 'Describe samples: and replicates' + title: Describe samples 2.15.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdescribe_samples%2Fdescribe_samples%2F2.15.1%2Bgalaxy0 homepage: '' id: describe_samples_replicates @@ -3841,7 +4221,9 @@ data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. galaxy: - - title: DESeq2 2.11.40.8+galaxy0 + - description: 'DESeq2: Determines differentially expressed features from count + tables' + title: DESeq2 2.11.40.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdeseq2%2Fdeseq2%2F2.11.40.8%2Bgalaxy0 homepage: http://bioconductor.org/packages/DESeq2/ id: deseq2 @@ -3867,11 +4249,14 @@ biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. galaxy: - - title: DEXSeq-Count 1.44+galaxy0 + - description: 'DEXSeq-Count: Prepare and count exon abundancies from RNA-seq data' + title: DEXSeq-Count 1.44+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdexseq%2Fdexseq_count%2F1.44%2Bgalaxy0 - - title: DEXSeq 1.44+galaxy0 + - description: 'DEXSeq: Determines differential exon usage from count tables' + title: DEXSeq 1.44+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdexseq%2Fdexseq%2F1.44%2Bgalaxy0 - - title: plotDEXSeq 1.44+galaxy0 + - description: 'plotDEXSeq: Visualization of the per gene DEXSeq results' + title: plotDEXSeq 1.44+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdexseq%2Fplotdexseq%2F1.44%2Bgalaxy0 homepage: http://bioconductor.org/packages/release/bioc/html/DEXSeq.html id: DEXSeq @@ -3927,7 +4312,8 @@ DiaNN.exe (a command-line tool) and DIA-NN.exe (a GUI implemented as a wrapper for DiaNN.exe)' galaxy: - - title: DIA-NN 1.8.1+galaxy3 + - description: 'DIA-NN: is a software for DIA/SWATH data processing' + title: DIA-NN 1.8.1+galaxy3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fdiann%2Fdiann%2F1.8.1%2Bgalaxy3 homepage: https://github.com/vdemichev/diann id: diann @@ -3956,7 +4342,8 @@ DIA data, and also incorporates targeted extraction to reduce the number of cases of missing quantitation. galaxy: - - title: DIA_Umpire_SE 2.1.3.0 + - description: 'DIA_Umpire_SE: DIA signal extraction' + title: DIA_Umpire_SE 2.1.3.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fdia_umpire%2Fdia_umpire_se%2F2.1.3.0 homepage: https://sourceforge.net/projects/diaumpire/ id: diaumpire @@ -3985,11 +4372,14 @@ sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. galaxy: - - title: Diamond 2.0.15+galaxy0 + - description: 'Diamond: alignment tool for short sequences against a protein database' + title: Diamond 2.0.15+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdiamond%2Fbg_diamond%2F2.0.15%2Bgalaxy0 - - title: Diamond view 2.0.15+galaxy0 + - description: 'Diamond view: generate formatted output from DAA files' + title: Diamond view 2.0.15+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdiamond%2Fbg_diamond_view%2F2.0.15%2Bgalaxy0 - - title: Diamond makedb 2.0.15+galaxy0 + - description: 'Diamond makedb: Build database from a FASTA file' + title: Diamond makedb 2.0.15+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdiamond%2Fbg_diamond_makedb%2F2.0.15%2Bgalaxy0 homepage: https://github.com/bbuchfink/diamond id: diamond @@ -4012,7 +4402,9 @@ description: diaPASEF is an appproch for parallel accumulation-serial fragmentation combined with data-independent acquisition. galaxy: - - title: diapysef library generation 0.3.5.0 + - description: 'diapysef library generation: generates spectral library for DIA + analysis' + title: diapysef library generation 0.3.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fdiapysef%2Fdiapysef%2F0.3.5.0 homepage: https://github.com/Roestlab/dia-pasef id: diapysef @@ -4039,7 +4431,8 @@ using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. galaxy: - - title: DiffBind 2.10.0+galaxy1 + - 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 homepage: http://bioconductor.org/packages/release/bioc/html/DiffBind.html id: diffbind @@ -4080,7 +4473,8 @@ bunya: '' description: '' galaxy: - - title: Draw Stacked Bar Plots 1.0.0 + - description: 'Draw Stacked Bar Plots: for different categories and different criteria' + title: Draw Stacked Bar Plots 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdraw_stacked_barplots%2Fdraw_stacked_barplots%2F1.0.0 homepage: '' id: draw_stacked_barplots @@ -4117,7 +4511,9 @@ identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. galaxy: - - title: DropletUtils 1.10.0+galaxy2 + - description: 'DropletUtils: Utilities for handling droplet-based single-cell RNA-seq + data' + title: DropletUtils 1.10.0+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdropletutils%2Fdropletutils%2F1.10.0%2Bgalaxy2 homepage: http://bioconductor.org/packages/release/bioc/html/DropletUtils.html id: dropletutils @@ -4165,16 +4561,25 @@ bunya: '' description: '' galaxy: - - title: Compute P-values and Correlation Coefficients for Feature Occurrences 1.0.1 + - description: 'Compute P-values and Correlation Coefficients for Feature Occurrences: + between two datasets using Discrete Wavelet Transfoms' + title: Compute P-values and Correlation Coefficients for Feature Occurrences 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdwt_cor_ava_perclass%2Fcompute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom%2F1.0.1 - - title: Compute P-values and Correlation Coefficients for Occurrences of Two Set + - description: 'Compute P-values and Correlation Coefficients for Occurrences of + Two Set of Features: between two datasets using Discrete Wavelet Transfoms' + title: Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdwt_cor_avb_all%2Fcompute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom%2F1.0.1 - - title: Compute P-values and Second Moments for Feature Occurrences 1.0.1 + - description: 'Compute P-values and Second Moments for Feature Occurrences: between + two datasets using Discrete Wavelet Transfoms' + title: Compute P-values and Second Moments for Feature Occurrences 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdwt_ivc_all%2Fcompute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom%2F1.0.1 - - title: Compute P-values and Max Variances for Feature Occurrences 1.0.1 + - description: 'Compute P-values and Max Variances for Feature Occurrences: in one + dataset using Discrete Wavelet Transfoms' + title: Compute P-values and Max Variances for Feature Occurrences 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdwt_var_perclass%2Fcompute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom%2F1.0.1 - - title: Wavelet variance 1.0.2 + - description: 'Wavelet variance: using Discrete Wavelet Transfoms' + title: Wavelet variance 1.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdwt_var_perfeature%2Fdwt_var1%2F1.0.2 homepage: '' id: dwt @@ -4233,7 +4638,8 @@ bunya: '' description: '' galaxy: - - title: EBI SRA 1.0.1 + - description: 'EBI SRA: ENA SRA' + title: EBI SRA 1.0.1 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=ebi_sra_main homepage: '' id: ebi_sra_main @@ -4277,7 +4683,8 @@ it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. galaxy: - - title: edgeR 3.36.0+galaxy4 + - description: 'edgeR: Perform differential expression of count data' + title: edgeR 3.36.0+galaxy4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fedger%2Fedger%2F3.36.0%2Bgalaxy4 homepage: http://bioconductor.org/packages/release/bioc/html/edgeR.html id: edger @@ -4311,7 +4718,9 @@ it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. galaxy: - - title: edgeR-repenrich 1.5.2 + - description: 'edgeR-repenrich: Determines differentially expressed features from + RepEnrich counts' + title: edgeR-repenrich 1.5.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fartbio%2Frepenrich%2Fedger-repenrich%2F1.5.2 homepage: http://bioconductor.org/packages/release/bioc/html/edgeR.html id: edger-repenrich @@ -4368,11 +4777,14 @@ than traditional homology searches, as it avoids transferring annotations from close paralogs.' galaxy: - - title: eggNOG Mapper 2.1.8+galaxy4 + - description: 'eggNOG Mapper: functional sequence annotation by orthology' + title: eggNOG Mapper 2.1.8+galaxy4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Feggnog_mapper%2Feggnog_mapper%2F2.1.8%2Bgalaxy4 - - title: eggNOG Mapper 2.1.8+galaxy4 + - description: 'eggNOG Mapper: annotation phase' + title: eggNOG Mapper 2.1.8+galaxy4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Feggnog_mapper%2Feggnog_mapper_annotate%2F2.1.8%2Bgalaxy4 - - title: eggNOG Mapper 2.1.8+galaxy4 + - description: 'eggNOG Mapper: search phase' + title: eggNOG Mapper 2.1.8+galaxy4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Feggnog_mapper%2Feggnog_mapper_search%2F2.1.8%2Bgalaxy4 homepage: http://beta-eggnogdb.embl.de/#/app/emapper id: eggnog-mapper @@ -4401,7 +4813,8 @@ description: This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. galaxy: - - title: EGSEA 1.20.0 + - description: 'EGSEA: easy and efficient ensemble gene set testing' + title: EGSEA 1.20.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fegsea%2Fegsea%2F1.20.0 homepage: http://bioconductor.org/packages/release/bioc/html/EGSEA.html id: egsea @@ -4469,219 +4882,328 @@ description: Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. galaxy: - - title: dreg 5.0.0+galaxy1 + - description: 'dreg: Regular expression search of a nucleotide sequence' + title: dreg 5.0.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+dreg27%2F5.0.0%2Bgalaxy1 - - title: octanol 5.0.0.1 + - description: 'octanol: Displays protein hydropathy' + title: octanol 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+octanol63%2F5.0.0.1 - - title: wordmatch 5.0.0.1 + - description: 'wordmatch: Finds all exact matches of a given size between 2 sequences' + title: wordmatch 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+wordmatch110%2F5.0.0.1 - - title: cpgreport 5.0.0.1 + - description: 'cpgreport: Reports all CpG rich regions' + title: cpgreport 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+cpgreport16%2F5.0.0.1 - - title: sixpack 5.0.0.1 + - description: 'sixpack: Display a DNA sequence with 6-frame translation and ORFs' + title: sixpack 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+sixpack90%2F5.0.0.1 - - title: plotorf 5.0.0 + - description: 'plotorf: Plot potential open reading frames' + title: plotorf 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+plotorf76%2F5.0.0 - - title: diffseq 5.0.0.1 + - description: 'diffseq: Find differences between nearly identical sequences' + title: diffseq 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+diffseq22%2F5.0.0.1 - - title: needle 5.0.0.1 + - description: 'needle: Needleman-Wunsch global alignment' + title: needle 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+needle56%2F5.0.0.1 - - title: pepcoil 5.0.0.1 + - description: 'pepcoil: Predicts coiled coil regions' + title: pepcoil 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+pepcoil68%2F5.0.0.1 - - title: pepinfo 5.0.0.1 + - description: 'pepinfo: Plots simple amino acid properties in parallel' + title: pepinfo 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+pepinfo69%2F5.0.0.1 - - title: revseq 5.0.0 + - description: 'revseq: Reverse and complement a sequence' + title: revseq 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+revseq82%2F5.0.0 - - title: sigcleave 5.0.0.1 + - description: 'sigcleave: Reports protein signal cleavage sites' + title: sigcleave 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+sigcleave88%2F5.0.0.1 - - title: newcpgseek 5.0.0.1 + - description: 'newcpgseek: Reports CpG rich region' + title: newcpgseek 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+newcpgseek58%2F5.0.0.1 - - title: pepwindow 5.0.0.1 + - description: 'pepwindow: Displays protein hydropathy' + title: pepwindow 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+pepwindow73%2F5.0.0.1 - - title: noreturn 5.0.0 + - description: 'noreturn: Removes carriage return from ASCII files' + title: noreturn 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+noreturn60%2F5.0.0 - - title: textsearch 5.0.0 + - description: 'textsearch: Search sequence documentation. Slow, use SRS and Entrez!' + title: textsearch 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+textsearch98%2F5.0.0 - - title: cusp 5.0.0 + - description: 'cusp: Create a codon usage table' + title: cusp 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+cusp17%2F5.0.0 - - title: showfeat 5.0.0.1 + - description: 'showfeat: Show features of a sequence' + title: showfeat 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+showfeat85%2F5.0.0.1 - - title: tranalign 5.0.0 + - description: 'tranalign: Align nucleic coding regions given the aligned proteins' + title: tranalign 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+tranalign100%2F5.0.0 - - title: geecee 5.0.0 + - description: 'geecee: Calculates fractional GC content of nucleic acid sequences' + title: geecee 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+geecee41%2F5.0.0 - - title: supermatcher 5.0.0.1 + - description: 'supermatcher: Match large sequences against one or more other sequences' + title: supermatcher 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+supermatcher95%2F5.0.0.1 - - title: codcmp 5.0.0 + - description: 'codcmp: Codon usage table comparison' + title: codcmp 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+codcmp12%2F5.0.0 - - title: etandem 5.0.0.1 + - description: 'etandem: Looks for tandem repeats in a nucleotide sequence' + title: etandem 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+etandem33%2F5.0.0.1 - - title: biosed 5.0.0 + - description: 'biosed: Replace or delete sequence sections' + title: biosed 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+biosed4%2F5.0.0 - - title: coderet 5.0.0 + - description: 'coderet: Extract CDS, mRNA and translations from feature tables' + title: coderet 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+coderet13%2F5.0.0 - - title: cai 5.0.0 + - description: 'cai: CAI codon adaptation index' + title: cai 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+cai6%2F5.0.0 - - title: est2genome 5.0.0.1 + - description: 'est2genome: Align EST and genomic DNA sequences' + title: est2genome 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+est2genome32%2F5.0.0.1 - - title: prettyplot 5.0.0.1 + - description: 'prettyplot: Displays aligned sequences, with colouring and boxing' + title: prettyplot 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+prettyplot79%2F5.0.0.1 - - title: nthseq 5.0.0.1 + - description: 'nthseq: Writes one sequence from a multiple set of sequences' + title: nthseq 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+nthseq62%2F5.0.0.1 - - title: lindna 5.0.0.1 + - description: 'lindna: Draws linear maps of DNA constructs' + title: lindna 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+lindna48%2F5.0.0.1 - - title: degapseq 5.0.0 + - description: 'degapseq: Removes gap characters from sequences' + title: degapseq 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+degapseq20%2F5.0.0 - - title: primersearch 5.0.0.1 + - description: 'primersearch: Searches DNA sequences for matches with primer pairs' + title: primersearch 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+primersearch81%2F5.0.0.1 - - title: tcode 5.0.0.1 + - description: 'tcode: Fickett TESTCODE statistic to identify protein-coding DNA' + title: tcode 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+tcode97%2F5.0.0.1 - - title: polydot 5.0.0.1 + - description: 'polydot: Displays all-against-all dotplots of a set of sequences' + title: polydot 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+polydot77%2F5.0.0.1 - - title: dotmatcher 5.0.0.1 + - description: 'dotmatcher: Displays a thresholded dotplot of two sequences' + title: dotmatcher 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+dotmatcher24%2F5.0.0.1 - - title: fuzznuc 5.0.3 + - description: 'fuzznuc: Nucleic acid pattern search' + title: fuzznuc 5.0.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+fuzznuc37%2F5.0.3 - - title: garnier 5.0.0 + - description: 'garnier: Predicts protein secondary structure' + title: garnier 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+garnier40%2F5.0.0 - - title: equicktandem 5.0.0.1 + - description: 'equicktandem: Finds tandem repeats' + title: equicktandem 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+equicktandem31%2F5.0.0.1 - - title: fuzzpro 5.0.0.1 + - description: 'fuzzpro: Protein pattern search' + title: fuzzpro 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+fuzzpro38%2F5.0.0.1 - - title: vectorstrip 5.0.0.1 + - description: 'vectorstrip: Strips out DNA between a pair of vector sequences' + title: vectorstrip 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+vectorstrip106%2F5.0.0.1 - - title: merger 5.0.0.1 + - description: 'merger: Merge two overlapping nucleic acid sequences' + title: merger 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+merger54%2F5.0.0.1 - - title: prettyseq 5.0.0.1 + - description: 'prettyseq: Output sequence with translated ranges' + title: prettyseq 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+prettyseq80%2F5.0.0.1 - - title: pepstats 5.0.0 + - description: 'pepstats: Protein statistics' + title: pepstats 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+pepstats71%2F5.0.0 - - title: plotcon 5.0.0.1 + - description: 'plotcon: Plot quality of conservation of a sequence alignment' + title: plotcon 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+plotcon75%2F5.0.0.1 - - title: notseq 5.0.0 + - description: 'notseq: Exclude a set of sequences and write out the remaining ones' + title: notseq 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+notseq61%2F5.0.0 - - title: skipseq 5.0.0.1 + - description: 'skipseq: Reads and writes sequences, skipping first few' + title: skipseq 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+skipseq91%2F5.0.0.1 - - title: dotpath 5.0.0.1 + - description: 'dotpath: Non-overlapping wordmatch dotplot of two sequences' + title: dotpath 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+dotpath25%2F5.0.0.1 - - title: shuffleseq 5.0.0.1 + - description: 'shuffleseq: Shuffles a set of sequences maintaining composition' + title: shuffleseq 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+shuffleseq87%2F5.0.0.1 - - title: patmatdb 5.0.0 + - description: 'patmatdb: Search a protein sequence with a motif' + title: patmatdb 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+patmatdb67%2F5.0.0 - - title: isochore 5.0.0.1 + - description: 'isochore: Plots isochores in large DNA sequences' + title: isochore 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+isochore47%2F5.0.0.1 - - title: dottup 5.0.0.1 + - description: 'dottup: Displays a wordmatch dotplot of two sequences' + title: dottup 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+dottup26%2F5.0.0.1 - - title: pepwindowall 5.0.0.1 + - description: 'pepwindowall: Displays protein hydropathy of a set of sequences' + title: pepwindowall 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+pepwindowall74%2F5.0.0.1 - - title: matcher 5.0.0.1 + - description: 'matcher: Finds the best local alignments between two sequences' + title: matcher 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+matcher52%2F5.0.0.1 - - title: pepwheel 5.0.0.1 + - description: 'pepwheel: Shows protein sequences as helices' + title: pepwheel 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+pepwheel72%2F5.0.0.1 - - title: maskseq 5.0.0 + - description: 'maskseq: Mask off regions of a sequence' + title: maskseq 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+maskseq51%2F5.0.0 - - title: trimseq 5.0.0.1 + - description: 'trimseq: Trim ambiguous bits off the ends of sequences' + title: trimseq 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+trimseq103%2F5.0.0.1 - - title: infoseq 5.0.0 + - description: 'infoseq: Displays some simple information about sequences' + title: infoseq 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+infoseq46%2F5.0.0 - - title: freak 5.0.0.1 + - description: 'freak: Residue/base frequency table or plot' + title: freak 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+freak36%2F5.0.0.1 - - title: hmoment 5.0.0.1 + - description: 'hmoment: Hydrophobic moment calculation' + title: hmoment 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+hmoment44%2F5.0.0.1 - - title: sirna 5.0.0 + - description: 'sirna: Finds siRNA duplexes in mRNA' + title: sirna 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+sirna89%2F5.0.0 - - title: backtranseq 6.6.0 + - description: 'backtranseq: Back translate a protein sequence' + title: backtranseq 6.6.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+backtranseq2%2F6.6.0 - - title: wobble 5.0.0.1 + - description: 'wobble: Wobble base plot' + title: wobble 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+wobble108%2F5.0.0.1 - - title: chips 5.0.0 + - description: 'chips: Codon usage statistics' + title: chips 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+chips10%2F5.0.0 - - title: marscan 5.0.0 + - description: 'marscan: Finds MAR/SAR sites in nucleic sequences' + title: marscan 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+marscan49%2F5.0.0 - - title: transeq 5.0.0 + - description: 'transeq: Translate nucleic acid sequences' + title: transeq 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+transeq101%2F5.0.0 - - title: twofeat 5.0.0.1 + - description: 'twofeat: Finds neighbouring pairs of features in sequences' + title: twofeat 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+twofeat104%2F5.0.0.1 - - title: union 5.0.0 + - description: 'union: Reads sequence fragments and builds one sequence' + title: union 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+union105%2F5.0.0 - - title: chaos 5.0.0 + - description: 'chaos: Create a chaos game representation plot for a sequence' + title: chaos 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+chaos7%2F5.0.0 - - title: pasteseq 5.0.0.1 + - description: 'pasteseq: Insert one sequence into another' + title: pasteseq 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+pasteseq66%2F5.0.0.1 - - title: megamerger 5.0.0.1 + - description: 'megamerger: Merge two large overlapping nucleic acid sequences' + title: megamerger 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+megamerger53%2F5.0.0.1 - - title: iep 5.0.0.1 + - description: 'iep: Calculates the isoelectric point of a protein' + title: iep 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+iep45%2F5.0.0.1 - - title: newcpgreport 5.0.0.1 + - description: 'newcpgreport: Report CpG rich areas' + title: newcpgreport 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+newcpgreport57%2F5.0.0.1 - - title: wordcount 5.0.0.1 + - description: 'wordcount: Counts words of a specified size in a DNA sequence' + title: wordcount 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+wordcount109%2F5.0.0.1 - - title: descseq 5.0.0 + - description: 'descseq: Alter the name or description of a sequence' + title: descseq 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+descseq21%2F5.0.0 - - title: extractseq 5.0.0 + - description: 'extractseq: Extract regions from a sequence' + title: extractseq 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+extractseq35%2F5.0.0 - - title: einverted 5.0.0.1 + - description: 'einverted: Finds DNA inverted repeats' + title: einverted 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+einverted28%2F5.0.0.1 - - title: fuzztran 5.0.0.1 + - description: 'fuzztran: Protein pattern search after translation' + title: fuzztran 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+fuzztran39%2F5.0.0.1 - - title: cutseq 5.0.0.1 + - description: 'cutseq: Removes a specified section from a sequence' + title: cutseq 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+cutseq18%2F5.0.0.1 - - title: dan 5.0.0.1 + - description: 'dan: Calculates DNA RNA/DNA melting temperature' + title: dan 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+dan19%2F5.0.0.1 - - title: banana 5.0.0 + - description: 'banana: Bending and curvature plot in B-DNA' + title: banana 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+banana3%2F5.0.0 - - title: compseq 5.0.0.1 + - description: 'compseq: Count composition of dimer/trimer/etc words in a sequence' + title: compseq 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+compseq14%2F5.0.0.1 - - title: splitter 5.0.0.1 + - description: 'splitter: Split a sequence into (overlapping) smaller sequences' + title: splitter 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+splitter92%2F5.0.0.1 - - title: tmap 5.0.0 + - description: 'tmap: Displays membrane spanning regions' + title: tmap 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+tmap99%2F5.0.0 - - title: msbar 5.0.0.1 + - description: 'msbar: Mutate sequence beyond all recognition' + title: msbar 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+msbar55%2F5.0.0.1 - - title: digest 5.0.0 + - description: 'digest: Protein proteolytic enzyme or reagent cleavage digest' + title: digest 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+digest23%2F5.0.0 - - title: trimest 5.0.0.1 + - description: 'trimest: Trim poly-A tails off EST sequences' + title: trimest 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+trimest102%2F5.0.0.1 - - title: oddcomp 5.0.0.1 + - description: 'oddcomp: Find protein sequence regions with a biased composition' + title: oddcomp 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+oddcomp64%2F5.0.0.1 - - title: maskfeat 5.0.0 + - description: 'maskfeat: Mask off features of a sequence' + title: maskfeat 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+maskfeat50%2F5.0.0 - - title: seqret 5.0.0 + - description: 'seqret: Reads and writes sequences' + title: seqret 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+seqret84%2F5.0.0 - - title: cirdna 5.0.0 + - description: 'cirdna: Draws circular maps of DNA constructs' + title: cirdna 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+cirdna11%2F5.0.0 - - title: syco 5.0.0.1 + - description: 'syco: Synonymous codon usage Gribskov statistic plot' + title: syco 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+syco96%2F5.0.0.1 - - title: btwisted 5.0.0 + - description: 'btwisted: Calculates the twisting in a B-DNA sequence' + title: btwisted 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+btwisted5%2F5.0.0 - - title: extractfeat 5.0.0.1 + - description: 'extractfeat: Extract features from a sequence' + title: extractfeat 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+extractfeat34%2F5.0.0.1 - - title: getorf 5.0.0.1 + - description: 'getorf: Finds and extracts open reading frames (ORFs)' + title: getorf 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+getorf42%2F5.0.0.1 - - title: newseq 5.0.0 + - description: 'newseq: Type in a short new sequence' + title: newseq 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+newseq59%2F5.0.0 - - title: antigenic 5.0.0.1 + - description: 'antigenic: Predicts potentially antigenic regions of a protein sequence, + using the method of Kolaskar and Tongaonkar.' + title: antigenic 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+antigenic1%2F5.0.0.1 - - title: charge 5.0.0.1 + - description: 'charge: Protein charge plot' + title: charge 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+charge8%2F5.0.0.1 - - title: helixturnhelix 5.0.0.1 + - description: 'helixturnhelix: Report nucleic acid binding motifs' + title: helixturnhelix 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+helixturnhelix43%2F5.0.0.1 - - title: checktrans 5.0.0.1 + - description: 'checktrans: Reports STOP codons and ORF statistics of a protein' + title: checktrans 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+checktrans9%2F5.0.0.1 - - title: water 5.0.0.1 + - description: 'water: Smith-Waterman local alignment' + title: water 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+water107%2F5.0.0.1 - - title: pepnet 5.0.0 + - description: 'pepnet: Displays proteins as a helical net' + title: pepnet 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+pepnet70%2F5.0.0 - - title: seqmatchall 5.0.0.1 + - description: 'seqmatchall: All-against-all comparison of a set of sequences' + title: seqmatchall 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+seqmatchall83%2F5.0.0.1 - - title: cai custom 5.0.0 + - description: 'cai custom: CAI codon adaptation index using custom codon usage + file' + title: cai custom 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+cai_custom6%2F5.0.0 - - title: epestfind 5.0.0.1 + - description: 'epestfind: Finds PEST motifs as potential proteolytic cleavage sites' + title: epestfind 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+epestfind29%2F5.0.0.1 - - title: cpgplot 5.0.0 + - description: 'cpgplot: Plot CpG rich areas' + title: cpgplot 5.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+cpgplot15%2F5.0.0 - - title: palindrome 5.0.0.1 + - description: 'palindrome: Looks for inverted repeats in a nucleotide sequence' + title: palindrome 5.0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+palindrome65%2F5.0.0.1 - - title: preg 5.0.0+galaxy1 + - description: 'preg: Regular expression search of a protein sequence' + title: preg 5.0.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Femboss_5%2FEMBOSS%3A+preg78%2F5.0.0%2Bgalaxy1 homepage: http://emboss.bioinformatics.nl/ id: emboss @@ -4707,9 +5229,12 @@ both as the database of record for the output of the world's sequencing activity and as a platform for the management, sharing and publication of sequence data. galaxy: - - title: ENA Upload tool 0.6.3+galaxy0 + - description: 'ENA Upload tool: ' + title: ENA Upload tool 0.6.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fena_upload%2Fena_upload%2F0.6.3%2Bgalaxy0 - - title: ENA upload table builder 0.1.0+galaxy0 + - description: 'ENA upload table builder: create tables for the ENA upload tool + from metadata templates' + title: ENA upload table builder 0.1.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=interactive_tool_ena_upload_table_builder homepage: http://www.ebi.ac.uk/ena id: ena_upload @@ -4736,13 +5261,21 @@ for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries. galaxy: - - title: SearchToLib 1.12.34+galaxy0 + - 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 - - title: EncyclopeDIA 1.2.2+galaxy0 + - 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 Quantify 1.12.34+galaxy0 + - 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 - - title: Walnut 1.2.2+galaxy0 + - 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 @@ -4849,7 +5382,8 @@ bunya: '' description: '' galaxy: - - title: EtherCalc 0.1 + - description: 'EtherCalc: ' + title: EtherCalc 0.1 url: https://usegalaxy.org.au/root?tool_id=interactive_tool_ethercalc homepage: '' id: ethercalc @@ -4869,7 +5403,8 @@ and Trypanosoma. The database portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. galaxy: - - title: EuPathDB 1.0.0 + - description: 'EuPathDB: server' + title: EuPathDB 1.0.0 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=eupathdb homepage: http://EuPathDB.org id: eupathdb @@ -4956,7 +5491,8 @@ description: A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. galaxy: - - title: Exonerate 2.4.0+galaxy2 + - description: 'Exonerate: pairwise sequence comparison' + title: Exonerate 2.4.0+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fexonerate%2Fexonerate%2F2.4.0%2Bgalaxy2 homepage: http://www.ebi.ac.uk/%7Eguy/exonerate id: exonerate @@ -4980,7 +5516,8 @@ bunya: '' description: '' galaxy: - - title: Export datasets 0.1.0 + - description: 'Export datasets: to remote files source' + title: Export datasets 0.1.0 url: https://usegalaxy.org.au/root?tool_id=export_remote homepage: '' id: export_remote @@ -4999,7 +5536,8 @@ and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. galaxy: - - title: Export to GraPhlAn 0.20+galaxy0 + - description: 'Export to GraPhlAn: ' + title: Export to GraPhlAn 0.20+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fexport2graphlan%2Fexport2graphlan%2F0.20%2Bgalaxy0 homepage: https://github.com/SegataLab/export2graphlan/ id: export2graphlan @@ -5027,7 +5565,9 @@ data. It can be used to resolve ambiguous mappings in other high-throughput sequencing based applications. galaxy: - - title: eXpress 1.1.1 + - description: 'eXpress: Quantify the abundances of a set of target sequences from + sampled subsequences' + title: eXpress 1.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fexpress%2Fexpress%2F1.1.1 homepage: https://pachterlab.github.io/eXpress/index.html id: eXpress @@ -5121,7 +5661,8 @@ bunya: '' description: Add length of sequence to fasta header. galaxy: - - title: Compute sequence length 1.0.3 + - description: 'Compute sequence length: ' + title: Compute sequence length 1.0.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffasta_compute_length%2Ffasta_compute_length%2F1.0.3 homepage: https://bioweb.pasteur.fr/packages/pack@pf1-tools@0.1 id: fasta_compute_length @@ -5146,7 +5687,8 @@ bunya: '' description: '' galaxy: - - title: Concatenate 0.0.1 + - description: 'Concatenate: FASTA alignment by species' + title: Concatenate 0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffasta_concatenate_by_species%2Ffasta_concatenate0%2F0.0.1 homepage: '' id: fasta_concatenate_by_species @@ -5178,7 +5720,8 @@ bunya: '' description: '' galaxy: - - title: Filter sequences by length 1.2 + - description: 'Filter sequences by length: ' + title: Filter sequences by length 1.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffasta_filter_by_length%2Ffasta_filter_by_length%2F1.2 homepage: '' id: fasta_filter_by_length @@ -5195,7 +5738,9 @@ bunya: '' description: '' galaxy: - - title: FASTA Merge Files and Filter Unique Sequences 1.2.0 + - description: 'FASTA Merge Files and Filter Unique Sequences: Concatenate FASTA + database files together' + title: FASTA Merge Files and Filter Unique Sequences 1.2.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Ffasta_merge_files_and_filter_unique_sequences%2Ffasta_merge_files_and_filter_unique_sequences%2F1.2.0 homepage: '' id: fasta_merge_files_and_filter_unique_sequences @@ -5212,7 +5757,8 @@ bunya: '' description: '' galaxy: - - title: Fasta Statistics 2.0 + - description: 'Fasta Statistics: display summary statistics for a FASTA file' + title: Fasta Statistics 2.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffasta_stats%2Ffasta-stats%2F2.0 homepage: '' id: fasta_stats @@ -5229,7 +5775,8 @@ bunya: '' description: '' galaxy: - - title: FASTA-to-Tabular 1.1.1 + - description: 'FASTA-to-Tabular: converter' + title: FASTA-to-Tabular 1.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffasta_to_tabular%2Ffasta2tab%2F1.1.1 homepage: '' id: fasta_to_tabular @@ -5327,7 +5874,8 @@ files. This tool is developed in C++ with multithreading supported to afford high performance. galaxy: - - title: fastp 0.23.4+galaxy0 + - 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 homepage: https://github.com/OpenGene/fastp id: fastp @@ -5371,7 +5919,8 @@ into a larger analysis pipeline for the systematic processing of large numbers of files. galaxy: - - title: FastQC 0.74+galaxy0 + - 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 homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ id: fastqc @@ -5396,7 +5945,8 @@ bunya: '' description: '' galaxy: - - title: FASTQE 0.2.6+galaxy2 + - 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 homepage: '' id: fastqe @@ -5457,7 +6007,8 @@ description: Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. galaxy: - - title: FASTTREE 2.1.10+galaxy1 + - description: 'FASTTREE: build maximum-likelihood phylogenetic trees' + title: FASTTREE 2.1.10+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffasttree%2Ffasttree%2F2.1.10%2Bgalaxy1 homepage: https://www.microbesonline.org/fasttree/ id: fasttree @@ -5482,23 +6033,32 @@ description: Collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. galaxy: - - title: Remove sequencing artifacts 1.0.1+galaxy2 + - description: 'Remove sequencing artifacts: ' + title: Remove sequencing artifacts 1.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastx_artifacts_filter%2Fcshl_fastx_artifacts_filter%2F1.0.1%2Bgalaxy2 - - title: Barcode Splitter 1.0.1+galaxy2 + - description: 'Barcode Splitter: ' + title: Barcode Splitter 1.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastx_barcode_splitter%2Fcshl_fastx_barcode_splitter%2F1.0.1%2Bgalaxy2 - - title: Clip 1.0.3+galaxy2 + - description: 'Clip: adapter sequences' + title: Clip 1.0.3+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastx_clipper%2Fcshl_fastx_clipper%2F1.0.3%2Bgalaxy2 - - title: Collapse 1.0.1+galaxy2 + - description: 'Collapse: sequences' + title: Collapse 1.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastx_collapser%2Fcshl_fastx_collapser%2F1.0.1%2Bgalaxy2 - - title: Rename sequences 0.0.14+galaxy2 + - description: 'Rename sequences: ' + title: Rename sequences 0.0.14+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastx_renamer%2Fcshl_fastx_renamer%2F0.0.14%2Bgalaxy2 - - title: Reverse-Complement 1.0.2+galaxy2 + - description: 'Reverse-Complement: ' + title: Reverse-Complement 1.0.2+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastx_reverse_complement%2Fcshl_fastx_reverse_complement%2F1.0.2%2Bgalaxy2 - - title: Trim sequences 1.0.2+galaxy2 + - description: 'Trim sequences: ' + title: Trim sequences 1.0.2+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastx_trimmer%2Fcshl_fastx_trimmer%2F1.0.2%2Bgalaxy2 - - title: Draw nucleotides distribution chart 1.0.1+galaxy2 + - description: 'Draw nucleotides distribution chart: ' + title: Draw nucleotides distribution chart 1.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastx_nucleotides_distribution%2Fcshl_fastx_nucleotides_distribution%2F1.0.1%2Bgalaxy2 - - title: Compute quality statistics 1.0.1+galaxy2 + - description: 'Compute quality statistics: ' + title: Compute quality statistics 1.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastx_quality_statistics%2Fcshl_fastx_quality_statistics%2F1.0.1%2Bgalaxy2 homepage: http://hannonlab.cshl.edu/fastx_toolkit/ id: fastx @@ -5519,15 +6079,20 @@ description: Collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. galaxy: - - title: Length Distribution 1.0.1+galaxy2 + - description: 'Length Distribution: chart' + title: Length Distribution 1.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffasta_clipping_histogram%2Fcshl_fasta_clipping_histogram%2F1.0.1%2Bgalaxy2 - - title: FASTA Width 1.0.1+galaxy2 + - description: 'FASTA Width: formatter' + title: FASTA Width 1.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffasta_formatter%2Fcshl_fasta_formatter%2F1.0.1%2Bgalaxy2 - - title: RNA/DNA 1.0.2+galaxy2 + - description: 'RNA/DNA: converter' + title: RNA/DNA 1.0.2+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffasta_nucleotide_changer%2Fcshl_fasta_nucleotides_changer%2F1.0.2%2Bgalaxy2 - - title: Filter by quality 1.0.2+galaxy2 + - description: 'Filter by quality: ' + title: Filter by quality 1.0.2+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_quality_filter%2Fcshl_fastq_quality_filter%2F1.0.2%2Bgalaxy2 - - title: Draw quality score boxplot 1.0.1+galaxy2 + - description: 'Draw quality score boxplot: ' + title: Draw quality score boxplot 1.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_quality_boxplot%2Fcshl_fastq_quality_boxplot%2F1.0.1%2Bgalaxy2 homepage: http://hannonlab.cshl.edu/fastx_toolkit/ id: fastx_toolkit @@ -5564,7 +6129,8 @@ description: HMM-based gene structure prediction (multiple genes, both chains); Program for predicting multiple genes in genomic DNA sequences. galaxy: - - title: FGENESH get protein 1.0.0+galaxy0 + - description: 'FGENESH get protein: sequences using rensn3 files' + title: FGENESH get protein 1.0.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=fgenesh_get_proteins homepage: http://nhjy.hzau.edu.cn/kech/swxxx/jakj/dianzi/Bioinf6/GeneFinding/GeneFinding2.htm id: fgenesh @@ -5587,7 +6153,8 @@ p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. galaxy: - - title: fgsea 1.8.0+galaxy1 + - description: 'fgsea: - fast preranked gene set enrichment analysis' + title: fgsea 1.8.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffgsea%2Ffgsea%2F1.8.0%2Bgalaxy1 homepage: http://bioconductor.org/packages/release/bioc/html/fgsea.html id: fgsea @@ -5607,7 +6174,8 @@ bunya: '' description: '' galaxy: - - title: Filter Combined Transcripts 0.1 + - description: 'Filter Combined Transcripts: using tracking file' + title: Filter Combined Transcripts 0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffilter_transcripts_via_tracking%2Ffilter_combined_via_tracking%2F0.1 homepage: '' id: filter_transcripts_via_tracking @@ -5642,7 +6210,8 @@ (longer is better) and read identity (higher is better) when choosing which reads pass the filter. galaxy: - - title: filtlong 0.2.1+galaxy0 + - description: 'filtlong: Filtering long reads by quality' + title: filtlong 0.2.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffiltlong%2Ffiltlong%2F0.2.1%2Bgalaxy0 homepage: https://github.com/rrwick/Filtlong id: filtlong @@ -5660,7 +6229,9 @@ description: FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. galaxy: - - title: FlashLFQ 1.0.3.1 + - description: 'FlashLFQ: ultrafast label-free quantification for mass-spectrometry + proteomics' + title: FlashLFQ 1.0.3.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fflashlfq%2Fflashlfq%2F1.0.3.1 homepage: https://github.com/smith-chem-wisc/FlashLFQ id: flashlfq @@ -5702,8 +6273,9 @@ assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.' galaxy: - - title: Flye 2.9.1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fflye%2Fflye%2F2.9.1%2Bgalaxy0 + - 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 homepage: https://github.com/fenderglass/Flye id: flye license: '' @@ -5732,7 +6304,8 @@ bunya: '' description: '' galaxy: - - title: Flymine 1.0.0 + - description: 'Flymine: server' + title: Flymine 1.0.0 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=flymine homepage: '' id: flymine @@ -5775,9 +6348,11 @@ insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket). galaxy: - - title: dpocket 4.0.0+galaxy0 + - description: 'dpocket: to calculate descriptors for protein pockets' + title: dpocket 4.0.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ffpocket%2Fdpocket%2F4.0.0%2Bgalaxy0 - - title: fpocket 4.0.0+galaxy0 + - description: 'fpocket: - find potential binding sites in protein structures' + title: fpocket 4.0.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ffpocket%2Ffpocket%2F4.0.0%2Bgalaxy0 homepage: https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::fpocket id: fpocket @@ -5799,7 +6374,8 @@ bunya: '' description: Application for finding (fragmented) genes in short reads galaxy: - - title: FragGeneScan 1.30.0 + - description: 'FragGeneScan: for finding (fragmented) genes in short reads' + title: FragGeneScan 1.30.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffraggenescan%2Ffraggenescan%2F1.30.0 homepage: https://sourceforge.net/projects/fraggenescan/ id: fraggenescan @@ -5826,9 +6402,11 @@ (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. galaxy: - - title: BamLeftAlign 1.3.6 + - description: 'BamLeftAlign: indels in BAM datasets' + title: BamLeftAlign 1.3.6 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffreebayes%2Fbamleftalign%2F1.3.6 - - title: FreeBayes 1.3.6+galaxy0 + - description: 'FreeBayes: bayesian genetic variant detector' + title: FreeBayes 1.3.6+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffreebayes%2Ffreebayes%2F1.3.6%2Bgalaxy0 homepage: https://github.com/ekg/freebayes id: freebayes @@ -5889,15 +6467,20 @@ description: funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). galaxy: - - title: Funannotate functional 1.8.15+galaxy5 + - 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 - - title: Funannotate assembly clean 1.8.15+galaxy4 + - 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 - - title: Funannotate compare 1.8.15+galaxy4 + - 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 - - title: Funannotate predict annotation 1.8.15+galaxy4 + - 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 - - title: Sort assembly 1.8.15+galaxy4 + - 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 @@ -5915,13 +6498,21 @@ bunya: '' description: Gene Annotation EVAluation. galaxy: - - title: AEGeAn CanonGFF3 0.16.0+galaxy1 + - description: 'AEGeAn CanonGFF3: pre-process GFF3 files, removing all features + not directly related to protein-coding genes' + title: AEGeAn CanonGFF3 0.16.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Faegean_canongff3%2Faegean_canongff3%2F0.16.0%2Bgalaxy1 - - title: AEGeAn GAEVAL 0.16.0+galaxy1 + - description: 'AEGeAn GAEVAL: compute coverage and integrity scores for gene models + using transcript alignments.' + title: AEGeAn GAEVAL 0.16.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Faegean_gaeval%2Faegean_gaeval%2F0.16.0%2Bgalaxy1 - - title: AEGeAn LocusPocus 0.16.0+galaxy1 + - description: 'AEGeAn LocusPocus: calculate locus coordinates for the given gene + annotation' + title: AEGeAn LocusPocus 0.16.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Faegean_locuspocus%2Faegean_locuspocus%2F0.16.0%2Bgalaxy1 - - title: AEGeAn ParsEval 0.16.0+galaxy1 + - description: 'AEGeAn ParsEval: compare two sets of gene annotations for the same + sequence.' + title: AEGeAn ParsEval 0.16.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Faegean_parseval%2Faegean_parseval%2F0.16.0%2Bgalaxy1 homepage: http://www.plantgdb.org/GAEVAL/docs/index.html id: gaeval @@ -5940,37 +6531,54 @@ bunya: '' description: '' galaxy: - - title: Bundle Collection 1.3.0 + - description: 'Bundle Collection: Package up and download a collection of files + as a single archive.' + title: Bundle Collection 1.3.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fbundle_collections%2Fbundle_collection%2F1.3.0 - - title: Collapse Collection 5.1.0 + - description: 'Collapse Collection: into single dataset in order of the collection' + title: Collapse Collection 5.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fcollapse_collections%2Fcollapse_dataset%2F5.1.0 - - title: Column join 0.0.3 + - description: 'Column join: on multiple datasets' + title: Column join 0.0.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcollection_column_join%2Fcollection_column_join%2F0.0.3 - - title: Unzip collection 1.0.0 + - description: 'Unzip collection: ' + title: Unzip collection 1.0.0 url: https://usegalaxy.org.au/root?tool_id=__UNZIP_COLLECTION__ - - title: Zip collections 1.0.0 + - description: 'Zip collections: ' + title: Zip collections 1.0.0 url: https://usegalaxy.org.au/root?tool_id=__ZIP_COLLECTION__ - - title: Filter failed datasets 1.0.0 + - description: 'Filter failed datasets: ' + title: Filter failed datasets 1.0.0 url: https://usegalaxy.org.au/root?tool_id=__FILTER_FAILED_DATASETS__ - - title: Filter empty datasets 1.0.0 + - description: 'Filter empty datasets: ' + title: Filter empty datasets 1.0.0 url: https://usegalaxy.org.au/root?tool_id=__FILTER_EMPTY_DATASETS__ - - title: Flatten collection 1.0.0 + - description: 'Flatten collection: ' + title: Flatten collection 1.0.0 url: https://usegalaxy.org.au/root?tool_id=__FLATTEN__ - - title: Merge collections 1.0.0 + - description: 'Merge collections: ' + title: Merge collections 1.0.0 url: https://usegalaxy.org.au/root?tool_id=__MERGE_COLLECTION__ - - title: Relabel identifiers 1.0.0 + - description: 'Relabel identifiers: ' + title: Relabel identifiers 1.0.0 url: https://usegalaxy.org.au/root?tool_id=__RELABEL_FROM_FILE__ - - title: Filter collection 1.0.0 + - description: 'Filter collection: ' + title: Filter collection 1.0.0 url: https://usegalaxy.org.au/root?tool_id=__FILTER_FROM_FILE__ - - title: Sort collection 1.0.0 + - description: 'Sort collection: ' + title: Sort collection 1.0.0 url: https://usegalaxy.org.au/root?tool_id=__SORTLIST__ - - title: Tag elements 1.0.0 + - description: 'Tag elements: ' + title: Tag elements 1.0.0 url: https://usegalaxy.org.au/root?tool_id=__TAG_FROM_FILE__ - - title: Apply rules 1.1.0 + - description: 'Apply rules: ' + title: Apply rules 1.1.0 url: https://usegalaxy.org.au/root?tool_id=__APPLY_RULES__ - - title: Build list 1.1.0 + - description: 'Build list: ' + title: Build list 1.1.0 url: https://usegalaxy.org.au/root?tool_id=__BUILD_LIST__ - - title: Extract dataset 1.0.1 + - description: 'Extract dataset: ' + title: Extract dataset 1.0.1 url: https://usegalaxy.org.au/root?tool_id=__EXTRACT_DATASET__ homepage: '' id: galaxy_collection_operations @@ -5987,11 +6595,15 @@ bunya: '' description: '' galaxy: - - title: AXT to concatenated FASTA 1.0.0 + - description: 'AXT to concatenated FASTA: Converts an AXT formatted file to a concatenated + FASTA alignment' + title: AXT to concatenated FASTA 1.0.0 url: https://usegalaxy.org.au/root?tool_id=axt_to_concat_fasta - - title: AXT to FASTA 1.0.0 + - description: 'AXT to FASTA: Converts an AXT formatted file to FASTA format' + title: AXT to FASTA 1.0.0 url: https://usegalaxy.org.au/root?tool_id=axt_to_fasta - - title: AXT to LAV 1.0.0 + - description: 'AXT to LAV: Converts an AXT formatted file to LAV format' + title: AXT to LAV 1.0.0 url: https://usegalaxy.org.au/root?tool_id=axt_to_lav_1 homepage: '' id: Galaxy CONVERTER @@ -6008,21 +6620,29 @@ bunya: '' description: '' galaxy: - - title: Filter FASTA 2.3 + - 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 - - title: Filter 1.1.1 + - description: 'Filter: data on any column using simple expressions' + title: Filter 1.1.1 url: https://usegalaxy.org.au/root?tool_id=Filter1 - - title: Sort 1.2.0 + - description: 'Sort: data in ascending or descending order' + title: Sort 1.2.0 url: https://usegalaxy.org.au/root?tool_id=sort1 - - title: Select 1.0.4 + - description: 'Select: lines that match an expression' + title: Select 1.0.4 url: https://usegalaxy.org.au/root?tool_id=Grep1 - - title: Extract features 1.0.0 + - description: 'Extract features: from GFF data' + title: Extract features 1.0.0 url: https://usegalaxy.org.au/root?tool_id=Extract_features1 - - title: Filter GFF data by attribute 0.2 + - description: 'Filter GFF data by attribute: using simple expressions' + title: Filter GFF data by attribute 0.2 url: https://usegalaxy.org.au/root?tool_id=gff_filter_by_attribute - - title: Filter GFF data by feature count 0.1.1 + - description: 'Filter GFF data by feature count: using simple expressions' + title: Filter GFF data by feature count 0.1.1 url: https://usegalaxy.org.au/root?tool_id=gff_filter_by_feature_count - - title: Filter GTF data by attribute values_list 0.2 + - description: 'Filter GTF data by attribute values_list: ' + title: Filter GTF data by attribute values_list 0.2 url: https://usegalaxy.org.au/root?tool_id=gtf_filter_by_attribute_values_list homepage: '' id: galaxy_filter_and_sort @@ -6039,7 +6659,8 @@ bunya: '' description: '' galaxy: - - title: Bar chart 1.0.0 + - description: 'Bar chart: for multiple columns' + title: Bar chart 1.0.0 url: https://usegalaxy.org.au/root?tool_id=barchart_gnuplot homepage: '' id: galaxy_graph_display @@ -6056,7 +6677,8 @@ bunya: '' description: '' galaxy: - - title: Gene BED To Exon/Intron/Codon BED 1.0.0 + - description: 'Gene BED To Exon/Intron/Codon BED: expander' + title: Gene BED To Exon/Intron/Codon BED 1.0.0 url: https://usegalaxy.org.au/root?tool_id=gene2exon1 homepage: '' id: galaxy_genomic_intervals @@ -6073,15 +6695,21 @@ bunya: '' description: '' galaxy: - - title: Reverse 1.8+galaxy0 + - description: 'Reverse: columns in a tabular file' + title: Reverse 1.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdatamash_reverse%2Fdatamash_reverse%2F1.8%2Bgalaxy0 - - title: Transpose 1.8+galaxy1 + - description: 'Transpose: rows/columns in a tabular file' + title: Transpose 1.8+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdatamash_transpose%2Fdatamash_transpose%2F1.8%2Bgalaxy1 - - title: Join two Datasets 2.1.3 + - description: 'Join two Datasets: side by side on a specified field' + title: Join two Datasets 2.1.3 url: https://usegalaxy.org.au/root?tool_id=join1 - - title: Compare two Datasets 1.0.2 + - description: 'Compare two Datasets: to find common or distinct rows' + title: Compare two Datasets 1.0.2 url: https://usegalaxy.org.au/root?tool_id=comp1 - - title: Group 2.1.4 + - description: 'Group: data by a column and perform aggregate operation on other + columns.' + title: Group 2.1.4 url: https://usegalaxy.org.au/root?tool_id=Grouping1 homepage: '' id: galaxy_join_subtract_and_group @@ -6098,59 +6726,86 @@ bunya: '' description: '' galaxy: - - title: Number lines 9.3+galaxy0 + - description: 'Number lines: ' + title: Number lines 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Fnl%2F9.3%2Bgalaxy0 - - title: Column Regex Find And Replace 1.0.3 + - description: 'Column Regex Find And Replace: ' + title: Column Regex Find And Replace 1.0.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fregex_find_replace%2FregexColumn1%2F1.0.3 - - title: Regex Find And Replace 1.0.3 + - description: 'Regex Find And Replace: ' + title: Regex Find And Replace 1.0.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fregex_find_replace%2Fregex1%2F1.0.3 - - title: Add column 1.0.1 + - description: 'Add column: to an existing dataset' + title: Add column 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fadd_value%2FaddValue%2F1.0.1 - - title: Extract element identifiers 0.0.2 + - description: 'Extract element identifiers: of a list collection' + title: Extract element identifiers 0.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcollection_element_identifiers%2Fcollection_element_identifiers%2F0.0.2 - - title: Column arrange 0.2 + - description: 'Column arrange: by header name' + title: Column arrange 0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fcolumn_arrange_by_header%2Fbg_column_arrange_by_header%2F0.2 - - title: Compute 2.0 + - description: 'Compute: on rows' + title: Compute 2.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcolumn_maker%2FAdd_a_column1%2F2.0 - - title: Concatenate multiple datasets 0.2 + - description: 'Concatenate multiple datasets: tail-to-head' + title: Concatenate multiple datasets 0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fmvdbeek%2Fconcatenate_multiple_datasets%2Fcat_multiple%2F0.2 - - title: Concatenate multiple datasets 1.0 + - description: 'Concatenate multiple datasets: tail-to-head by specifying how' + title: Concatenate multiple datasets 1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fartbio%2Fconcatenate_multiple_datasets%2Fcat_multi_datasets%2F1.0 - - title: Condense 1.0.0 + - description: 'Condense: consecutive characters' + title: Condense 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcondense_characters%2FCondense+characters1%2F1.0.0 - - title: cut_francais 1.0 + - description: 'cut_francais: keep or remove selected column' + title: cut_francais 1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fr-lannes%2Fcut_include_exclude%2Fcut_fr%2F1.0 - - title: Filter Tabular 3.3.0 + - description: 'Filter Tabular: ' + title: Filter Tabular 3.3.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffilter_tabular%2Ffilter_tabular%2F3.3.0 - - title: Add column 1.0.0 + - description: 'Add column: to an existing dataset' + title: Add column 1.0.0 url: https://usegalaxy.org.au/root?tool_id=addValue - - title: Concatenate datasets 1.0.0 + - description: 'Concatenate datasets: tail-to-head' + title: Concatenate datasets 1.0.0 url: https://usegalaxy.org.au/root?tool_id=cat1 - - title: Cut 1.0.2 + - description: 'Cut: columns from a table' + title: Cut 1.0.2 url: https://usegalaxy.org.au/root?tool_id=Cut1 - - title: Merge Columns 1.0.1 + - description: 'Merge Columns: together' + title: Merge Columns 1.0.1 url: https://usegalaxy.org.au/root?tool_id=mergeCols1 - - title: Convert 1.0.0 + - description: 'Convert: delimiters to TAB' + title: Convert 1.0.0 url: https://usegalaxy.org.au/root?tool_id=Convert+characters1 - - title: Create single interval 1.0.0 + - description: 'Create single interval: as a new dataset' + title: Create single interval 1.0.0 url: https://usegalaxy.org.au/root?tool_id=createInterval - - title: Change Case 1.0.0 + - description: 'Change Case: of selected columns' + title: Change Case 1.0.0 url: https://usegalaxy.org.au/root?tool_id=ChangeCase - - title: Paste 1.0.0 + - description: 'Paste: two files side by side' + title: Paste 1.0.0 url: https://usegalaxy.org.au/root?tool_id=Paste1 - - title: Remove beginning 1.0.0 + - description: 'Remove beginning: of a file' + title: Remove beginning 1.0.0 url: https://usegalaxy.org.au/root?tool_id=Remove+beginning1 - - title: Select random lines 2.0.2 + - description: 'Select random lines: from a file' + title: Select random lines 2.0.2 url: https://usegalaxy.org.au/root?tool_id=random_lines1 - - title: Select first 1.0.2 + - description: 'Select first: lines from a dataset' + title: Select first 1.0.2 url: https://usegalaxy.org.au/root?tool_id=Show+beginning1 - - title: Select last 1.0.1 + - description: 'Select last: lines from a dataset' + title: Select last 1.0.1 url: https://usegalaxy.org.au/root?tool_id=Show+tail1 - - title: Trim 0.0.2 + - description: 'Trim: leading or trailing characters' + title: Trim 0.0.2 url: https://usegalaxy.org.au/root?tool_id=trimmer - - title: Line/Word/Character count 1.0.0 + - description: 'Line/Word/Character count: of a dataset' + title: Line/Word/Character count 1.0.0 url: https://usegalaxy.org.au/root?tool_id=wc_gnu - - title: Secure Hash / Message Digest 0.0.2 + - description: 'Secure Hash / Message Digest: on a dataset' + title: Secure Hash / Message Digest 0.0.2 url: https://usegalaxy.org.au/root?tool_id=secure_hash_message_digest homepage: '' id: galaxy_text_manipulation @@ -6167,39 +6822,56 @@ bunya: '' description: '' galaxy: - - title: Combine FASTA and QUAL 1.1.5 + - description: 'Combine FASTA and QUAL: into FASTQ' + title: Combine FASTA and QUAL 1.1.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_combiner%2Ffastq_combiner%2F1.1.5 - - title: Filter FASTQ 1.1.5 + - description: 'Filter FASTQ: reads by quality score and length' + title: Filter FASTQ 1.1.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_filter%2Ffastq_filter%2F1.1.5 - - title: FASTQ Groomer 1.1.5 + - description: 'FASTQ Groomer: convert between various FASTQ quality formats' + title: FASTQ Groomer 1.1.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_groomer%2Ffastq_groomer%2F1.1.5 - - title: Manipulate FASTQ 1.1.5 + - description: 'Manipulate FASTQ: reads on various attributes' + title: Manipulate FASTQ 1.1.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_manipulation%2Ffastq_manipulation%2F1.1.5 - - title: FASTQ Masker 1.1.5 + - description: 'FASTQ Masker: by quality score' + title: FASTQ Masker 1.1.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_masker_by_quality%2Ffastq_masker_by_quality%2F1.1.5 - - title: FASTQ de-interlacer 1.1.5 + - description: 'FASTQ de-interlacer: on paired end reads' + title: FASTQ de-interlacer 1.1.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_paired_end_deinterlacer%2Ffastq_paired_end_deinterlacer%2F1.1.5 - - title: FASTQ interlacer 1.2.0.1+galaxy0 + - description: 'FASTQ interlacer: on paired end reads' + title: FASTQ interlacer 1.2.0.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_paired_end_interlacer%2Ffastq_paired_end_interlacer%2F1.2.0.1%2Bgalaxy0 - - title: FASTQ joiner 2.0.1.1+galaxy0 + - description: 'FASTQ joiner: on paired end reads' + title: FASTQ joiner 2.0.1.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_paired_end_joiner%2Ffastq_paired_end_joiner%2F2.0.1.1%2Bgalaxy0 - - title: FASTQ splitter 1.1.5+galaxy1 + - description: 'FASTQ splitter: on joined paired end reads' + title: FASTQ splitter 1.1.5+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_paired_end_splitter%2Ffastq_paired_end_splitter%2F1.1.5%2Bgalaxy1 - - title: Quality format converter 1.0.1+galaxy2 + - description: 'Quality format converter: (ASCII-Numeric)' + title: Quality format converter 1.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_quality_converter%2Fcshl_fastq_quality_converter%2F1.0.1%2Bgalaxy2 - - title: FASTQ Summary Statistics 1.1.5 + - description: 'FASTQ Summary Statistics: by column' + title: FASTQ Summary Statistics 1.1.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_stats%2Ffastq_stats%2F1.1.5 - - title: FASTQ to FASTA 1.1.5 + - description: 'FASTQ to FASTA: converter' + title: FASTQ to FASTA 1.1.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastqtofasta%2Ffastq_to_fasta_python%2F1.1.5 - - title: FASTQ Trimmer 1.1.5 + - description: 'FASTQ Trimmer: by column' + title: FASTQ Trimmer 1.1.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_trimmer%2Ffastq_trimmer%2F1.1.5 - - title: FASTQ Quality Trimmer 1.1.5 + - description: 'FASTQ Quality Trimmer: by sliding window' + title: FASTQ Quality Trimmer 1.1.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_trimmer_by_quality%2Ffastq_quality_trimmer%2F1.1.5 - - title: FASTQ to FASTA 1.0.2+galaxy2 + - description: 'FASTQ to FASTA: converter from FASTX-toolkit' + title: FASTQ to FASTA 1.0.2+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_to_fasta%2Fcshl_fastq_to_fasta%2F1.0.2%2Bgalaxy2 - - title: FASTQ to Tabular 1.1.5 + - description: 'FASTQ to Tabular: converter' + title: FASTQ to Tabular 1.1.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_to_tabular%2Ffastq_to_tabular%2F1.1.5 - - title: Tabular to FASTQ 1.1.5 + - description: 'Tabular to FASTQ: converter' + title: Tabular to FASTQ 1.1.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftabular_to_fastq%2Ftabular_to_fastq%2F1.1.5 homepage: '' id: galaxy_sequence_utils @@ -6216,15 +6888,20 @@ bunya: '' description: '' galaxy: - - title: Categorize Elements 1.0.0 + - description: 'Categorize Elements: satisfying criteria' + title: Categorize Elements 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcategorize_elements_satisfying_criteria%2Fcategorize_elements_satisfying_criteria%2F1.0.0 - - title: Compute Motif Frequencies For All Motifs 1.0.0 + - description: 'Compute Motif Frequencies For All Motifs: motif by motif' + title: Compute Motif Frequencies For All Motifs 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcompute_motif_frequencies_for_all_motifs%2Fcompute_motif_frequencies_for_all_motifs%2F1.0.0 - - title: Compute Motif Frequencies 1.0.0 + - description: 'Compute Motif Frequencies: in indel flanking regions' + title: Compute Motif Frequencies 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcompute_motifs_frequency%2Fcompute_motifs_frequency%2F1.0.0 - - title: Correlation 1.0.0 + - description: 'Correlation: for numeric columns' + title: Correlation 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcorrelation%2Fcor2%2F1.0.0 - - title: Count GFF Features 0.2 + - description: 'Count GFF Features: ' + title: Count GFF Features 0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcount_gff_features%2Fcount_gff_features%2F0.2 homepage: '' id: galaxy_statistics @@ -6274,7 +6951,9 @@ bunya: '' description: Cleaning aligned sequences. galaxy: - - title: Gblocks 0.91b + - description: 'Gblocks: Selection of conserved blocks from multiple alignments + for their use in phylogenetic analysis' + title: Gblocks 0.91b url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fearlhaminst%2Fgblocks%2Fgblocks%2F0.91b homepage: http://www.embl-heidelberg.de/~castresa/Gblocks/Gblocks.html id: gblock @@ -6323,7 +7002,8 @@ results (equivalent to MUMmer) with controlled memory consumption and comparable or faster execution times particularly with long sequences. galaxy: - - title: Gecko 1.2 + - description: 'Gecko: Ungapped genome comparison' + title: Gecko 1.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgecko%2Fgecko%2F1.2 homepage: http://bitlab-es.com/gecko/ id: gecko @@ -6348,53 +7028,84 @@ a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. galaxy: - - title: GEMINI actionable_mutations 0.20.1 + - description: 'GEMINI actionable_mutations: Retrieve genes with actionable somatic + mutations via COSMIC and DGIdb' + title: GEMINI actionable_mutations 0.20.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_actionable_mutations%2Fgemini_actionable_mutations%2F0.20.1 - - title: GEMINI amend 0.20.1 + - description: 'GEMINI amend: Amend an already loaded GEMINI database.' + title: GEMINI amend 0.20.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_amend%2Fgemini_amend%2F0.20.1 - - title: GEMINI annotate 0.20.1+galaxy2 + - description: 'GEMINI annotate: the variants in an existing GEMINI database with + additional information' + title: GEMINI annotate 0.20.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_annotate%2Fgemini_annotate%2F0.20.1%2Bgalaxy2 - - title: GEMINI burden 0.20.1 + - description: 'GEMINI burden: perform sample-wise gene-level burden calculations' + title: GEMINI burden 0.20.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_burden%2Fgemini_burden%2F0.20.1 - - title: GEMINI comp_hets 0.18.1.1 + - description: 'GEMINI comp_hets: Identifying potential compound heterozygotes' + title: GEMINI comp_hets 0.18.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_comp_hets%2Fgemini_comp_hets%2F0.18.1.1 - - title: GEMINI database info 0.20.1 + - description: 'GEMINI database info: Retrieve information about tables, columns + and annotation data stored in a GEMINI database' + title: GEMINI database info 0.20.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_db_info%2Fgemini_db_info%2F0.20.1 - - title: GEMINI de_novo 0.18.1.1 + - description: 'GEMINI de_novo: Identifying potential de novo mutations' + title: GEMINI de_novo 0.18.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_de_novo%2Fgemini_de_novo%2F0.18.1.1 - - title: GEMINI dump 0.18.1.1 + - description: 'GEMINI dump: Extract data from the Gemini DB' + title: GEMINI dump 0.18.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_dump%2Fgemini_dump%2F0.18.1.1 - - title: GEMINI fusions 0.20.1 + - description: 'GEMINI fusions: Identify somatic fusion genes from a GEMINI database' + title: GEMINI fusions 0.20.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_fusions%2Fgemini_fusions%2F0.20.1 - - title: GEMINI gene_wise 0.20.1 + - description: 'GEMINI gene_wise: Discover per-gene variant patterns across families' + title: GEMINI gene_wise 0.20.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_gene_wise%2Fgemini_gene_wise%2F0.20.1 - - title: GEMINI inheritance pattern 0.20.1 + - description: 'GEMINI inheritance pattern: based identification of candidate genes' + title: GEMINI inheritance pattern 0.20.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_inheritance%2Fgemini_inheritance%2F0.20.1 - - title: GEMINI interactions 0.20.1 + - description: 'GEMINI interactions: Find genes among variants that are interacting + partners' + title: GEMINI interactions 0.20.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_interactions%2Fgemini_interactions%2F0.20.1 - - title: GEMINI load 0.20.1+galaxy2 + - description: 'GEMINI load: Loading a VCF file into GEMINI' + title: GEMINI load 0.20.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_load%2Fgemini_load%2F0.20.1%2Bgalaxy2 - - title: GEMINI lof_sieve 0.20.1 + - description: 'GEMINI lof_sieve: Filter LoF variants by transcript position and + type' + title: GEMINI lof_sieve 0.20.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_lof_sieve%2Fgemini_lof_sieve%2F0.20.1 - - title: GEMINI mendel_errors 0.18.1.1 + - description: 'GEMINI mendel_errors: Identify candidate violations of Mendelian + inheritance' + title: GEMINI mendel_errors 0.18.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_mendel_errors%2Fgemini_mendel_errors%2F0.18.1.1 - - title: GEMINI pathways 0.20.1 + - description: 'GEMINI pathways: Map genes and variants to KEGG pathways' + title: GEMINI pathways 0.20.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_pathways%2Fgemini_pathways%2F0.20.1 - - title: GEMINI qc 0.20.1 + - description: 'GEMINI qc: Quality control tool' + title: GEMINI qc 0.20.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_qc%2Fgemini_qc%2F0.20.1 - - title: GEMINI query 0.20.1+galaxy1 + - description: 'GEMINI query: Querying the GEMINI database' + title: GEMINI query 0.20.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_query%2Fgemini_query%2F0.20.1%2Bgalaxy1 - - title: GEMINI autosomal recessive/dominant 0.18.1.1 + - description: 'GEMINI autosomal recessive/dominant: Find variants meeting an autosomal + recessive/dominant model' + title: GEMINI autosomal recessive/dominant 0.18.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_recessive_and_dominant%2Fgemini_recessive_and_dominant%2F0.18.1.1 - - title: GEMINI region 0.18.1.1 + - description: 'GEMINI region: Extracting variants from specific regions or genes' + title: GEMINI region 0.18.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_region%2Fgemini_region%2F0.18.1.1 - - title: GEMINI roh 0.20.1 + - description: 'GEMINI roh: Identifying runs of homozygosity' + title: GEMINI roh 0.20.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_roh%2Fgemini_roh%2F0.20.1 - - title: GEMINI set_somatic 0.20.1 + - description: 'GEMINI set_somatic: Tag somatic mutations in a GEMINI database' + title: GEMINI set_somatic 0.20.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_set_somatic%2Fgemini_set_somatic%2F0.20.1 - - title: GEMINI stats 0.20.1 + - description: 'GEMINI stats: Compute useful variant statistics' + title: GEMINI stats 0.20.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_stats%2Fgemini_stats%2F0.20.1 - - title: GEMINI windower 0.20.1 + - description: 'GEMINI windower: Compute sliding window statistics from variants' + title: GEMINI windower 0.20.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgemini_windower%2Fgemini_windower%2F0.20.1 homepage: https://gemini.readthedocs.io/en/latest/index.html id: gemini @@ -6440,7 +7151,8 @@ bunya: '' description: '' galaxy: - - title: Stitch Gene blocks 1.0.1 + - description: 'Stitch Gene blocks: given a set of coding exon intervals' + title: Stitch Gene blocks 1.0.1 url: https://usegalaxy.org.au/root?tool_id=GeneBed_Maf_Fasta2 homepage: '' id: GeneBed_Maf_Fasta2 @@ -6457,7 +7169,9 @@ bunya: '' description: '' galaxy: - - title: gene.iobio visualisation 4.7.1+galaxy1 + - description: 'gene.iobio visualisation: analyses VCFs for single and trio analysis + to find causative variants using gene.iobio''s public server' + title: gene.iobio visualisation 4.7.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgeneiobio%2Fgene_iobio_display_generation_iframe%2F4.7.1%2Bgalaxy1 homepage: '' id: geneiobio @@ -6499,7 +7213,8 @@ bunya: '' description: '' galaxy: - - title: Generate count matrix 1.0 + - description: 'Generate count matrix: from individual files' + title: Generate count matrix 1.0 url: https://usegalaxy.org.au/root?tool_id=testtoolshed.g2.bx.psu.edu%2Frepos%2Fjchung%2Fgenerate_count_matrix%2Fgenerate_count_matrix%2F1.0 homepage: '' id: generate_count_matrix @@ -6516,7 +7231,8 @@ bunya: '' description: '' galaxy: - - title: Generate A Matrix 1.0.0 + - description: 'Generate A Matrix: for using PC and LDA' + title: Generate A Matrix 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fgenerate_pc_lda_matrix%2Fgenerate_matrix_for_pca_and_lda1%2F1.0.0 homepage: '' id: generate_pc_lda_matrix @@ -6553,7 +7269,8 @@ and polyploid genomes | Average k-mer coverage for polyploid genome | Upload results from running Jellyfish or KMC galaxy: - - title: GenomeScope 2.0+galaxy2 + - 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 homepage: https://github.com/tbenavi1/genomescope2.0 id: genomescope @@ -6622,7 +7339,8 @@ bunya: '' description: '' galaxy: - - title: Genrich 0.5+galaxy2 + - description: 'Genrich: Detecting sites of genomic enrichment' + title: Genrich 0.5+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgenrich%2Fgenrich%2F0.5%2Bgalaxy2 homepage: '' id: genrich @@ -6639,7 +7357,8 @@ bunya: '' description: '' galaxy: - - title: Get PDB file 0.1.0 + - description: 'Get PDB file: from Protein Data Bank' + title: Get PDB file 0.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fget_pdb%2Fget_pdb%2F0.1.0 homepage: '' id: get_pdb_file @@ -6660,7 +7379,8 @@ This toolkit assemblies organelle genome from genomic skimming data.' galaxy: - - title: Get organelle from reads 1.7.7.0+galaxy1 + - description: 'Get organelle from reads: ' + title: Get organelle from reads 1.7.7.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgetorganelle%2Fget_organelle_from_reads%2F1.7.7.0%2Bgalaxy1 homepage: https://github.com/Kinggerm/GetOrganelle id: getorganelle @@ -6685,7 +7405,9 @@ bunya: '' description: '' galaxy: - - title: GFA to FASTA 0.1.2 + - description: 'GFA to FASTA: Convert Graphical Fragment Assembly files to FASTA + format' + title: GFA to FASTA 0.1.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgfa_to_fa%2Fgfa_to_fa%2F0.1.2 homepage: '' id: gfa_to_fa @@ -6704,7 +7426,8 @@ and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. galaxy: - - title: gfastats 1.3.6+galaxy0 + - description: 'gfastats: the swiss army knife for genome assembly' + title: gfastats 1.3.6+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fgfastats%2Fgfastats%2F1.3.6%2Bgalaxy0 homepage: https://github.com/vgl-hub/gfastats id: gfastats @@ -6768,7 +7491,8 @@ bunya: '' description: '' galaxy: - - title: GFF-to-BED 1.0.1 + - description: 'GFF-to-BED: converter' + title: GFF-to-BED 1.0.1 url: https://usegalaxy.org.au/root?tool_id=gff2bed1 homepage: '' id: gff2bed1 @@ -6803,7 +7527,8 @@ description: Program for comparing, annotating, merging and tracking transcripts in GFF files. galaxy: - - title: GffCompare 0.12.6+galaxy0 + - description: 'GffCompare: compare assembled transcripts to a reference annotation' + title: GffCompare 0.12.6+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgffcompare%2Fgffcompare%2F0.12.6%2Bgalaxy0 homepage: https://ccb.jhu.edu/software/stringtie/gff.shtml id: gffcompare @@ -6822,7 +7547,8 @@ bunya: '' description: '' galaxy: - - title: Convert gffCompare annotated GTF to BED 0.2.1 + - description: 'Convert gffCompare annotated GTF to BED: for StringTie results' + title: Convert gffCompare annotated GTF to BED 0.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fgffcompare_to_bed%2Fgffcompare_to_bed%2F0.2.1 homepage: '' id: gffcompare_to_bed @@ -6840,7 +7566,8 @@ - 0.12.7-gcccore-10.3.0 description: program for filtering, converting and manipulating GFF files galaxy: - - title: gffread 2.2.1.4+galaxy0 + - description: 'gffread: Filters and/or converts GFF3/GTF2 records' + title: gffread 2.2.1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fgffread%2Fgffread%2F2.2.1.4%2Bgalaxy0 homepage: https://ccb.jhu.edu/software/stringtie/gff.shtml id: gffread @@ -6860,17 +7587,23 @@ bunya: '' description: Plotting system for R, based on the grammar of graphics. galaxy: - - title: heatmap2 3.1.3.1+galaxy0 + - description: 'heatmap2: ' + title: heatmap2 3.1.3.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fggplot2_heatmap2%2Fggplot2_heatmap2%2F3.1.3.1%2Bgalaxy0 - - title: Histogram with ggplot2 3.4.0+galaxy0 + - description: 'Histogram with ggplot2: ' + title: Histogram with ggplot2 3.4.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fggplot2_histogram%2Fggplot2_histogram%2F3.4.0%2Bgalaxy0 - - title: Heatmap w ggplot 3.4.0+galaxy0 + - description: 'Heatmap w ggplot: ' + title: Heatmap w ggplot 3.4.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fggplot2_heatmap%2Fggplot2_heatmap%2F3.4.0%2Bgalaxy0 - - title: Scatterplot with ggplot2 3.4.0+galaxy1 + - description: 'Scatterplot with ggplot2: ' + title: Scatterplot with ggplot2 3.4.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fggplot2_point%2Fggplot2_point%2F3.4.0%2Bgalaxy1 - - title: PCA plot w ggplot2 3.4.0+galaxy0 + - description: 'PCA plot w ggplot2: ' + title: PCA plot w ggplot2 3.4.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fggplot2_pca%2Fggplot2_pca%2F3.4.0%2Bgalaxy0 - - title: Violin plot w ggplot2 3.4.0+galaxy0 + - description: 'Violin plot w ggplot2: ' + title: Violin plot w ggplot2 3.4.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fggplot2_violin%2Fggplot2_violin%2F3.4.0%2Bgalaxy0 homepage: http://ggplot2.org/ id: ggplot2 @@ -6955,7 +7688,8 @@ bunya: '' description: '' galaxy: - - title: GMAJ 2.0.1 + - description: 'GMAJ: Multiple Alignment Viewer' + title: GMAJ 2.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fgmaj%2Fgmaj_1%2F2.0.1 homepage: '' id: GMAJ @@ -7099,9 +7833,12 @@ \ in the set of enriched GO terms and simplify its output.\nIt was developed by\ \ the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ci\xEAncia." galaxy: - - title: GOEnrichment 2.0.1 + - description: 'GOEnrichment: performs GO enrichment analysis of a set of gene products' + title: GOEnrichment 2.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgoenrichment%2Fgoenrichment%2F2.0.1 - - title: GOSlimmer 1.0.1 + - description: 'GOSlimmer: converts a set of annotation from GO to a given GOSlim + version' + title: GOSlimmer 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgoslimmer%2Fgoslimmer%2F1.0.1 homepage: https://github.com/DanFaria/GOEnrichment id: goenrichment @@ -7120,7 +7857,8 @@ description: Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. galaxy: - - title: goseq 1.50.0+galaxy0 + - description: 'goseq: tests for overrepresented gene categories' + title: goseq 1.50.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgoseq%2Fgoseq%2F1.50.0%2Bgalaxy0 homepage: https://bioconductor.org/packages/release/bioc/html/goseq.html id: goseq @@ -7162,7 +7900,8 @@ bunya: '' description: '' galaxy: - - title: GrameneMart 1.0.1 + - description: 'GrameneMart: Central server' + title: GrameneMart 1.0.1 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=gramenemart homepage: '' id: gramenemart @@ -7182,9 +7921,11 @@ informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. galaxy: - - title: GraPhlAn 1.1.3 + - description: 'GraPhlAn: to produce graphical output of an input tree' + title: GraPhlAn 1.1.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgraphlan%2Fgraphlan%2F1.1.3 - - title: Generation, personalization and annotation of tree 1.1.3 + - description: 'Generation, personalization and annotation of tree: for GraPhlAn' + title: Generation, personalization and annotation of tree 1.1.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgraphlan_annotate%2Fgraphlan_annotate%2F1.1.3 homepage: https://github.com/biobakery/graphlan id: graphlan @@ -7229,21 +7970,31 @@ fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. galaxy: - - title: Modify/convert and concatate GROMACS trajectories 2022+galaxy2 + - description: 'Modify/convert and concatate GROMACS trajectories: using trjconv + and trjcat' + title: Modify/convert and concatate GROMACS trajectories 2022+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fchemteam%2Fgmx_trj%2Fgmx_trj%2F2022%2Bgalaxy2 - - title: GROMACS structure configuration 2022+galaxy0 + - description: 'GROMACS structure configuration: using editconf' + title: GROMACS structure configuration 2022+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fchemteam%2Fgmx_editconf%2Fgmx_editconf%2F2022%2Bgalaxy0 - - title: GROMACS energy minimization 2022+galaxy0 + - description: 'GROMACS energy minimization: of the system prior to equilibration + and production MD' + title: GROMACS energy minimization 2022+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fchemteam%2Fgmx_em%2Fgmx_em%2F2022%2Bgalaxy0 - - title: Extract energy components with GROMACS 2022+galaxy1 + - description: 'Extract energy components with GROMACS: ' + title: Extract energy components with GROMACS 2022+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fchemteam%2Fgmx_energy%2Fgmx_energy%2F2022%2Bgalaxy1 - - title: Merge GROMACS topologies 3.4.3+galaxy0 + - description: 'Merge GROMACS topologies: and GRO files' + title: Merge GROMACS topologies 3.4.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fchemteam%2Fgmx_merge_topology_files%2Fgmx_merge_topology_files%2F3.4.3%2Bgalaxy0 - - title: GROMACS initial setup 2022+galaxy0 + - description: 'GROMACS initial setup: of topology and GRO structure file' + title: GROMACS initial setup 2022+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fchemteam%2Fgmx_setup%2Fgmx_setup%2F2022%2Bgalaxy0 - - title: GROMACS simulation 2022+galaxy0 + - description: 'GROMACS simulation: for system equilibration or data collection' + title: GROMACS simulation 2022+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fchemteam%2Fgmx_sim%2Fgmx_sim%2F2022%2Bgalaxy0 - - title: GROMACS solvation and adding ions 2022+galaxy0 + - description: 'GROMACS solvation and adding ions: to structure and topology files' + title: GROMACS solvation and adding ions 2022+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fchemteam%2Fgmx_solvate%2Fgmx_solvate%2F2022%2Bgalaxy0 homepage: http://www.gromacs.org/ id: gromacs @@ -7346,8 +8097,9 @@ samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).' galaxy: - - title: GTDB-Tk Classify genomes 2.3.2+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgtdbtk_classify_wf%2Fgtdbtk_classify_wf%2F2.3.2%2Bgalaxy0 + - description: 'GTDB-Tk Classify genomes: by placement in GTDB reference tree' + title: GTDB-Tk Classify genomes 2.3.2+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgtdbtk_classify_wf%2Fgtdbtk_classify_wf%2F2.3.2%2Bgalaxy1 homepage: https://github.com/ecogenomics/gtdbtk id: gtdb-tk license: GPL-3.0 @@ -7385,7 +8137,8 @@ bunya: '' description: '' galaxy: - - title: GTF-to-BEDGraph 1.0.0 + - description: 'GTF-to-BEDGraph: converter' + title: GTF-to-BEDGraph 1.0.0 url: https://usegalaxy.org.au/root?tool_id=gtf2bedgraph homepage: '' id: gtf2bedgraph @@ -7402,7 +8155,9 @@ bunya: '' description: '' galaxy: - - title: GTF2GeneList 1.52.0+galaxy0 + - description: 'GTF2GeneList: extracts a complete annotation table or subsets thereof + from an Ensembl GTF using rtracklayer' + title: GTF2GeneList 1.52.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fgtf2gene_list%2F_ensembl_gtf2gene_list%2F1.52.0%2Bgalaxy0 homepage: '' id: gtf2gene_list @@ -7420,7 +8175,8 @@ description: Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. galaxy: - - title: Gubbins 3.2.1+galaxy0 + - description: 'Gubbins: Recombination detection in Bacteria' + title: Gubbins 3.2.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgubbins%2Fgubbins%2F3.2.1%2Bgalaxy0 homepage: https://github.com/nickjcroucher/gubbins id: gubbins @@ -7459,7 +8215,8 @@ - 1.12-gcccore-11.3.0 (D) description: '' galaxy: - - title: Compress file(s) 0.1.0 + - description: 'Compress file(s): ' + title: Compress file(s) 0.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcompress_file%2Fcompress_file%2F0.1.0 homepage: '' id: gzip @@ -7501,7 +8258,8 @@ The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md' galaxy: - - title: Hapcut2 1.3.3+galaxy0+ga1 + - description: 'Hapcut2: - haplotype assembly for diploid organisms' + title: Hapcut2 1.3.3+galaxy0+ga1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxy-australia%2Fhapcut2%2Fhapcut2%2F1.3.3%2Bgalaxy0%2Bga1 homepage: https://github.com/vibansal/HapCUT2 id: hapcut2 @@ -7518,7 +8276,8 @@ bunya: '' description: '' galaxy: - - title: HbVar 2.0.0 + - description: 'HbVar: Human Hemoglobin Variants and Thalassemias' + title: HbVar 2.0.0 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=hbvar homepage: '' id: hbvar @@ -7553,13 +8312,17 @@ bunya: '' description: Tool for single-species active module discovery. galaxy: - - title: Calculate a Heinz score 1.0 + - description: 'Calculate a Heinz score: for each node' + title: Calculate a Heinz score 1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fheinz%2Fheinz_scoring%2F1.0 - - title: Visualize 0.1.1 + - description: 'Visualize: the optimal scoring subnetwork' + title: Visualize 0.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fheinz%2Fheinz_visualization%2F0.1.1 - - title: Fit a BUM model 1.0 + - description: 'Fit a BUM model: with p-values' + title: Fit a BUM model 1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fheinz%2Fheinz_bum%2F1.0 - - title: Identify optimal scoring subnetwork 1.0 + - description: 'Identify optimal scoring subnetwork: using Heinz' + title: Identify optimal scoring subnetwork 1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fheinz%2Fheinz%2F1.0 homepage: https://software.cwi.nl/software/heinz id: heinz @@ -7583,7 +8346,8 @@ description: This tool provides functional annotation for a list of genes by connecting with DAVID database. galaxy: - - title: DAVID 1.0.1 + - description: 'DAVID: functional annotation for a list of genes' + title: DAVID 1.0.1 url: https://usegalaxy.org.au/root?tool_id=hgv_david homepage: https://github.com/galaxyproject/galaxy/tree/dev/tools id: hgv_david @@ -7611,7 +8375,8 @@ description: This tool can be used to analyze the patterns of linkage disequilibrium (LD) between polymorphic sites in a locus. galaxy: - - title: LD 1.0.0 + - description: 'LD: linkage disequilibrium and tag SNPs' + title: LD 1.0.0 url: https://usegalaxy.org.au/root?tool_id=hgv_ldtools homepage: https://github.com/galaxyproject/galaxy/tree/dev/tools id: hgv_ldtools @@ -7641,7 +8406,8 @@ description: This tool creates a link to the g:GOSt tool (Gene Group Functional Profiling), which provides functional profiling of gene lists. galaxy: - - title: g:Profiler 1.0.0 + - description: 'g:Profiler: tools for functional profiling of gene lists' + title: g:Profiler 1.0.0 url: https://usegalaxy.org.au/root?tool_id=hgv_linkToGProfile homepage: https://github.com/galaxyproject/galaxy/tree/dev/tools id: hgv_linkToGProfile @@ -7672,15 +8438,22 @@ \ 3.6 documentation.\n\nscHiCExplorer \u2014 scHiCExplorer 7 documentation.\n\n\ Free document hosting provided by Read the Docs." galaxy: - - title: hicPCA 3.7.2+galaxy0 + - 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 - - title: hicFindTADs 3.7.2+galaxy0 + - description: 'hicFindTADs: identify TAD boundaries by computing the degree of + separation of each Hi-C matrix bin' + title: hicFindTADs 3.7.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicfindtads%2Fhicexplorer_hicfindtads%2F3.7.2%2Bgalaxy0 - - title: hicPlotMatrix 3.7.2+galaxy0 + - 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 - - title: hicMergeMatrixBins 3.7.2+galaxy0 + - 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 - - title: hicBuildMatrix 3.7.2+galaxy0 + - description: 'hicBuildMatrix: create a contact matrix' + title: hicBuildMatrix 3.7.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicbuildmatrix%2Fhicexplorer_hicbuildmatrix%2F3.7.2%2Bgalaxy0 homepage: https://hicexplorer.usegalaxy.eu id: hicexplorer @@ -7706,7 +8479,9 @@ description: Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz). galaxy: - - title: HiFi Adapter Filter 2.0.0+galaxy0 + - description: 'HiFi Adapter Filter: Remove CCS reads with remnant PacBio adapter + sequences' + title: HiFi Adapter Filter 2.0.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxy-australia%2Fhifiadapterfilt%2Fhifiadapterfilt%2F2.0.0%2Bgalaxy0 homepage: https://github.com/sheinasim/HiFiAdapterFilt id: hifiadapterfilt @@ -7733,7 +8508,8 @@ - 0.16.1-gcccore-10.3.0 description: 'Hifiasm: a haplotype-resolved assembler for accurate Hifi reads' galaxy: - - title: Hifiasm 0.19.8+galaxy1 + - 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 homepage: https://github.com/chhylp123/hifiasm id: hifiasm @@ -7756,7 +8532,8 @@ bunya: '' description: '' galaxy: - - title: Hifiasm_meta 0.3.1+galaxy0 + - description: 'Hifiasm_meta: for metagenome assembly using Hifi reads' + title: Hifiasm_meta 0.3.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxy-australia%2Fhifiasm_meta%2Fhifiasm_meta%2F0.3.1%2Bgalaxy0 homepage: '' id: hifiasm_meta @@ -7778,7 +8555,8 @@ DNA and RNA) to a population of human genomes (as well as to a single reference genome). galaxy: - - title: HISAT2 2.2.1+galaxy1 + - description: 'HISAT2: A fast and sensitive alignment program' + title: HISAT2 2.2.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhisat2%2Fhisat2%2F2.2.1%2Bgalaxy1 homepage: https://ccb.jhu.edu/software/hisat2/index.shtml id: hisat2 @@ -7804,7 +8582,8 @@ bunya: '' description: '' galaxy: - - title: Histogram 1.0.4 + - 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 homepage: '' id: histogram @@ -7842,29 +8621,42 @@ using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. galaxy: - - title: hmmconvert 0.1.0 + - description: 'hmmconvert: convert profile file to a HMMER format' + title: hmmconvert 0.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhmmer3%2Fhmmer_hmmconvert%2F0.1.0 - - title: hmmalign 0.1.0 + - description: 'hmmalign: align sequences to a profile HMM' + title: hmmalign 0.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhmmer3%2Fhmmer_hmmalign%2F0.1.0 - - title: phmmer 0.1.0 + - description: 'phmmer: search a protein sequence against a protein database (BLASTP-like)' + title: phmmer 0.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhmmer3%2Fhmmer_phmmer%2F0.1.0 - - title: nhmmer 0.1.0 + - description: 'nhmmer: search a DNA model or alignment against a DNA database (BLASTN-like)' + title: nhmmer 0.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhmmer3%2Fhmmer_nhmmer%2F0.1.0 - - title: alimask 0.1.0 + - description: 'alimask: append modelmask line to a multiple sequence alignments' + title: alimask 0.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhmmer3%2Fhmmer_alimask%2F0.1.0 - - title: hmmscan 0.1.0 + - description: 'hmmscan: search sequence(s) against a profile database' + title: hmmscan 0.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhmmer3%2Fhmmer_hmmscan%2F0.1.0 - - title: jackhmmer 0.1.0 + - description: 'jackhmmer: iteratively search a protein sequence against a protein + database (PSIBLAST-like)' + title: jackhmmer 0.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhmmer3%2Fhmmer_jackhmmer%2F0.1.0 - - title: hmmsearch 0.1.0 + - description: 'hmmsearch: search profile(s) against a sequence database' + title: hmmsearch 0.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhmmer3%2Fhmmer_hmmsearch%2F0.1.0 - - title: nhmmscan 0.1.0 + - description: 'nhmmscan: search DNA sequence(s) against a DNA profile database' + title: nhmmscan 0.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhmmer3%2Fhmmer_nhmmscan%2F0.1.0 - - title: hmmbuild 0.1.0 + - description: 'hmmbuild: Build a profile HMM from an input multiple alignment' + title: hmmbuild 0.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhmmer3%2Fhmmer_hmmbuild%2F0.1.0 - - title: hmmfetch 0.1.0 + - description: 'hmmfetch: retrieve profile HMM(s) from a file' + title: hmmfetch 0.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhmmer3%2Fhmmer_hmmfetch%2F0.1.0 - - title: hmmemit 0.1.0 + - description: 'hmmemit: sample sequence(s) from a profile HMM' + title: hmmemit 0.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhmmer3%2Fhmmer_hmmemit%2F0.1.0 homepage: http://hmmer.org/ id: hmmer @@ -7916,7 +8708,9 @@ description: Python framework to process and analyse high-throughput sequencing (HTS) data galaxy: - - title: htseq-count 2.0.5+galaxy0 + - description: 'htseq-count: - Count aligned reads in a BAM file that overlap features + in a GFF file' + title: htseq-count 2.0.5+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Flparsons%2Fhtseq_count%2Fhtseq_count%2F2.0.5%2Bgalaxy0 homepage: http://htseq.readthedocs.io/en/release_0.9.1/ id: htseq @@ -7970,29 +8764,43 @@ \ profiling answers the question \u201CWhat are the microbes in my community-of-interest\ \ doing (or are capable of doing)?\u201D" galaxy: - - title: Join (merge) 3.8+galaxy0 + - description: 'Join (merge): gene, pathway, or taxonomy HUMAnN/MetaPhlAn tables + into a single table' + title: Join (merge) 3.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhumann_join_tables%2Fhumann_join_tables%2F3.8%2Bgalaxy0 - - title: Make strain profiles 3.8+galaxy0 + - description: 'Make strain profiles: ' + title: Make strain profiles 3.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhumann_strain_profiler%2Fhumann_strain_profiler%2F3.8%2Bgalaxy0 - - title: Split 3.8+galaxy0 + - description: 'Split: a merged HUMAnN table' + title: Split 3.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhumann_split_table%2Fhumann_split_table%2F3.8%2Bgalaxy0 - - title: Reduce 3.8+galaxy0 + - description: 'Reduce: a joined HUMAnN table' + title: Reduce 3.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhumann_reduce_table%2Fhumann_reduce_table%2F3.8%2Bgalaxy0 - - title: Barplot 3.8+galaxy0 + - description: 'Barplot: stratified HUMAnN features' + title: Barplot 3.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhumann_barplot%2Fhumann_barplot%2F3.8%2Bgalaxy0 - - title: Regroup 3.8+galaxy0 + - description: 'Regroup: HUMAnN table features' + title: Regroup 3.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhumann_regroup_table%2Fhumann_regroup_table%2F3.8%2Bgalaxy0 - - title: Renormalize 3.8+galaxy0 + - description: 'Renormalize: a HUMAnN generated table' + title: Renormalize 3.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhumann_renorm_table%2Fhumann_renorm_table%2F3.8%2Bgalaxy0 - - title: Split a HUMAnN table 3.8+galaxy0 + - description: 'Split a HUMAnN table: into 2 tables (one stratified and one unstratified)' + title: Split a HUMAnN table 3.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhumann_split_stratified_table%2Fhumann_split_stratified_table%2F3.8%2Bgalaxy0 - - title: Unpack pathway abundances 3.8+galaxy0 + - description: 'Unpack pathway abundances: to show the genes for each' + title: Unpack pathway abundances 3.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhumann_unpack_pathways%2Fhumann_unpack_pathways%2F3.8%2Bgalaxy0 - - title: HUMAnN 3.8+galaxy0 + - description: 'HUMAnN: to profile presence/absence and abundance of microbial pathways + and gene families' + title: HUMAnN 3.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhumann%2Fhumann%2F3.8%2Bgalaxy0 - - title: Rename features 3.8+galaxy0 + - description: 'Rename features: of a HUMAnN generated table' + title: Rename features 3.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhumann_rename_table%2Fhumann_rename_table%2F3.8%2Bgalaxy0 - - title: Perform metadata association 3.8+galaxy0 + - description: 'Perform metadata association: on HUMAnN generated table' + title: Perform metadata association 3.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhumann_associate%2Fhumann_associate%2F3.8%2Bgalaxy0 homepage: https://huttenhower.sph.harvard.edu/humann id: humann @@ -8020,17 +8828,24 @@ \ functional profiling answers the question \u201CWhat are the microbes in my\ \ community-of-interest doing (or capable of doing)?\u201D" galaxy: - - title: HUMAnN2 0.11.1.3 + - description: 'HUMAnN2: to profile presence/absence and abundance of microbial + pathways and gene families' + title: HUMAnN2 0.11.1.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhumann2%2Fhumann2%2F0.11.1.3 - - title: Create a genus level gene families file 0.11.1.1 + - description: 'Create a genus level gene families file: ' + title: Create a genus level gene families file 0.11.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhumann2_genefamilies_genus_level%2Fhumann2_genefamilies_genus_level%2F0.11.1.1 - - title: Regroup 0.11.1.1 + - description: 'Regroup: a HUMAnN2 generated table by features' + title: Regroup 0.11.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhumann2_regroup_table%2Fhumann2_regroup_table%2F0.11.1.1 - - title: Renormalize 0.11.1.1 + - description: 'Renormalize: a HUMAnN2 generated table' + title: Renormalize 0.11.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhumann2_renorm_table%2Fhumann2_renorm_table%2F0.11.1.1 - - title: Unpack pathway abundances to show genes included 0.11.1.1 + - description: 'Unpack pathway abundances to show genes included: ' + title: Unpack pathway abundances to show genes included 0.11.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhumann2_unpack_pathways%2Fhumann2_unpack_pathways%2F0.11.1.1 - - title: Join 0.11.1.2 + - description: 'Join: HUMAnN2 generated tables' + title: Join 0.11.1.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhumann2_join_tables%2Fhumann2_join_tables%2F0.11.1.2 homepage: http://huttenhower.sph.harvard.edu/humann2 id: humann2 @@ -8049,7 +8864,8 @@ bunya: '' description: '' galaxy: - - title: HybPiper 2.1.6+galaxy0 + - description: 'HybPiper: Analyse targeted sequence capture data' + title: HybPiper 2.1.6+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhybpiper%2Fhybpiper%2F2.1.6%2Bgalaxy0 homepage: '' id: hybpiper @@ -8067,9 +8883,11 @@ description: Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. galaxy: - - title: HyPhy-aBSREL 2.5.47+galaxy0 + - description: 'HyPhy-aBSREL: adaptive Branch Site Random Effects Likelihood' + title: HyPhy-aBSREL 2.5.47+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhyphy_absrel%2Fhyphy_absrel%2F2.5.47%2Bgalaxy0 - - title: HyPhy-GARD 2.5.47+galaxy0 + - description: 'HyPhy-GARD: Genetic Algorithm for Recombination Detection' + title: HyPhy-GARD 2.5.47+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhyphy_gard%2Fhyphy_gard%2F2.5.47%2Bgalaxy0 homepage: https://hyphy.org id: HyPhy @@ -8173,17 +8991,24 @@ is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence. galaxy: - - title: cmscan 1.1.4+galaxy0 + - description: 'cmscan: Search sequences against collections of covariance models' + title: cmscan 1.1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Finfernal%2Finfernal_cmscan%2F1.1.4%2Bgalaxy0 - - title: cmalign 1.1.4+galaxy0 + - description: 'cmalign: Align sequences to a covariance model against a sequence + database' + title: cmalign 1.1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Finfernal%2Finfernal_cmalign%2F1.1.4%2Bgalaxy0 - - title: cmsearch 1.1.4+galaxy0 + - description: 'cmsearch: Search covariance model(s) against a sequence database' + title: cmsearch 1.1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Finfernal%2Finfernal_cmsearch%2F1.1.4%2Bgalaxy0 - - title: cmpress 1.1.4+galaxy0 + - description: 'cmpress: Prepare a covariance model database for cmscan' + title: cmpress 1.1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Finfernal%2Finfernal_cmpress%2F1.1.4%2Bgalaxy0 - - title: cmbuild 1.1.4+galaxy0 + - description: 'cmbuild: Build covariance models from sequence alignments' + title: cmbuild 1.1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Finfernal%2Finfernal_cmbuild%2F1.1.4%2Bgalaxy0 - - title: cmstat 1.1.4+galaxy0 + - description: 'cmstat: Summary statistics for covariance model' + title: cmstat 1.1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Finfernal%2Finfernal_cmstat%2F1.1.4%2Bgalaxy0 homepage: http://eddylab.org/infernal/ id: infernal @@ -8199,6 +9024,7 @@ resource-documentation: .nan topics: - Sequence sites, features and motifs + - Structural genomics - biocontainers: '' bunya: '' description: '' @@ -8249,7 +9075,8 @@ bunya: '' description: A tool to detect Integron in DNA sequences. galaxy: - - title: Integron Finder 2.0.2+galaxy1 + - description: 'Integron Finder: is a program that detects integrons in DNA sequences' + title: Integron Finder 2.0.2+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fintegron_finder%2Fintegron_finder%2F2.0.2%2Bgalaxy1 homepage: https://github.com/gem-pasteur/Integron_Finder id: integron_finder @@ -8276,7 +9103,8 @@ bunya: '' description: '' galaxy: - - title: InterMine 1.0.0 + - description: 'InterMine: server' + title: InterMine 1.0.0 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=intermine homepage: '' id: intermine @@ -8293,7 +9121,8 @@ bunya: '' description: '' galaxy: - - title: Create InterMine Interchange 0.0.1 + - description: 'Create InterMine Interchange: Dataset' + title: Create InterMine Interchange 0.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fintermine_galaxy_exchange%2Fgalaxy_intermine_exchange%2F0.0.1 homepage: '' id: intermine_galaxy_exchange @@ -8311,7 +9140,8 @@ - 5.55-88.0-foss-2021a description: Scan sequences against the InterPro protein signature databases. galaxy: - - title: InterProScan 5.59-91.0+galaxy3 + - description: 'InterProScan: functional annotation' + title: InterProScan 5.59-91.0+galaxy3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Finterproscan%2Finterproscan%2F5.59-91.0%2Bgalaxy3 homepage: http://www.ebi.ac.uk/Tools/pfa/iprscan/ id: interproscan @@ -8334,7 +9164,8 @@ bunya: '' description: '' galaxy: - - title: Stitch MAF blocks 1.0.1 + - description: 'Stitch MAF blocks: given a set of genomic intervals' + title: Stitch MAF blocks 1.0.1 url: https://usegalaxy.org.au/root?tool_id=Interval_Maf_Merged_Fasta2 homepage: '' id: Interval_Maf_Merged_Fasta2 @@ -8351,7 +9182,8 @@ bunya: '' description: '' galaxy: - - title: Extract Pairwise MAF blocks 1.0.1 + - description: 'Extract Pairwise MAF blocks: given a set of genomic intervals' + title: Extract Pairwise MAF blocks 1.0.1 url: https://usegalaxy.org.au/root?tool_id=Interval2Maf_pairwise1 homepage: '' id: Interval2Maf_pairwise1 @@ -8368,7 +9200,8 @@ bunya: '' description: '' galaxy: - - title: Extract MAF blocks 1.0.1 + - description: 'Extract MAF blocks: given a set of genomic intervals' + title: Extract MAF blocks 1.0.1 url: https://usegalaxy.org.au/root?tool_id=Interval2Maf1 homepage: '' id: Interval2Maf1 @@ -8415,7 +9248,9 @@ It is based on the IQPNNI algorithm with 10-fold speedup together with substantially additional features. galaxy: - - title: IQ-TREE 2.1.2+galaxy2 + - description: 'IQ-TREE: Phylogenomic / evolutionary tree construction from multiple + sequences' + title: IQ-TREE 2.1.2+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fiqtree%2Fiqtree%2F2.1.2%2Bgalaxy2 homepage: http://www.cibiv.at/software/iqtree/ id: iq-tree @@ -8442,7 +9277,8 @@ in a SingleCellExperiment object with visualization of dimensionality reduction results. galaxy: - - title: iSEE 1.0.0 + - description: 'iSEE: ' + title: iSEE 1.0.0 url: https://usegalaxy.org.au/root?tool_id=interactive_tool_isee homepage: http://bioconductor.org/packages/release/bioc/html/iSEE.html id: isee @@ -8465,7 +9301,8 @@ description: Automated identification of insertion sequence elements in prokaryotic genomes. galaxy: - - title: ISEScan 1.7.2.3+galaxy1 + - description: 'ISEScan: Insertion Sequence Elements detection in prokaryotic genomes' + title: ISEScan 1.7.2.3+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fisescan%2Fisescan%2F1.7.2.3%2Bgalaxy1 homepage: https://github.com/xiezhq/ISEScan id: isescan @@ -8508,7 +9345,8 @@ supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. galaxy: - - title: IsoformSwitchAnalyzeR 1.20.0+galaxy5 + - description: 'IsoformSwitchAnalyzeR: statistical identification of isoform switching' + title: IsoformSwitchAnalyzeR 1.20.0+galaxy5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fisoformswitchanalyzer%2Fisoformswitchanalyzer%2F1.20.0%2Bgalaxy5 homepage: http://bioconductor.org/packages/IsoformSwitchAnalyzeR/ id: isoformswitchanalyzer @@ -8553,17 +9391,25 @@ iVar - DataBase of Genomics Variants.' galaxy: - - title: ivar consensus 1.4.2+galaxy0 + - description: 'ivar consensus: Call consensus from aligned BAM file' + title: ivar consensus 1.4.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_consensus%2Fivar_consensus%2F1.4.2%2Bgalaxy0 - - title: ivar filtervariants 1.4.2+galaxy0 + - description: 'ivar filtervariants: Filter variants across replicates or multiple + samples aligned using the same reference' + title: ivar filtervariants 1.4.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_filtervariants%2Fivar_filtervariants%2F1.4.2%2Bgalaxy0 - - title: ivar getmasked 1.2.2+galaxy0 + - description: 'ivar getmasked: Detect primer mismatches and get primer indices + for the amplicon to be masked' + title: ivar getmasked 1.2.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_getmasked%2Fivar_getmasked%2F1.2.2%2Bgalaxy0 - - title: ivar removereads 1.4.2+galaxy0 + - description: 'ivar removereads: Remove reads from trimmed BAM file' + title: ivar removereads 1.4.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_removereads%2Fivar_removereads%2F1.4.2%2Bgalaxy0 - - title: ivar trim 1.4.2+galaxy0 + - 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 - - title: ivar variants 1.4.2+galaxy1 + - description: 'ivar variants: Call variants from aligned BAM file' + title: ivar variants 1.4.2+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_variants%2Fivar_variants%2F1.4.2%2Bgalaxy1 homepage: https://github.com/CGR-UNIMORE/iVar id: ivar @@ -8588,11 +9434,14 @@ of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset. galaxy: - - title: IWTomics Load 1.0.0.0 + - description: 'IWTomics Load: Smooth and Plot' + title: IWTomics Load 1.0.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fiwtomics_loadandplot%2Fiwtomics_loadandplot%2F1.0.0.0 - - title: IWTomics Plot with Threshold 1.0.0.0 + - description: 'IWTomics Plot with Threshold: on Test Scale' + title: IWTomics Plot with Threshold 1.0.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fiwtomics_plotwithscale%2Fiwtomics_plotwithscale%2F1.0.0.0 - - title: IWTomics Test 1.0.0.0 + - description: 'IWTomics Test: and Plot' + title: IWTomics Test 1.0.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fiwtomics_testandplot%2Fiwtomics_testandplot%2F1.0.0.0 homepage: http://bioconductor.org/packages/release/bioc/html/IWTomics.html id: iwtomics @@ -8697,9 +9546,12 @@ for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. galaxy: - - title: JBrowse 1.16.11+galaxy1 + - description: 'JBrowse: genome browser' + title: JBrowse 1.16.11+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fjbrowse%2Fjbrowse%2F1.16.11%2Bgalaxy1 - - title: JBrowse - Data Directory to Standalone 1.16.11+galaxy1 + - description: 'JBrowse - Data Directory to Standalone: upgrades the bare data directory + to a full JBrowse instance' + title: JBrowse - Data Directory to Standalone 1.16.11+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fjbrowse%2Fjbrowse_to_standalone%2F1.16.11%2Bgalaxy1 homepage: https://gmod.org/wiki/JBrowse id: jbrowse @@ -8719,7 +9571,8 @@ bunya: '' description: '' galaxy: - - title: Genome annotation statistics 0.8.4 + - description: 'Genome annotation statistics: ' + title: Genome annotation statistics 0.8.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fjcvi_gff_stats%2Fjcvi_gff_stats%2F0.8.4 homepage: https://github.com/tanghaibao/jcvi id: jcvi @@ -8738,7 +9591,8 @@ - 2.3.0-gcc-11.3.0 (D) description: A command-line algorithm for counting k-mers in DNA sequence. galaxy: - - title: jellyfish 2.3.0+galaxy1 + - description: 'jellyfish: ' + title: jellyfish 2.3.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fjellyfish%2Fjellyfish%2F2.3.0%2Bgalaxy1 homepage: http://www.genome.umd.edu/jellyfish.html id: jellyfish @@ -8760,7 +9614,8 @@ bunya: '' description: '' galaxy: - - title: Join two files 1.0.1 + - description: 'Join two files: on column allowing a small difference' + title: Join two files 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fjoin_files_on_column_fuzzy%2Fjoin_files_on_column_fuzzy%2F1.0.1 homepage: '' id: join_files_on_column_fuzzy @@ -8777,7 +9632,8 @@ bunya: '' description: '' galaxy: - - title: JQ 1.0 + - description: 'JQ: process JSON' + title: JQ 1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fjq%2Fjq%2F1.0 homepage: https://stedolan.github.io/jq/ id: jq @@ -8862,9 +9718,11 @@ It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. galaxy: - - title: Kallisto pseudo 0.48.0+galaxy1 + - description: 'Kallisto pseudo: run pseudoalignment on RNA-Seq transcripts' + title: Kallisto pseudo 0.48.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkallisto_pseudo%2Fkallisto_pseudo%2F0.48.0%2Bgalaxy1 - - title: Kallisto quant 0.48.0+galaxy1 + - description: 'Kallisto quant: quantify abundances of RNA-Seq transcripts' + title: Kallisto quant 0.48.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkallisto_quant%2Fkallisto_quant%2F0.48.0%2Bgalaxy1 homepage: https://pachterlab.github.io/kallisto/about.html id: kallisto @@ -8927,21 +9785,35 @@ de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. galaxy: - - title: 'khmer: Abundance Distribution 3.0.0a3+galaxy2' + - description: 'khmer: Abundance Distribution: Calculate abundance distribution + of k-mers using pre-made k-mer countgraphs' + title: 'khmer: Abundance Distribution 3.0.0a3+galaxy2' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkhmer_abundance_distribution%2Fkhmer_abundance_distribution%2F3.0.0a3%2Bgalaxy2 - - title: 'khmer: Abundance Distribution (all-in-one) 3.0.0a3+galaxy2' + - description: 'khmer: Abundance Distribution (all-in-one): Calculate abundance + distribution of k-mers' + title: 'khmer: Abundance Distribution (all-in-one) 3.0.0a3+galaxy2' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkhmer_abundance_distribution_single%2Fkhmer_abundance_distribution_single%2F3.0.0a3%2Bgalaxy2 - - title: 'khmer: Count Median 3.0.0a3+galaxy2' + - description: 'khmer: Count Median: Count the median/avg k-mer abundance for each + sequence' + title: 'khmer: Count Median 3.0.0a3+galaxy2' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkhmer_count_median%2Fkhmer_count_median%2F3.0.0a3%2Bgalaxy2 - - title: 'khmer: Extract partitions 3.0.0a3+galaxy2' + - description: 'khmer: Extract partitions: Separate sequences that are annotated + with partitions into grouped files' + title: 'khmer: Extract partitions 3.0.0a3+galaxy2' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkhmer_extract_partitions%2Fkhmer_extract_partitions%2F3.0.0a3%2Bgalaxy2 - - title: 'khmer: Filter reads 3.0.0a3+galaxy2' + - description: 'khmer: Filter reads: by minimal k-mer abundance' + title: 'khmer: Filter reads 3.0.0a3+galaxy2' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkhmer_filter_abundance%2Fkhmer_filter_abundance%2F3.0.0a3%2Bgalaxy2 - - title: 'khmer: Filter reads 3.0.0a3+galaxy2' + - description: 'khmer: Filter reads: below k-mer abundance of 50' + title: 'khmer: Filter reads 3.0.0a3+galaxy2' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkhmer_filter_below_abundance_cutoff%2Fkhmer_filter_below_abundance_cutoff%2F3.0.0a3%2Bgalaxy2 - - title: 'khmer: Normalize By Median 3.0.0a3+galaxy2' + - description: 'khmer: Normalize By Median: Filter reads using digital normalization + via k-mer abundances' + title: 'khmer: Normalize By Median 3.0.0a3+galaxy2' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkhmer_normalize_by_median%2Fkhmer_normalize_by_median%2F3.0.0a3%2Bgalaxy2 - - title: 'khmer: Sequence partition all-in-one 3.0.0a3+galaxy2' + - description: 'khmer: Sequence partition all-in-one: Load, partition, and annotate + sequences' + title: 'khmer: Sequence partition all-in-one 3.0.0a3+galaxy2' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkhmer_partition%2Fkhmer_partition%2F3.0.0a3%2Bgalaxy2 homepage: http://khmer.readthedocs.org/en/v2.0/ id: khmer @@ -9029,23 +9901,33 @@ and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. galaxy: - - title: Convert Kraken 1.2+galaxy0 + - description: 'Convert Kraken: data to Galaxy taxonomy representation' + title: Convert Kraken 1.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fkraken2tax%2FKraken2Tax%2F1.2%2Bgalaxy0 - - title: Kraken 1.3.1 + - description: 'Kraken: assign taxonomic labels to sequencing reads' + title: Kraken 1.3.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fkraken%2Fkraken%2F1.3.1 - - title: Kraken-filter 1.3.1 + - description: 'Kraken-filter: filter classification by confidence score' + title: Kraken-filter 1.3.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fkraken_filter%2Fkraken-filter%2F1.3.1 - - title: Kraken-report 1.3.1 + - description: 'Kraken-report: view sample report of a classification' + title: Kraken-report 1.3.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fkraken_report%2Fkraken-report%2F1.3.1 - - title: Kraken-mpa-report 1.2.4 + - description: 'Kraken-mpa-report: view report of classification for multiple samples' + title: Kraken-mpa-report 1.2.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fkraken_report%2Fkraken-mpa-report%2F1.2.4 - - title: Kraken-translate 1.3.1 + - description: 'Kraken-translate: convert taxonomy IDs to names' + title: Kraken-translate 1.3.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fkraken_translate%2Fkraken-translate%2F1.3.1 - - title: 'Krakentools: Convert kraken report file 1.2+galaxy1' + - description: 'Krakentools: Convert kraken report file: to krona text file' + title: 'Krakentools: Convert kraken report file 1.2+galaxy1' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkrakentools_kreport2krona%2Fkrakentools_kreport2krona%2F1.2%2Bgalaxy1 - - title: Kraken-biom 1.2.0+galaxy1 + - description: 'Kraken-biom: Create BIOM-format tables from kraken output' + title: Kraken-biom 1.2.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkraken_biom%2Fkraken_biom%2F1.2.0%2Bgalaxy1 - - title: 'Krakentools: Extract Kraken Reads By ID 1.2+galaxy1' + - description: 'Krakentools: Extract Kraken Reads By ID: Extract reads that were + classified by the Kraken family at specified taxonomic IDs' + title: 'Krakentools: Extract Kraken Reads By ID 1.2+galaxy1' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkrakentools_extract_kraken_reads%2Fkrakentools_extract_kraken_reads%2F1.2%2Bgalaxy1 homepage: https://ccb.jhu.edu/software/kraken/ id: kraken @@ -9072,7 +9954,8 @@ common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. galaxy: - - title: Kraken2 2.1.1+galaxy1 + - 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 homepage: https://ccb.jhu.edu/software/kraken2/ id: kraken2 @@ -9094,13 +9977,20 @@ description: KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files galaxy: - - title: 'Krakentools: Combine multiple Kraken reports 1.2+galaxy1' + - 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: calculates beta diversity (Bray-Curtis dissimilarity) 1.2+galaxy1' + - 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' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkrakentools_beta_diversity%2Fkrakentools_beta_diversity%2F1.2%2Bgalaxy1 - - title: 'Krakentools: Calculates alpha diversity 1.2+galaxy1' + - description: 'Krakentools: Calculates alpha diversity: from the Bracken abundance + estimation file' + title: 'Krakentools: Calculates alpha diversity 1.2+galaxy1' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkrakentools_alpha_diversity%2Fkrakentools_alpha_diversity%2F1.2%2Bgalaxy1 - - title: 'Krakentools: Convert kraken report file 1.2+galaxy1' + - description: 'Krakentools: Convert kraken report file: to MetaPhlAn-style' + title: 'Krakentools: Convert kraken report file 1.2+galaxy1' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkrakentools_kreport2mpa%2Fkrakentools_kreport2mpa%2F1.2%2Bgalaxy1 homepage: https://github.com/jenniferlu717/KrakenTools id: krakentools @@ -9120,9 +10010,11 @@ description: Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). galaxy: - - title: Krona pie chart 2.7.1+galaxy0 + - description: 'Krona pie chart: from taxonomic profile' + title: Krona pie chart 2.7.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fcrs4%2Ftaxonomy_krona_chart%2Ftaxonomy_krona_chart%2F2.7.1%2Bgalaxy0 - - title: Visualize with Krona 1 + - description: 'Visualize with Krona: Visualise any hierarchical data' + title: Visualize with Krona 1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fsaskia-hiltemann%2Fkrona_text%2Fkrona-text%2F1 homepage: https://github.com/marbl/Krona/wiki id: krona @@ -9190,11 +10082,14 @@ description: A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. galaxy: - - title: LASTZ_D 1.04.22+galaxy0 + - description: 'LASTZ_D: : estimate substitution scores matrix' + title: LASTZ_D 1.04.22+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Flastz%2Flastz_d_wrapper%2F1.04.22%2Bgalaxy0 - - title: LASTZ 1.04.22+galaxy0 + - description: 'LASTZ: : align long sequences' + title: LASTZ 1.04.22+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Flastz%2Flastz_wrapper_2%2F1.04.22%2Bgalaxy0 - - title: Lastz paired reads 1.1.1 + - description: 'Lastz paired reads: map short paired reads against reference sequence' + title: Lastz paired reads 1.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Flastz_paired_reads%2Flastz_paired_reads_wrapper%2F1.1.1 homepage: http://www.bx.psu.edu/~rsharris/lastz/ id: lastz @@ -9213,7 +10108,8 @@ bunya: '' description: '' galaxy: - - title: LAV to BED 1.0.0 + - 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 homepage: '' id: lav_to_bed1 @@ -9230,7 +10126,8 @@ bunya: '' description: '' galaxy: - - title: Gene length and GC content 0.1.2 + - description: 'Gene length and GC content: from GTF and FASTA file' + title: Gene length and GC content 0.1.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Flength_and_gc_content%2Flength_and_gc_content%2F0.1.2 homepage: '' id: length_and_gc_content @@ -9257,7 +10154,9 @@ \ tables to facilitate statistical and exploratory analysis of label-free quantitative\ \ datasets" galaxy: - - title: LFQ Analyst 1.2.5+galaxy0 + - description: 'LFQ Analyst: Analyze and Visualize Label-Free Proteomics output + from MaxQuant' + title: LFQ Analyst 1.2.5+galaxy0 url: https://usegalaxy.org.au/root?tool_id=interactive_tool_lfqanalyst homepage: https://bioinformatics.erc.monash.edu/apps/LFQ-Analyst id: LFQ-Analyst @@ -9282,7 +10181,8 @@ bunya: '' description: '' galaxy: - - title: Convert genome coordinates 1.0.6 + - description: 'Convert genome coordinates: between assemblies and genomes' + title: Convert genome coordinates 1.0.6 url: https://usegalaxy.org.au/root?tool_id=liftOver1 homepage: '' id: liftOver1 @@ -9300,7 +10200,8 @@ description: Data analysis, linear models and differential expression for microarray data. galaxy: - - title: limma 3.58.1+galaxy0 + - description: 'limma: Perform differential expression with limma-voom or limma-trend' + title: limma 3.58.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Flimma_voom%2Flimma_voom%2F3.58.1%2Bgalaxy0 homepage: http://bioconductor.org/packages/release/bioc/html/limma.html id: limma @@ -9326,7 +10227,8 @@ assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. galaxy: - - title: LINKS 2.0.1+galaxy+1 + - description: 'LINKS: - scaffold genome assemblies with long reads' + title: LINKS 2.0.1+galaxy+1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Flinks%2Flinks%2F2.0.1%2Bgalaxy%2B1 homepage: https://github.com/bcgsc/LINKS id: links @@ -9382,15 +10284,20 @@ (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering. galaxy: - - title: Add LoFreq alignment quality scores 2.1.5+galaxy1 + - description: 'Add LoFreq alignment quality scores: to aligned read SAM/BAM records' + title: Add LoFreq alignment quality scores 2.1.5+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Flofreq_alnqual%2Flofreq_alnqual%2F2.1.5%2Bgalaxy1 - - title: Call variants 2.1.5+galaxy2 + - description: 'Call variants: with LoFreq' + title: Call variants 2.1.5+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Flofreq_call%2Flofreq_call%2F2.1.5%2Bgalaxy2 - - title: Lofreq filter 2.1.5+galaxy0 + - description: 'Lofreq filter: called variants posteriorly' + title: Lofreq filter 2.1.5+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Flofreq_filter%2Flofreq_filter%2F2.1.5%2Bgalaxy0 - - title: Insert indel qualities 2.1.5+galaxy1 + - description: 'Insert indel qualities: into a BAM file' + title: Insert indel qualities 2.1.5+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Flofreq_indelqual%2Flofreq_indelqual%2F2.1.5%2Bgalaxy1 - - title: Realign reads 2.1.5+galaxy0 + - description: 'Realign reads: with LoFreq viterbi' + title: Realign reads 2.1.5+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Flofreq_viterbi%2Flofreq_viterbi%2F2.1.5%2Bgalaxy0 homepage: https://csb5.github.io/lofreq/ id: lofreq @@ -9559,25 +10466,38 @@ - 2.2.9.1 description: Model-based Analysis of ChIP-seq data. galaxy: - - title: MACS2 bdgdiff 2.2.9.1+galaxy0 + - description: 'MACS2 bdgdiff: Differential peak detection based on paired four + bedgraph files' + title: MACS2 bdgdiff 2.2.9.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmacs2%2Fmacs2_bdgdiff%2F2.2.9.1%2Bgalaxy0 - - title: MACS2 refinepeak 2.2.9.1+galaxy0 + - description: 'MACS2 refinepeak: Refine peak summits and give scores measuring + balance of forward- backward tags (Experimental)' + title: MACS2 refinepeak 2.2.9.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmacs2%2Fmacs2_refinepeak%2F2.2.9.1%2Bgalaxy0 - - title: MACS2 randsample 2.2.9.1+galaxy0 + - description: 'MACS2 randsample: Randomly sample number or percentage of total + reads' + title: MACS2 randsample 2.2.9.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmacs2%2Fmacs2_randsample%2F2.2.9.1%2Bgalaxy0 - - title: MACS2 bdgbroadcall 2.2.9.1+galaxy0 + - description: 'MACS2 bdgbroadcall: Call broad peaks from bedGraph output' + title: MACS2 bdgbroadcall 2.2.9.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmacs2%2Fmacs2_bdgbroadcall%2F2.2.9.1%2Bgalaxy0 - - title: MACS2 filterdup 2.2.9.1+galaxy0 + - description: 'MACS2 filterdup: Remove duplicate reads at the same position' + title: MACS2 filterdup 2.2.9.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmacs2%2Fmacs2_filterdup%2F2.2.9.1%2Bgalaxy0 - - title: MACS2 bdgpeakcall 2.2.9.1+galaxy0 + - description: 'MACS2 bdgpeakcall: Call peaks from bedGraph output' + title: MACS2 bdgpeakcall 2.2.9.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmacs2%2Fmacs2_bdgpeakcall%2F2.2.9.1%2Bgalaxy0 - - title: MACS2 callpeak 2.2.9.1+galaxy0 + - description: 'MACS2 callpeak: Call peaks from alignment results' + title: MACS2 callpeak 2.2.9.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmacs2%2Fmacs2_callpeak%2F2.2.9.1%2Bgalaxy0 - - title: MACS2 bdgcmp 2.2.9.1+galaxy0 + - description: 'MACS2 bdgcmp: Deduct noise by comparing two signal tracks in bedGraph' + title: MACS2 bdgcmp 2.2.9.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmacs2%2Fmacs2_bdgcmp%2F2.2.9.1%2Bgalaxy0 - - title: MACS2 predictd 2.2.9.1+galaxy0 + - description: 'MACS2 predictd: Predict ''d'' or fragment size from alignment results' + title: MACS2 predictd 2.2.9.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmacs2%2Fmacs2_predictd%2F2.2.9.1%2Bgalaxy0 - - title: MACS2.1.2 2.1.2.0 + - description: 'MACS2.1.2: Model-based Analysis of ChIP-Seq: peak calling' + title: MACS2.1.2 2.1.2.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fpjbriggs%2Fmacs21%2Fmacs2_1_peakcalling%2F2.1.2.0 homepage: http://liulab.dfci.harvard.edu/MACS/ id: macs2 @@ -9616,7 +10536,9 @@ bunya: '' description: '' galaxy: - - title: Extract MAF by block number 1.0.1 + - description: 'Extract MAF by block number: given a set of block numbers and a + MAF file' + title: Extract MAF by block number 1.0.1 url: https://usegalaxy.org.au/root?tool_id=maf_by_block_number1 homepage: '' id: maf_by_block_number1 @@ -9633,7 +10555,8 @@ bunya: '' description: '' galaxy: - - title: Filter MAF 1.0.1 + - description: 'Filter MAF: by specified attributes' + title: Filter MAF 1.0.1 url: https://usegalaxy.org.au/root?tool_id=MAF_filter homepage: '' id: MAF_filter @@ -9650,7 +10573,8 @@ bunya: '' description: '' galaxy: - - title: Filter MAF blocks 1.0.1 + - description: 'Filter MAF blocks: by Size' + title: Filter MAF blocks 1.0.1 url: https://usegalaxy.org.au/root?tool_id=maf_limit_size1 homepage: '' id: maf_limit_size1 @@ -9667,7 +10591,8 @@ bunya: '' description: '' galaxy: - - title: Filter MAF blocks 1.0.0 + - description: 'Filter MAF blocks: by Species' + title: Filter MAF blocks 1.0.0 url: https://usegalaxy.org.au/root?tool_id=MAF_Limit_To_Species1 homepage: '' id: MAF_Limit_To_Species1 @@ -9684,7 +10609,8 @@ bunya: '' description: '' galaxy: - - title: Reverse Complement 1.0.1 + - description: 'Reverse Complement: a MAF file' + title: Reverse Complement 1.0.1 url: https://usegalaxy.org.au/root?tool_id=MAF_Reverse_Complement_1 homepage: '' id: MAF_Reverse_Complement_1 @@ -9701,7 +10627,8 @@ bunya: '' description: '' galaxy: - - title: Split MAF blocks 1.0.0 + - description: 'Split MAF blocks: by Species' + title: Split MAF blocks 1.0.0 url: https://usegalaxy.org.au/root?tool_id=MAF_split_blocks_by_species1 homepage: '' id: MAF_split_blocks_by_species1 @@ -9718,7 +10645,8 @@ bunya: '' description: '' galaxy: - - title: MAF Coverage Stats 1.0.1 + - description: 'MAF Coverage Stats: Alignment coverage information' + title: MAF Coverage Stats 1.0.1 url: https://usegalaxy.org.au/root?tool_id=maf_stats1 homepage: '' id: maf_stats1 @@ -9735,7 +10663,8 @@ bunya: '' description: '' galaxy: - - title: Join MAF blocks 1.0.0 + - description: 'Join MAF blocks: by Species' + title: Join MAF blocks 1.0.0 url: https://usegalaxy.org.au/root?tool_id=MAF_Thread_For_Species1 homepage: '' id: MAF_Thread_For_Species1 @@ -9752,7 +10681,8 @@ bunya: '' description: '' galaxy: - - title: MAF to BED 1.0.0 + - description: 'MAF to BED: Converts a MAF formatted file to the BED format' + title: MAF to BED 1.0.0 url: https://usegalaxy.org.au/root?tool_id=MAF_To_BED1 homepage: '' id: MAF_To_BED1 @@ -9769,7 +10699,8 @@ bunya: '' description: '' galaxy: - - title: MAF to FASTA 1.0.1 + - description: 'MAF to FASTA: Converts a MAF formatted file to FASTA format' + title: MAF to FASTA 1.0.1 url: https://usegalaxy.org.au/root?tool_id=MAF_To_Fasta1 homepage: '' id: MAF_To_Fasta1 @@ -9786,7 +10717,8 @@ bunya: '' description: '' galaxy: - - title: MAF to Interval 1.0.0 + - description: 'MAF to Interval: Converts a MAF formatted file to the Interval format' + title: MAF to Interval 1.0.0 url: https://usegalaxy.org.au/root?tool_id=MAF_To_Interval1 homepage: '' id: MAF_To_Interval1 @@ -9805,9 +10737,12 @@ description: MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. galaxy: - - title: MAFFT 7.508+galaxy1 + - description: 'MAFFT: Multiple alignment program for amino acid or nucleotide sequences' + title: MAFFT 7.508+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fmafft%2Frbc_mafft%2F7.508%2Bgalaxy1 - - title: MAFFT add 7.508+galaxy1 + - description: 'MAFFT add: Align a sequence,alignment or fragments to an existing + alignment.' + title: MAFFT add 7.508+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fmafft%2Frbc_mafft_add%2F7.508%2Bgalaxy1 homepage: http://mafft.cbrc.jp/alignment/server/index.html id: mafft @@ -9841,15 +10776,23 @@ description: Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. galaxy: - - title: MAGeCK count 0.5.9.2.4 + - description: 'MAGeCK count: - collect sgRNA read counts from read mapping files' + title: MAGeCK count 0.5.9.2.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmageck_count%2Fmageck_count%2F0.5.9.2.4 - - title: MAGeCK GSEA 0.5.9.2 + - description: 'MAGeCK GSEA: - a fast implementation of Gene Set Enrichment Analysis' + title: MAGeCK GSEA 0.5.9.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmageck_gsea%2Fmageck_gsea%2F0.5.9.2 - - title: MAGeCK mle 0.5.9.2.1 + - description: 'MAGeCK mle: - perform maximum-likelihood estimation of gene essentiality + scores' + title: MAGeCK mle 0.5.9.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmageck_mle%2Fmageck_mle%2F0.5.9.2.1 - - title: MAGeCK pathway 0.5.9.2 + - description: 'MAGeCK pathway: - given a ranked gene list, test whether one pathway + is enriched' + title: MAGeCK pathway 0.5.9.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmageck_pathway%2Fmageck_pathway%2F0.5.9.2 - - title: MAGeCKs test 0.5.9.2.1 + - description: 'MAGeCKs test: - given a table of read counts, perform the sgRNA + and gene ranking' + title: MAGeCKs test 0.5.9.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmageck_test%2Fmageck_test%2F0.5.9.2.1 homepage: https://bitbucket.org/johanneskoester/mageck id: MAGeCK @@ -9874,9 +10817,11 @@ s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently\ \ annotate their genomes and to create genome databases." galaxy: - - title: Maker 2.31.11+galaxy2 + - description: 'Maker: genome annotation pipeline' + title: Maker 2.31.11+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmaker%2Fmaker%2F2.31.11%2Bgalaxy2 - - title: Map annotation ids 2.31.11 + - description: 'Map annotation ids: on a Maker annotation' + title: Map annotation ids 2.31.11 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmaker_map_ids%2Fmaker_map_ids%2F2.31.11 homepage: https://www.yandell-lab.org/software/maker.html id: maker @@ -9908,9 +10853,13 @@ peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions. galaxy: - - title: MALDIquant peak detection 1.22.0.0 + - description: 'MALDIquant peak detection: Peak detection, binning and filtering + for mass-spectrometry imaging data' + title: MALDIquant peak detection 1.22.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmaldi_quant_peak_detection%2Fmaldi_quant_peak_detection%2F1.22.0.0 - - title: MALDIquant preprocessing 1.22.0.0 + - description: 'MALDIquant preprocessing: Preprocessing of mass-spectrometry imaging + data' + title: MALDIquant preprocessing 1.22.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmaldi_quant_preprocessing%2Fmaldi_quant_preprocessing%2F1.22.0.0 homepage: https://cran.r-project.org/package=MALDIquant id: maldi_quant @@ -9955,7 +10904,9 @@ bunya: '' description: '' galaxy: - - title: mash screen 2.3+galaxy3 + - description: 'mash screen: determines how well query sequences are contained within + a pool of sequences' + title: mash screen 2.3+galaxy3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmash%2Fmash_screen%2F2.3%2Bgalaxy3 homepage: '' id: mash_screen @@ -9972,7 +10923,9 @@ bunya: '' description: '' galaxy: - - title: mash sketch 2.3+galaxy0 + - description: 'mash sketch: Create a reduced representation of a sequence or set + of sequences, based on min-hashes' + title: mash sketch 2.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmash_sketch%2Fmash_sketch%2F2.3%2Bgalaxy0 homepage: '' id: mash_sketch @@ -10007,7 +10960,8 @@ bunya: '' description: '' galaxy: - - title: MasterVar to pgSnp 1.0.0 + - description: 'MasterVar to pgSnp: Convert from MasterVar to pgSnp format' + title: MasterVar to pgSnp 1.0.0 url: https://usegalaxy.org.au/root?tool_id=master2pgSnp homepage: '' id: master2pgSnp @@ -10027,7 +10981,9 @@ \ assemble data sets containing only short reads from Illumina sequencing or a\ \ mixture of short reads and long reads (Sanger, 454)." galaxy: - - title: MaSuRCA simple 4.0.6+galaxy0 + - description: 'MaSuRCA simple: The MaSuRCA (Maryland Super Read Cabog Assembler) + genome assembly and analysis toolkit without config' + title: MaSuRCA simple 4.0.6+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdnbenso%2Fmasurca_simple%2Fmasurca_simple%2F4.0.6%2Bgalaxy0 homepage: http://www.genome.umd.edu/masurca.html id: masurca @@ -10049,27 +11005,45 @@ bunya: '' description: Tool to import, process, clean, and compare mass spectrometry data. galaxy: - - title: matchms convert 0.20.0+galaxy0 + - 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 - - title: matchms filtering 0.20.0+galaxy0 + - 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 - - title: matchms fingerprint similarity 0.20.0+galaxy0 + - 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 scores formatter 0.20.0+galaxy0 + - 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 - - title: matchms metadata export 0.20.0+galaxy0 + - 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 metadata match 0.20.0+galaxy0 + - 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 - - title: matchms networking 0.20.0+galaxy0 + - 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 similarity 0.20.0+galaxy0 + - 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 - - title: matchms spectral similarity 0.20.0+galaxy0 + - 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 - - title: matchms split library 0.20.0+galaxy0 + - 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 - - title: recetox-xMSannotator 0.10.0+galaxy0 + - 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 homepage: https://github.com/matchms/matchms id: matchms @@ -10127,7 +11101,8 @@ description: Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. galaxy: - - title: MaxBin2 2.2.7+galaxy2 + - description: 'MaxBin2: clusters metagenomic contigs into bins' + title: MaxBin2 2.2.7+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fmbernt%2Fmaxbin2%2Fmaxbin2%2F2.2.7%2Bgalaxy2 homepage: https://sourceforge.net/projects/maxbin/ id: maxbin @@ -10151,11 +11126,14 @@ description: Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. galaxy: - - title: MaxQuant (using mqpar.xml) 2.0.3.0+galaxy0 + - description: 'MaxQuant (using mqpar.xml): ' + title: MaxQuant (using mqpar.xml) 2.0.3.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmaxquant%2Fmaxquant_mqpar%2F2.0.3.0%2Bgalaxy0 - - title: MaxQuant 2.0.3.0+galaxy0 + - description: 'MaxQuant: ' + title: MaxQuant 2.0.3.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmaxquant%2Fmaxquant%2F2.0.3.0%2Bgalaxy0 - - title: MaxQuant (using mqpar.xml) 1.6.10.43 + - description: 'MaxQuant (using mqpar.xml): ' + title: MaxQuant (using mqpar.xml) 1.6.10.43 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmaxquant_mqpar%2Fmaxquant_mqpar%2F1.6.10.43 homepage: http://www.maxquant.org/ id: maxquant @@ -10238,7 +11216,8 @@ supported coordinate formats for the full list). It can write most of these formats, too, together with atom selections for use in Gromacs, CHARMM, VMD and PyMol galaxy: - - title: Cosine Content 1.0.0+galaxy0 + - description: 'Cosine Content: - measure the cosine content of the PCA projection' + title: Cosine Content 1.0.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fchemteam%2Fmdanalysis_cosine_analysis%2Fmdanalysis_cosine_analysis%2F1.0.0%2Bgalaxy0 homepage: https://www.mdanalysis.org id: mdanalysis @@ -10258,9 +11237,12 @@ bunya: '' description: '' galaxy: - - title: Slice MD trajectories 1.9.7+galaxy0 + - description: 'Slice MD trajectories: using the MDTraj package' + title: Slice MD trajectories 1.9.7+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fchemteam%2Fmd_converter%2Fmd_slicer%2F1.9.7%2Bgalaxy0 - - title: MDTraj file converter 1.9.6+galaxy0 + - description: 'MDTraj file converter: - interconvert between MD trajectory file + formats.' + title: MDTraj file converter 1.9.6+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fchemteam%2Fmd_converter%2Fmd_converter%2F1.9.6%2Bgalaxy0 homepage: '' id: MDTraj @@ -10280,13 +11262,18 @@ nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. galaxy: - - title: medaka variant pipeline 1.4.4+galaxy1 + - description: 'medaka variant pipeline: via neural networks' + title: medaka variant pipeline 1.4.4+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmedaka_variant_pipeline%2Fmedaka_variant_pipeline%2F1.4.4%2Bgalaxy1 - - title: medaka consensus tool 1.7.2+galaxy0 + - description: 'medaka consensus tool: Assembly polishing via neural networks' + title: medaka consensus tool 1.7.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmedaka_consensus%2Fmedaka_consensus%2F1.7.2%2Bgalaxy0 - - title: medaka consensus pipeline 1.7.2+galaxy1 + - description: 'medaka consensus pipeline: Assembly polishing via neural networks' + title: medaka consensus pipeline 1.7.2+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmedaka_consensus_pipeline%2Fmedaka_consensus_pipeline%2F1.7.2%2Bgalaxy1 - - title: medaka variant tool 1.7.2+galaxy1 + - description: 'medaka variant tool: decodes variant calls from medaka consensus + output' + title: medaka variant tool 1.7.2+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmedaka_variant%2Fmedaka_variant%2F1.7.2%2Bgalaxy1 homepage: https://github.com/nanoporetech/medaka id: medaka @@ -10309,7 +11296,8 @@ such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. galaxy: - - title: MEGAHIT 1.2.9+galaxy1 + - 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 homepage: https://github.com/voutcn/megahit id: megahit @@ -10333,7 +11321,8 @@ bunya: '' description: '' galaxy: - - title: Merge Columns 1.0.3 + - description: 'Merge Columns: together' + title: Merge Columns 1.0.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fmerge_cols%2FmergeCols1%2F1.0.3 homepage: '' id: merge_cols @@ -10375,9 +11364,11 @@ Merqury provides a set of tools for this purpose.' galaxy: - - title: Merqury 1.3+galaxy3 + - description: 'Merqury: evaluate the assembly quality' + title: Merqury 1.3+galaxy3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmerqury%2Fmerqury%2F1.3%2Bgalaxy3 - - title: Merqury histogram plot 1.3+galaxy3 + - description: 'Merqury histogram plot: evaluate the assembly quality' + title: Merqury histogram plot 1.3+galaxy3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmerqury%2Fmerquryplot%2F1.3%2Bgalaxy3 homepage: https://github.com/marbl/merqury id: merqury @@ -10401,7 +11392,8 @@ originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. galaxy: - - title: Meryl 1.3+galaxy6 + - description: 'Meryl: a genomic k-mer counter and sequence utility' + title: Meryl 1.3+galaxy6 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmeryl%2Fmeryl%2F1.3%2Bgalaxy6 homepage: https://github.com/marbl/meryl id: meryl @@ -10428,7 +11420,8 @@ composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning galaxy: - - title: MetaBAT2 2.15+galaxy3 + - description: 'MetaBAT2: metagenome binning' + title: MetaBAT2 2.15+galaxy3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmetabat2%2Fmetabat2%2F2.15%2Bgalaxy3 homepage: https://bitbucket.org/berkeleylab/metabat id: metabat @@ -10454,7 +11447,8 @@ bunya: '' description: '' galaxy: - - title: metabolicMine 1.0.0 + - description: 'metabolicMine: server' + title: metabolicMine 1.0.0 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=metabolicmine homepage: '' id: metabolicmine @@ -10502,23 +11496,36 @@ This history is empty. You can load your own data or get data from an external source' galaxy: - - title: PEAR Statistics 1.0.0 + - description: 'PEAR Statistics: Generate paired-end reads overlap Statistic from + PEAR log file' + title: PEAR Statistics 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fqfabrepo%2Fmetadegalaxy_pear_stats%2FpearStat%2F1.0.0 - - title: Phyloseq Abundance plot 1.22.3.3 + - description: 'Phyloseq Abundance plot: Phyloseq Abundance Plot with the factors + of choice' + title: Phyloseq Abundance plot 1.22.3.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fqfabrepo%2Fmetadegalaxy_phyloseq_abundance_factor%2Fphyloseq_abundance%2F1.22.3.3 - - title: Phyloseq Abundance Taxonomy 1.22.3.3 + - description: 'Phyloseq Abundance Taxonomy: Phyloseq Abundance Plot on Taxonomy + level' + title: Phyloseq Abundance Taxonomy 1.22.3.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fqfabrepo%2Fmetadegalaxy_phyloseq_abundance_taxonomy%2Fphyloseq_taxonomy%2F1.22.3.3 - - title: Phyloseq DESeq2 1.22.3 + - description: 'Phyloseq DESeq2: Perform differential expression analysis of BIOM + file' + title: Phyloseq DESeq2 1.22.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fqfabrepo%2Fmetadegalaxy_phyloseq_deseq2%2Fphyloseq_DESeq2%2F1.22.3 - - title: Phyloseq Network Plot 1.24.2 + - description: 'Phyloseq Network Plot: Phyloseq Network Plot' + title: Phyloseq Network Plot 1.24.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fqfabrepo%2Fmetadegalaxy_phyloseq_net%2Fphyloseq_net%2F1.24.2 - - title: Phyloseq Richness 1.22.3.2 + - description: 'Phyloseq Richness: Phyloseq Richness Plot' + title: Phyloseq Richness 1.22.3.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fqfabrepo%2Fmetadegalaxy_phyloseq_richness%2Fphyloseq_richness%2F1.22.3.2 - - title: reheader 1.0.0 + - description: 'reheader: Rename sequence header in FASTQ file' + title: reheader 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fqfabrepo%2Fmetadegalaxy_reheader%2Frename%2F1.0.0 - - title: Symmetric Plot 1.0.1 + - description: 'Symmetric Plot: Symmetric Plot' + title: Symmetric Plot 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fqfabrepo%2Fmetadegalaxy_symmetric_plot%2FsymmetricPlot%2F1.0.1 - - title: OTUTable 1.0.0 + - description: 'OTUTable: Convert UCLUST format from Vsearch to OTU Table' + title: OTUTable 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fqfabrepo%2Fmetadegalaxy_uc2otutable%2Fuclust2otutable%2F1.0.0 homepage: http://203.101.224.202/galaxy/ id: MetaDEGalaxy @@ -10587,13 +11594,17 @@ description: Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. galaxy: - - title: MetaPhlAn 4.0.6+galaxy2 + - description: 'MetaPhlAn: to profile the composition of microbial communities' + title: MetaPhlAn 4.0.6+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmetaphlan%2Fmetaphlan%2F4.0.6%2Bgalaxy2 - - title: Merge 4.0.6+galaxy2 + - description: 'Merge: MetaPhlAn abundance tables' + title: Merge 4.0.6+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmerge_metaphlan_tables%2Fmerge_metaphlan_tables%2F4.0.6%2Bgalaxy2 - - title: MetaPhlAn2 2.6.0.1 + - 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 - - title: Format MetaPhlAn2 2.6.0.0 + - description: 'Format MetaPhlAn2: output for Krona' + title: Format MetaPhlAn2 2.6.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmetaphlan2krona%2Fmetaphlan2krona%2F2.6.0.0 homepage: http://huttenhower.sph.harvard.edu/metaphlan id: metaphlan @@ -10619,17 +11630,26 @@ analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. galaxy: - - title: 'metaQuantome: database 2.0.2+galaxy0' + - description: 'metaQuantome: database: download the GO, EC, and NCBI databases' + title: 'metaQuantome: database 2.0.2+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmetaquantome_db%2Fmetaquantome_db%2F2.0.2%2Bgalaxy0 - - title: 'metaQuantome: expand 2.0.2+galaxy0' + - description: 'metaQuantome: expand: a set of functional or taxonomy annotations' + title: 'metaQuantome: expand 2.0.2+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmetaquantome_expand%2Fmetaquantome_expand%2F2.0.2%2Bgalaxy0 - - title: 'metaQuantome: filter 2.0.2+galaxy0' + - description: 'metaQuantome: filter: for quality, redundancy, and sample coverage' + title: 'metaQuantome: filter 2.0.2+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmetaquantome_filter%2Fmetaquantome_filter%2F2.0.2%2Bgalaxy0 - - title: 'metaQuantome: create samples file 2.0.2+galaxy0' + - description: 'metaQuantome: create samples file: by specifying the experiment''s + groups and associated column names' + title: 'metaQuantome: create samples file 2.0.2+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmetaquantome_sample%2Fmetaquantome_sample%2F2.0.2%2Bgalaxy0 - - title: 'metaQuantome: stat 2.0.2+galaxy0' + - description: 'metaQuantome: stat: differential analysis of functional expression + and taxonomic abundance' + title: 'metaQuantome: stat 2.0.2+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmetaquantome_stat%2Fmetaquantome_stat%2F2.0.2%2Bgalaxy0 - - title: 'metaQuantome: visualize 2.0.2+galaxy0' + - description: 'metaQuantome: visualize: taxonomic analysis, functional analysis, + and function-taxonomy analysis results' + title: 'metaQuantome: visualize 2.0.2+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmetaquantome_viz%2Fmetaquantome_viz%2F2.0.2%2Bgalaxy0 homepage: https://github.com/galaxyproteomics/metaquantome id: metaQuantome @@ -10656,7 +11676,8 @@ bunya: '' description: Genome assembler for metagenomics datasets. galaxy: - - title: metaSPAdes 3.15.5+galaxy1 + - description: 'metaSPAdes: metagenome assembler' + title: metaSPAdes 3.15.5+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fmetaspades%2Fmetaspades%2F3.15.5%2Bgalaxy1 homepage: http://cab.spbu.ru/software/spades/ id: metaspades @@ -10686,7 +11707,8 @@ quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.' galaxy: - - title: MetaWRAP 1.3.0+galaxy0 + - description: 'MetaWRAP: metagenome binning pipeline' + title: MetaWRAP 1.3.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxy-australia%2Fmetawrapmg_binning%2Fmetawrapmg_binning%2F1.3.0%2Bgalaxy0 homepage: https://github.com/bxlab/metaWRAP id: metawrap @@ -10710,7 +11732,8 @@ bunya: '' description: A (mostly) universal methylation extractor for BS-seq experiments. galaxy: - - title: MethylDackel 0.5.2+galaxy0 + - description: 'MethylDackel: A tool for processing bisulfite sequencing alignments' + title: MethylDackel 0.5.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fpileometh%2Fpileometh%2F0.5.2%2Bgalaxy0 homepage: https://github.com/dpryan79/MethylDackel id: MethylDackel @@ -10728,7 +11751,9 @@ bunya: '' description: '' galaxy: - - title: metilene 0.2.6.1 + - description: 'metilene: calling differentially methylated regions from bisulfite + sequencing data' + title: metilene 0.2.6.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fmetilene%2Fmetilene%2F0.2.6.1 homepage: '' id: metilene @@ -10792,33 +11817,61 @@ bunya: '' description: '' galaxy: - - title: MiModD Read Alignment 0.1.9 + - description: 'MiModD Read Alignment: maps sequence reads to a reference genome + using SNAP' + title: MiModD Read Alignment 0.1.9 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fwolma%2Fmimodd_aln%2Fmimodd_align%2F0.1.9 - - title: MiModD Variant Calling 0.1.9 + - description: 'MiModD Variant Calling: generates a BCF file of position-specific + variant likelihoods and coverage information based on a reference sequence and + reads aligned against it' + title: MiModD Variant Calling 0.1.9 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fwolma%2Fmimodd_main%2Fmimodd_varcall%2F0.1.9 - - title: MiModD Coverage Statistics 0.1.9 + - description: 'MiModD Coverage Statistics: calculates coverage statistics for a + BCF file as generated by the MiModd Variant Calling tool' + title: MiModD Coverage Statistics 0.1.9 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fwolma%2Fmimodd_main%2Fmimodd_covstats%2F0.1.9 - - title: MiModD Run Annotation 0.1.9 + - description: 'MiModD Run Annotation: writes run metadata in SAM format for attaching + it to sequenced reads data' + title: MiModD Run Annotation 0.1.9 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fwolma%2Fmimodd_main%2Fmimodd_header%2F0.1.9 - - title: MiModD File Information 0.1.9 + - description: 'MiModD File Information: provides summary reports for supported + sequence data formats.' + title: MiModD File Information 0.1.9 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fwolma%2Fmimodd_main%2Fmimodd_info%2F0.1.9 - - title: MiModD Reheader 0.1.9 + - description: 'MiModD Reheader: takes a BAM file and generates a copy with the + original header (if any) replaced or modified by that found in a template SAM + file' + title: MiModD Reheader 0.1.9 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fwolma%2Fmimodd_main%2Fmimodd_reheader%2F0.1.9 - - title: MiModD NacreousMap 0.1.9 + - description: 'MiModD NacreousMap: maps phenotypically selected variants by multi-variant + linkage analysis' + title: MiModD NacreousMap 0.1.9 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fwolma%2Fmimodd_main%2Fmimodd_map%2F0.1.9 - - title: MiModD Report Variants 0.1.9 + - description: 'MiModD Report Variants: in a human-friendly format that simplifies + data exploration' + title: MiModD Report Variants 0.1.9 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fwolma%2Fmimodd_main%2Fmimodd_varreport%2F0.1.9 - - title: MiModD Deletion Calling (for PE data) 0.1.9 + - description: 'MiModD Deletion Calling (for PE data): predicts deletions in one + or more aligned paired-end read samples based on coverage of the reference genome + and on insert sizes' + title: MiModD Deletion Calling (for PE data) 0.1.9 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fwolma%2Fmimodd_main%2Fmimodd_delcall%2F0.1.9 - - title: MiModD Extract Variant Sites 0.1.9 + - description: 'MiModD Extract Variant Sites: from a BCF file' + title: MiModD Extract Variant Sites 0.1.9 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fwolma%2Fmimodd_main%2Fmimodd_varextract%2F0.1.9 - - title: MiModD Rebase Sites 0.1.9 + - description: 'MiModD Rebase Sites: from a VCF file' + title: MiModD Rebase Sites 0.1.9 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fwolma%2Fmimodd_main%2Fmimodd_rebase%2F0.1.9 - - title: MiModD Convert 0.1.9 + - description: 'MiModD Convert: converts sequence data into different formats' + title: MiModD Convert 0.1.9 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fwolma%2Fmimodd_main%2Fmimodd_convert%2F0.1.9 - - title: MiModD Sort 0.1.9 + - description: 'MiModD Sort: takes a SAM/BAM dataset and generates a coordinate/name-sorted + copy' + title: MiModD Sort 0.1.9 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fwolma%2Fmimodd_main%2Fmimodd_sort%2F0.1.9 - - title: MiModD VCF Filter 0.1.9 + - description: 'MiModD VCF Filter: extracts lines from a vcf variant file based + on field-specific filters' + title: MiModD VCF Filter 0.1.9 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fwolma%2Fmimodd_main%2Fmimodd_vcf_filter%2F0.1.9 homepage: https://mimodd.readthedocs.io/en/latest/nacreousmap.html id: mimodd @@ -10836,7 +11889,8 @@ description: Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. galaxy: - - title: Minia 3.2.6 + - description: 'Minia: Short-read assembler based on a de Bruijn graph' + title: Minia 3.2.6 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fminia%2Fminia%2F3.2.6 homepage: http://minia.genouest.org/ id: minia @@ -10859,7 +11913,8 @@ It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. galaxy: - - title: miniasm 0.3_r179+galaxy1 + - description: 'miniasm: Ultrafast de novo assembly for long noisy reads' + title: miniasm 0.3_r179+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fminiasm%2Fminiasm%2F0.3_r179%2Bgalaxy1 homepage: https://github.com/lh3/miniasm id: miniasm @@ -10917,7 +11972,9 @@ - 2.24-gcccore-11.3.0 description: Pairwise aligner for genomic and spliced nucleotide sequences galaxy: - - title: Map with minimap2 2.26+galaxy0 + - 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 homepage: https://github.com/lh3/minimap2 id: minimap2 @@ -10981,7 +12038,8 @@ bunya: '' description: '' galaxy: - - title: miRcounts 1.4.0 + - description: 'miRcounts: Counts miRNA alignments from small RNA sequence data' + title: miRcounts 1.4.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fartbio%2Fmircounts%2Fmircounts%2F1.4.0 homepage: https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts id: mircounts @@ -10999,11 +12057,15 @@ description: miRDeep2 discovers active known or novel miRNAs from deep sequencing data. galaxy: - - title: MiRDeep2 2.0.1.2+galaxy0 + - description: 'MiRDeep2: identification of novel and known miRNAs' + title: MiRDeep2 2.0.1.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fmirdeep2%2Frbc_mirdeep2%2F2.0.1.2%2Bgalaxy0 - - title: MiRDeep2 Mapper 2.0.0.8.1 + - description: 'MiRDeep2 Mapper: process and map reads to a reference genome' + title: MiRDeep2 Mapper 2.0.0.8.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fmirdeep2_mapper%2Frbc_mirdeep2_mapper%2F2.0.0.8.1 - - title: MiRDeep2 Quantifier 2.0.0 + - description: 'MiRDeep2 Quantifier: fast quantitation of reads mapping to known + miRBase precursors' + title: MiRDeep2 Quantifier 2.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fmirdeep2_quantifier%2Frbc_mirdeep2_quantifier%2F2.0.0 homepage: https://github.com/rajewsky-lab/mirdeep2 id: mirdeep2 @@ -11043,7 +12105,8 @@ bunya: '' description: '' galaxy: - - title: MITObim 1.9.1 + - description: 'MITObim: mitochondrial baiting and iterative mapping' + title: MITObim 1.9.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmitobim%2Fmitobim%2F1.9.1 homepage: '' id: mitobim @@ -11060,7 +12123,8 @@ bunya: '' description: Find, circularise and annotate mitogenome from PacBio assemblies galaxy: - - title: MitoHiFi 3+galaxy0 + - description: 'MitoHiFi: assembly mitogenomes from Pacbio HiFi reads' + title: MitoHiFi 3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fmitohifi%2Fmitohifi%2F3%2Bgalaxy0 homepage: https://github.com/marcelauliano/MitoHiFi id: mitohifi @@ -11083,7 +12147,8 @@ bunya: '' description: De novo metazoan mitochondrial genome annotation. galaxy: - - title: MITOS2 2.1.7+galaxy1 + - description: 'MITOS2: de-novo annotation of metazoan mitochondrial genomes' + title: MITOS2 2.1.7+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmitos2%2Fmitos2%2F2.1.7%2Bgalaxy1 homepage: https://mitos.bioinf.uni-leipzig.de/index.py id: mitos2 @@ -11106,9 +12171,11 @@ description: Multi Locus Sequence Typing from an assembled genome or from a set of reads. galaxy: - - title: MLST 2.22.0 + - description: 'MLST: Scans genomes against PubMLST schemes' + title: MLST 2.22.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmlst%2Fmlst%2F2.22.0 - - title: MLST List 2.22.0 + - description: 'MLST List: Lists available schemes for the MLST tool' + title: MLST List 2.22.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmlst%2Fmlst_list%2F2.22.0 homepage: http://cge.cbs.dtu.dk/services/MLST/ id: mlst @@ -11185,9 +12252,11 @@ to different genetic backgrounds. The MOB-suite is designed to be a modular set of tools for the typing and reconstruction of plasmid sequences from WGS assemblies.' galaxy: - - title: MOB-Recon 3.0.3+galaxy0 + - description: 'MOB-Recon: Type contigs and extract plasmid sequences' + title: MOB-Recon 3.0.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fmob_suite%2Fmob_recon%2F3.0.3%2Bgalaxy0 - - title: MOB-Typer 3.0.3+galaxy0 + - description: 'MOB-Typer: Get the plasmid type and mobility given its sequence' + title: MOB-Typer 3.0.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fmob_suite%2Fmob_typer%2F3.0.3%2Bgalaxy0 homepage: https://github.com/phac-nml/mob-suite id: mob-suite @@ -11212,7 +12281,8 @@ bunya: '' description: '' galaxy: - - title: modENCODE fly 1.0.1 + - description: 'modENCODE fly: server' + title: modENCODE fly 1.0.1 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=modENCODEfly homepage: '' id: modENCODEfly @@ -11229,7 +12299,8 @@ bunya: '' description: '' galaxy: - - title: modENCODE worm 1.0.1 + - description: 'modENCODE worm: server' + title: modENCODE worm 1.0.1 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=modENCODEworm homepage: '' id: modENCODEworm @@ -11246,7 +12317,8 @@ bunya: '' description: '' galaxy: - - title: modENCODE modMine 1.0.0 + - description: 'modENCODE modMine: server' + title: modENCODE modMine 1.0.0 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=modmine homepage: '' id: modmine @@ -11263,7 +12335,8 @@ bunya: '' description: A modest Feature Finder to extract features in MS1 Data. galaxy: - - title: moFF 2.0.3.0 + - description: 'moFF: extracts MS1 intensities from spectrum files' + title: moFF 2.0.3.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fproteomics_moff%2Fproteomics_moff%2F2.0.3.0 homepage: https://github.com/compomics/moFF id: moff @@ -11301,7 +12374,9 @@ description: A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. galaxy: - - title: Morpheus 2.255.0 + - 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 homepage: https://cwenger.github.io/Morpheus/ id: morpheus @@ -11323,267 +12398,423 @@ description: Open-source, platform-independent, community-supported software for describing and comparing microbial communities galaxy: - - title: Align.check 1.39.5.0 + - description: 'Align.check: Calculate the number of potentially misaligned bases' + title: Align.check 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_align_check%2Fmothur_align_check%2F1.39.5.0 - - title: Align.seqs 1.39.5.0 + - description: 'Align.seqs: Align sequences to a template alignment' + title: Align.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_align_seqs%2Fmothur_align_seqs%2F1.39.5.0 - - title: Amova 1.39.5.0 + - description: 'Amova: Analysis of molecular variance' + title: Amova 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_amova%2Fmothur_amova%2F1.39.5.0 - - title: Anosim 1.39.5.0 + - description: 'Anosim: Non-parametric multivariate analysis of changes in community + structure' + title: Anosim 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_anosim%2Fmothur_anosim%2F1.39.5.0 - - title: Bin.seqs 1.39.5.0 + - description: 'Bin.seqs: Order Sequences by OTU' + title: Bin.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_bin_seqs%2Fmothur_bin_seqs%2F1.39.5.0 - - title: Biom.info 1.39.5.0 + - description: 'Biom.info: create shared and taxonomy files from biom' + title: Biom.info 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_biom_info%2Fmothur_biom_info%2F1.39.5.0 - - title: Chimera.bellerophon 1.39.5.0 + - description: 'Chimera.bellerophon: Find putative chimeras using bellerophon' + title: Chimera.bellerophon 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_chimera_bellerophon%2Fmothur_chimera_bellerophon%2F1.39.5.0 - - title: Chimera.ccode 1.39.5.0 + - description: 'Chimera.ccode: Find putative chimeras using ccode' + title: Chimera.ccode 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_chimera_ccode%2Fmothur_chimera_ccode%2F1.39.5.0 - - title: Chimera.check 1.39.5.0 + - description: 'Chimera.check: Find putative chimeras using chimeraCheck' + title: Chimera.check 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_chimera_check%2Fmothur_chimera_check%2F1.39.5.0 - - title: Chimera.perseus 1.39.5.0 + - description: 'Chimera.perseus: Find putative chimeras using chimeraCheck' + title: Chimera.perseus 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_chimera_perseus%2Fmothur_chimera_perseus%2F1.39.5.0 - - title: Chimera.pintail 1.39.5.0 + - description: 'Chimera.pintail: Find putative chimeras using pintail' + title: Chimera.pintail 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_chimera_pintail%2Fmothur_chimera_pintail%2F1.39.5.0 - - title: Chimera.slayer 1.39.5.0 + - description: 'Chimera.slayer: Find putative chimeras using slayer' + title: Chimera.slayer 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_chimera_slayer%2Fmothur_chimera_slayer%2F1.39.5.0 - - title: Chimera.uchime 1.39.5.0 + - description: 'Chimera.uchime: Find putative chimeras using uchime' + title: Chimera.uchime 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_chimera_uchime%2Fmothur_chimera_uchime%2F1.39.5.0 - - title: Chimera.vsearch 1.39.5.2 + - description: 'Chimera.vsearch: find potential chimeric sequences using vsearch' + title: Chimera.vsearch 1.39.5.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_chimera_vsearch%2Fmothur_chimera_vsearch%2F1.39.5.2 - - title: Chop.seqs 1.39.5.0 + - description: 'Chop.seqs: Trim sequences to a specified length' + title: Chop.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_chop_seqs%2Fmothur_chop_seqs%2F1.39.5.0 - - title: Classify.otu 1.39.5.0 + - description: 'Classify.otu: Assign sequences to taxonomy' + title: Classify.otu 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_classify_otu%2Fmothur_classify_otu%2F1.39.5.0 - - title: Classify.rf 1.36.1.0 + - description: 'Classify.rf: description' + title: Classify.rf 1.36.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_classify_rf%2Fmothur_classify_rf%2F1.36.1.0 - - title: Classify.seqs 1.39.5.0 + - description: 'Classify.seqs: Assign sequences to taxonomy' + title: Classify.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_classify_seqs%2Fmothur_classify_seqs%2F1.39.5.0 - - title: Classify.tree 1.39.5.0 + - description: 'Classify.tree: Get a consensus taxonomy for each node on a tree' + title: Classify.tree 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_classify_tree%2Fmothur_classify_tree%2F1.39.5.0 - - title: Clearcut 1.39.5.0 + - description: 'Clearcut: Generate a tree using relaxed neighbor joining' + title: Clearcut 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_clearcut%2Fmothur_clearcut%2F1.39.5.0 - - title: Cluster 1.39.5.0 + - description: 'Cluster: Assign sequences to OTUs (Operational Taxonomic Unit)' + title: Cluster 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_cluster%2Fmothur_cluster%2F1.39.5.0 - - title: Cluster.classic 1.39.5.0 + - description: 'Cluster.classic: Assign sequences to OTUs (Dotur implementation)' + title: Cluster.classic 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_cluster_classic%2Fmothur_cluster_classic%2F1.39.5.0 - - title: Cluster.fragments 1.39.5.0 + - description: 'Cluster.fragments: Group sequences that are part of a larger sequence' + title: Cluster.fragments 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_cluster_fragments%2Fmothur_cluster_fragments%2F1.39.5.0 - - title: Cluster.split 1.39.5.0 + - description: 'Cluster.split: Assign sequences to OTUs and split large matrices' + title: Cluster.split 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_cluster_split%2Fmothur_cluster_split%2F1.39.5.0 - - title: Collect.shared 1.39.5.0 + - description: 'Collect.shared: Generate collector''s curves for calculators on + OTUs' + title: Collect.shared 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_collect_shared%2Fmothur_collect_shared%2F1.39.5.0 - - title: Collect.single 1.39.5.0 + - description: 'Collect.single: Generate collector''s curves for OTUs' + title: Collect.single 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_collect_single%2Fmothur_collect_single%2F1.39.5.0 - - title: Consensus.seqs 1.39.5.0 + - description: 'Consensus.seqs: Find a consensus sequence for each OTU or phylotype' + title: Consensus.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_consensus_seqs%2Fmothur_consensus_seqs%2F1.39.5.0 - - title: Cooccurrence 1.39.5.0 + - description: 'Cooccurrence: tests whether presence-absence patterns differ from + chance' + title: Cooccurrence 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_cooccurrence%2Fmothur_cooccurrence%2F1.39.5.0 - - title: Corr.axes 1.39.5.0 + - description: 'Corr.axes: correlation of data to axes' + title: Corr.axes 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_corr_axes%2Fmothur_corr_axes%2F1.39.5.0 - - title: Count.groups 1.39.5.0 + - description: 'Count.groups: counts the number of sequences represented by a specific + group or set of groups' + title: Count.groups 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_count_groups%2Fmothur_count_groups%2F1.39.5.0 - - title: Count.seqs 1.39.5.0 + - description: 'Count.seqs: (aka make.table) counts the number of sequences represented + by the representative' + title: Count.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_count_seqs%2Fmothur_count_seqs%2F1.39.5.0 - - title: Create.database 1.39.5.0 + - description: 'Create.database: creates a database file from a list, repnames, + repfasta and contaxonomy file' + title: Create.database 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_create_database%2Fmothur_create_database%2F1.39.5.0 - - title: Degap.seqs 1.39.5.0 + - description: 'Degap.seqs: Remove gap characters from sequences' + title: Degap.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_degap_seqs%2Fmothur_degap_seqs%2F1.39.5.0 - - title: Deunique.seqs 1.39.5.0 + - description: 'Deunique.seqs: Return all sequences' + title: Deunique.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_deunique_seqs%2Fmothur_deunique_seqs%2F1.39.5.0 - - title: Deunique.tree 1.39.5.0 + - description: 'Deunique.tree: Reinsert the redundant sequence identiers back into + a unique tree.' + title: Deunique.tree 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_deunique_tree%2Fmothur_deunique_tree%2F1.39.5.0 - - title: Dist.seqs 1.39.5.0 + - description: 'Dist.seqs: calculate uncorrected pairwise distances between aligned + sequences' + title: Dist.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_dist_seqs%2Fmothur_dist_seqs%2F1.39.5.0 - - title: Dist.shared 1.39.5.0 + - description: 'Dist.shared: Generate a phylip-formatted dissimilarity distance + matrix among multiple groups' + title: Dist.shared 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_dist_shared%2Fmothur_dist_shared%2F1.39.5.0 - - title: Fastq.info 1.39.5.0 + - description: 'Fastq.info: Convert fastq to fasta and quality' + title: Fastq.info 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_fastq_info%2Fmothur_fastq_info%2F1.39.5.0 - - title: Filter.seqs 1.39.5.0 + - description: 'Filter.seqs: removes columns from alignments' + title: Filter.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_filter_seqs%2Fmothur_filter_seqs%2F1.39.5.0 - - title: Filter.shared 1.39.5.0 + - description: 'Filter.shared: remove OTUs based on various critieria' + title: Filter.shared 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_filter_shared%2Fmothur_filter_shared%2F1.39.5.0 - - title: Get.communitytype 1.39.5.0 + - description: 'Get.communitytype: description' + title: Get.communitytype 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_get_communitytype%2Fmothur_get_communitytype%2F1.39.5.0 - - title: Get.coremicrobiome 1.39.5.0 + - description: 'Get.coremicrobiome: fraction of OTUs for samples or abundances' + title: Get.coremicrobiome 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_get_coremicrobiome%2Fmothur_get_coremicrobiome%2F1.39.5.0 - - title: Get.dists 1.39.5.0 + - description: 'Get.dists: selects distances from a phylip or column file' + title: Get.dists 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_get_dists%2Fmothur_get_dists%2F1.39.5.0 - - title: Get.group 1.39.5.0 + - description: 'Get.group: group names from shared or from list and group' + title: Get.group 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_get_group%2Fmothur_get_group%2F1.39.5.0 - - title: Get.groups 1.39.5.0 + - description: 'Get.groups: Select groups' + title: Get.groups 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_get_groups%2Fmothur_get_groups%2F1.39.5.0 - - title: Get.label 1.39.5.0 + - description: 'Get.label: label names from list, sabund, or rabund file' + title: Get.label 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_get_label%2Fmothur_get_label%2F1.39.5.0 - - title: Get.lineage 1.39.5.0 + - description: 'Get.lineage: Picks by taxon' + title: Get.lineage 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_get_lineage%2Fmothur_get_lineage%2F1.39.5.0 - - title: Get.mimarkspackage 1.39.5.0 + - description: 'Get.mimarkspackage: creates a mimarks package form with your groups' + title: Get.mimarkspackage 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_get_mimarkspackage%2Fmothur_get_mimarkspackage%2F1.39.5.0 - - title: Get.otulabels 1.39.5.0 + - description: 'Get.otulabels: Selects OTU labels' + title: Get.otulabels 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_get_otulabels%2Fmothur_get_otulabels%2F1.39.5.0 - - title: Get.otulist 1.39.5.0 + - description: 'Get.otulist: Get otus for each distance in a otu list' + title: Get.otulist 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_get_otulist%2Fmothur_get_otulist%2F1.39.5.0 - - title: Get.oturep 1.39.5.0 + - description: 'Get.oturep: Generate a fasta with a representative sequence for + each OTU' + title: Get.oturep 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_get_oturep%2Fmothur_get_oturep%2F1.39.5.0 - - title: Get.otus 1.39.5.0 + - description: 'Get.otus: Get otus containing sequences from specified groups' + title: Get.otus 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_get_otus%2Fmothur_get_otus%2F1.39.5.0 - - title: Get.rabund 1.39.5.0 + - description: 'Get.rabund: Get rabund from a otu list or sabund' + title: Get.rabund 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_get_rabund%2Fmothur_get_rabund%2F1.39.5.0 - - title: Get.relabund 1.39.5.0 + - description: 'Get.relabund: Calculate the relative abundance of each otu' + title: Get.relabund 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_get_relabund%2Fmothur_get_relabund%2F1.39.5.0 - - title: Get.sabund 1.39.5.0 + - description: 'Get.sabund: Get sabund from a otu list or rabund' + title: Get.sabund 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_get_sabund%2Fmothur_get_sabund%2F1.39.5.0 - - title: Get.seqs 1.39.5.0 + - description: 'Get.seqs: Picks sequences by name' + title: Get.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_get_seqs%2Fmothur_get_seqs%2F1.39.5.0 - - title: Get.sharedseqs 1.39.5.0 + - description: 'Get.sharedseqs: Get shared sequences at each distance from list + and group' + title: Get.sharedseqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_get_sharedseqs%2Fmothur_get_sharedseqs%2F1.39.5.0 - - title: Hcluster 1.36.1.0 + - description: 'Hcluster: Assign sequences to OTUs (Operational Taxonomic Unit)' + title: Hcluster 1.36.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_hcluster%2Fmothur_hcluster%2F1.36.1.0 - - title: Heatmap.bin 1.39.5.0 + - description: 'Heatmap.bin: Generate a heatmap for OTUs' + title: Heatmap.bin 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_heatmap_bin%2Fmothur_heatmap_bin%2F1.39.5.0 - - title: Heatmap.sim 1.39.5.0 + - description: 'Heatmap.sim: Generate a heatmap for pariwise similarity' + title: Heatmap.sim 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_heatmap_sim%2Fmothur_heatmap_sim%2F1.39.5.0 - - title: Homova 1.39.5.0 + - description: 'Homova: Homogeneity of molecular variance' + title: Homova 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_homova%2Fmothur_homova%2F1.39.5.0 - - title: Indicator 1.39.5.0 + - description: 'Indicator: Identify indicator "species" for nodes on a tree' + title: Indicator 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_indicator%2Fmothur_indicator%2F1.39.5.0 - - title: Lefse 1.39.5.0 + - description: 'Lefse: description' + title: Lefse 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_lefse%2Fmothur_lefse%2F1.39.5.0 - - title: Libshuff 1.39.5.0 + - description: 'Libshuff: Cramer-von Mises tests communities for the same structure' + title: Libshuff 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_libshuff%2Fmothur_libshuff%2F1.39.5.0 - - title: List.otulabels 1.39.5.0 + - description: 'List.otulabels: Lists otu labels from shared or relabund file' + title: List.otulabels 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_list_otulabels%2Fmothur_list_otulabels%2F1.39.5.0 - - title: List.seqs 1.39.5.0 + - description: 'List.seqs: Lists the names (accnos) of the sequences' + title: List.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_list_seqs%2Fmothur_list_seqs%2F1.39.5.0 - - title: Make.biom 1.39.5.0 + - description: 'Make.biom: Make biom files from a shared file' + title: Make.biom 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_make_biom%2Fmothur_make_biom%2F1.39.5.0 - - title: Make.contigs 1.39.5.1 + - description: 'Make.contigs: Aligns paired forward and reverse fastq files to contigs + as fasta and quality' + title: Make.contigs 1.39.5.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_make_contigs%2Fmothur_make_contigs%2F1.39.5.1 - - title: Make Design 1.39.5.0 + - description: 'Make Design: Assign groups to Sets' + title: Make Design 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_make_design%2Fmothur_make_design%2F1.39.5.0 - - title: Make.fastq 1.39.5.0 + - description: 'Make.fastq: Convert fasta and quality to fastq' + title: Make.fastq 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_make_fastq%2Fmothur_make_fastq%2F1.39.5.0 - - title: Make.group 1.39.5.0 + - description: 'Make.group: Make a group file' + title: Make.group 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_make_group%2Fmothur_make_group%2F1.39.5.0 - - title: Make.lefse 1.39.5.0 + - description: 'Make.lefse: create a lefse formatted input file from mothur''s output + files' + title: Make.lefse 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_make_lefse%2Fmothur_make_lefse%2F1.39.5.0 - - title: Make.lookup 1.39.5.0 + - description: 'Make.lookup: allows you to create custom lookup files for use with + shhh.flows' + title: Make.lookup 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_make_lookup%2Fmothur_make_lookup%2F1.39.5.0 - - title: Make.shared 1.39.5.0 + - description: 'Make.shared: Make a shared file from a list and a group' + title: Make.shared 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_make_shared%2Fmothur_make_shared%2F1.39.5.0 - - title: Make.sra 1.39.5.0 + - description: 'Make.sra: creates the necessary files for a NCBI submission' + title: Make.sra 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_make_sra%2Fmothur_make_sra%2F1.39.5.0 - - title: Mantel 1.39.5.0 + - description: 'Mantel: Mantel correlation coefficient between two matrices.' + title: Mantel 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_mantel%2Fmothur_mantel%2F1.39.5.0 - - title: Merge.count 1.39.5.0 + - description: 'Merge.count: Merge count tables' + title: Merge.count 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_merge_count%2Fmothur_merge_count%2F1.39.5.0 - - title: Merge.files 1.39.5.0 + - description: 'Merge.files: Merge data' + title: Merge.files 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_merge_files%2Fmothur_merge_files%2F1.39.5.0 - - title: Merge.groups 1.39.5.0 + - description: 'Merge.groups: Merge groups in a shared file' + title: Merge.groups 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_merge_groups%2Fmothur_merge_groups%2F1.39.5.0 - - title: Merge.sfffiles 1.39.5.0 + - description: 'Merge.sfffiles: Merge SFF files' + title: Merge.sfffiles 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_merge_sfffiles%2Fmothur_merge_sfffiles%2F1.39.5.0 - - title: Merge.taxsummary 1.39.5.0 + - description: 'Merge.taxsummary: Merge tax.summary files' + title: Merge.taxsummary 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_merge_taxsummary%2Fmothur_merge_taxsummary%2F1.39.5.0 - - title: Metastats 1.39.5.0 + - description: 'Metastats: generate principle components plot data' + title: Metastats 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_metastats%2Fmothur_metastats%2F1.39.5.0 - - title: Mimarks.attributes 1.39.5.0 + - description: 'Mimarks.attributes: Reads bioSample Attributes xml and generates + source for get.mimarkspackage command' + title: Mimarks.attributes 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_mimarks_attributes%2Fmothur_mimarks_attributes%2F1.39.5.0 - - title: Nmds 1.39.5.0 + - description: 'Nmds: generate non-metric multidimensional scaling data' + title: Nmds 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_nmds%2Fmothur_nmds%2F1.39.5.0 - - title: Normalize.shared 1.39.5.0 + - description: 'Normalize.shared: Normalize the number of sequences per group to + a specified level' + title: Normalize.shared 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_normalize_shared%2Fmothur_normalize_shared%2F1.39.5.0 - - title: Otu.association 1.39.5.0 + - description: 'Otu.association: Calculate the correlation coefficient for the otus' + title: Otu.association 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_otu_association%2Fmothur_otu_association%2F1.39.5.0 - - title: Otu.hierarchy 1.39.5.0 + - description: 'Otu.hierarchy: Relate OTUs at different distances' + title: Otu.hierarchy 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_otu_hierarchy%2Fmothur_otu_hierarchy%2F1.39.5.0 - - title: Pairwise.seqs 1.39.5.0 + - description: 'Pairwise.seqs: calculate uncorrected pairwise distances between + sequences' + title: Pairwise.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_pairwise_seqs%2Fmothur_pairwise_seqs%2F1.39.5.0 - - title: Parse.list 1.39.5.0 + - description: 'Parse.list: Generate a List file for each group' + title: Parse.list 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_parse_list%2Fmothur_parse_list%2F1.39.5.0 - - title: Parsimony 1.39.5.0 + - description: 'Parsimony: Describes whether two or more communities have the same + structure' + title: Parsimony 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_parsimony%2Fmothur_parsimony%2F1.39.5.0 - - title: Pca 1.39.5.0 + - description: 'Pca: Principal Coordinate Analysis for a shared file' + title: Pca 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_pca%2Fmothur_pca%2F1.39.5.0 - - title: Pcoa 1.39.5.0 + - description: 'Pcoa: Principal Coordinate Analysis for a distance matrix' + title: Pcoa 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_pcoa%2Fmothur_pcoa%2F1.39.5.0 - - title: Pcr.seqs 1.39.5.0 + - description: 'Pcr.seqs: Trim sequences' + title: Pcr.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_pcr_seqs%2Fmothur_pcr_seqs%2F1.39.5.0 - - title: Phylo.diversity 1.39.5.0 + - description: 'Phylo.diversity: Alpha Diversity calculates unique branch length' + title: Phylo.diversity 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_phylo_diversity%2Fmothur_phylo_diversity%2F1.39.5.0 - - title: Phylotype 1.39.5.0 + - description: 'Phylotype: Assign sequences to OTUs based on taxonomy' + title: Phylotype 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_phylotype%2Fmothur_phylotype%2F1.39.5.0 - - title: Pre.cluster 1.39.5.0 + - description: 'Pre.cluster: Remove sequences due to pyrosequencing errors' + title: Pre.cluster 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_pre_cluster%2Fmothur_pre_cluster%2F1.39.5.0 - - title: Primer.design 1.39.5.0 + - description: 'Primer.design: identify sequence fragments that are specific to + particular OTUs' + title: Primer.design 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_primer_design%2Fmothur_primer_design%2F1.39.5.0 - - title: Rarefaction.shared 1.39.5.0 + - description: 'Rarefaction.shared: Generate inter-sample rarefaction curves for + OTUs' + title: Rarefaction.shared 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_rarefaction_shared%2Fmothur_rarefaction_shared%2F1.39.5.0 - - title: Rarefaction.single 1.39.5.0 + - description: 'Rarefaction.single: Generate intra-sample rarefaction curves for + OTUs' + title: Rarefaction.single 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_rarefaction_single%2Fmothur_rarefaction_single%2F1.39.5.0 - - title: Remove.dists 1.39.5.0 + - description: 'Remove.dists: Removes distances from a phylip or column file' + title: Remove.dists 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_remove_dists%2Fmothur_remove_dists%2F1.39.5.0 - - title: Remove.groups 1.39.5.0 + - description: 'Remove.groups: Remove groups from groups,fasta,names,list,taxonomy' + title: Remove.groups 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_remove_groups%2Fmothur_remove_groups%2F1.39.5.0 - - title: Remove.lineage 1.39.5.0 + - description: 'Remove.lineage: Picks by taxon' + title: Remove.lineage 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_remove_lineage%2Fmothur_remove_lineage%2F1.39.5.0 - - title: Remove.otulabels 1.39.5.0 + - description: 'Remove.otulabels: Removes OTU labels' + title: Remove.otulabels 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_remove_otulabels%2Fmothur_remove_otulabels%2F1.39.5.0 - - title: Remove.otus 1.39.5.0 + - description: 'Remove.otus: Removes OTUs from various file formats' + title: Remove.otus 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_remove_otus%2Fmothur_remove_otus%2F1.39.5.0 - - title: Remove.rare 1.39.5.0 + - description: 'Remove.rare: Remove rare OTUs' + title: Remove.rare 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_remove_rare%2Fmothur_remove_rare%2F1.39.5.0 - - title: Remove.seqs 1.39.5.0 + - description: 'Remove.seqs: Remove sequences by name' + title: Remove.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_remove_seqs%2Fmothur_remove_seqs%2F1.39.5.0 - - title: Rename.seqs 1.39.5.0 + - description: 'Rename.seqs: Rename sequences by concatenating the group name' + title: Rename.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_rename_seqs%2Fmothur_rename_seqs%2F1.39.5.0 - - title: Reverse.seqs 1.39.5.0 + - description: 'Reverse.seqs: Reverse complement the sequences' + title: Reverse.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_reverse_seqs%2Fmothur_reverse_seqs%2F1.39.5.0 - - title: Screen.seqs 1.39.5.1 + - description: 'Screen.seqs: Screen sequences' + title: Screen.seqs 1.39.5.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_screen_seqs%2Fmothur_screen_seqs%2F1.39.5.1 - - title: Sens.spec 1.39.5.0 + - description: 'Sens.spec: Determine the quality of OTU assignment' + title: Sens.spec 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_sens_spec%2Fmothur_sens_spec%2F1.39.5.0 - - title: Seq.error 1.39.5.0 + - description: 'Seq.error: assess error rates in sequencing data' + title: Seq.error 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_seq_error%2Fmothur_seq_error%2F1.39.5.0 - - title: Sffinfo 1.39.5.0 + - description: 'Sffinfo: Summarize the quality of sequences' + title: Sffinfo 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_sffinfo%2Fmothur_sffinfo%2F1.39.5.0 - - title: Shhh.flows 1.39.5.0 + - description: 'Shhh.flows: Denoise flowgrams (PyroNoise algorithm)' + title: Shhh.flows 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_shhh_flows%2Fmothur_shhh_flows%2F1.39.5.0 - - title: Shhh.seqs 1.39.5.0 + - description: 'Shhh.seqs: Denoise program (Quince SeqNoise)' + title: Shhh.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_shhh_seqs%2Fmothur_shhh_seqs%2F1.39.5.0 - - title: Sort.seqs 1.39.5.0 + - description: 'Sort.seqs: put sequences in different files in the same order' + title: Sort.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_sort_seqs%2Fmothur_sort_seqs%2F1.39.5.0 - - title: Split.abund 1.39.5.0 + - description: 'Split.abund: Separate sequences into rare and abundant groups' + title: Split.abund 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_split_abund%2Fmothur_split_abund%2F1.39.5.0 - - title: Split.groups 1.39.5.0 + - description: 'Split.groups: Generates a fasta file for each group' + title: Split.groups 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_split_groups%2Fmothur_split_groups%2F1.39.5.0 - - title: Sub.sample 1.39.5.0 + - description: 'Sub.sample: Create a sub sample' + title: Sub.sample 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_sub_sample%2Fmothur_sub_sample%2F1.39.5.0 - - title: Summary.qual 1.39.5.0 + - description: 'Summary.qual: Summarize the quality scores' + title: Summary.qual 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_summary_qual%2Fmothur_summary_qual%2F1.39.5.0 - - title: Summary.seqs 1.39.5.0 + - description: 'Summary.seqs: Summarize the quality of sequences' + title: Summary.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_summary_seqs%2Fmothur_summary_seqs%2F1.39.5.0 - - title: Summary.shared 1.39.5.0 + - description: 'Summary.shared: Summary of calculator values for OTUs' + title: Summary.shared 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_summary_shared%2Fmothur_summary_shared%2F1.39.5.0 - - title: Summary.single 1.39.5.2 + - description: 'Summary.single: Summary of calculator values for OTUs' + title: Summary.single 1.39.5.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_summary_single%2Fmothur_summary_single%2F1.39.5.2 - - title: Summary.tax 1.39.5.0 + - description: 'Summary.tax: Assign sequences to taxonomy' + title: Summary.tax 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_summary_tax%2Fmothur_summary_tax%2F1.39.5.0 - - title: Taxonomy-to-Krona 1.0 + - description: 'Taxonomy-to-Krona: convert a mothur taxonomy file to Krona input + format' + title: Taxonomy-to-Krona 1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_taxonomy_to_krona%2Fmothur_taxonomy_to_krona%2F1.0 - - title: Tree.shared 1.39.5.0 + - description: 'Tree.shared: Generate a newick tree for dissimilarity among groups' + title: Tree.shared 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_tree_shared%2Fmothur_tree_shared%2F1.39.5.0 - - title: Trim.flows 1.39.5.0 + - description: 'Trim.flows: partition by barcode, trim to length, cull by length + and mismatches' + title: Trim.flows 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_trim_flows%2Fmothur_trim_flows%2F1.39.5.0 - - title: Trim.seqs 1.39.5.0 + - description: 'Trim.seqs: Trim sequences - primers, barcodes, quality' + title: Trim.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_trim_seqs%2Fmothur_trim_seqs%2F1.39.5.0 - - title: unifrac.unweighted 1.39.5.0 + - description: 'unifrac.unweighted: Describes whether two or more communities have + the same structure' + title: unifrac.unweighted 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_unifrac_unweighted%2Fmothur_unifrac_unweighted%2F1.39.5.0 - - title: unifrac.weighted 1.39.5.0 + - description: 'unifrac.weighted: Describes whether two or more communities have + the same structure' + title: unifrac.weighted 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_unifrac_weighted%2Fmothur_unifrac_weighted%2F1.39.5.0 - - title: Unique.seqs 1.39.5.0 + - description: 'Unique.seqs: Return unique sequences' + title: Unique.seqs 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_unique_seqs%2Fmothur_unique_seqs%2F1.39.5.0 - - title: Venn 1.39.5.0 + - description: 'Venn: Generate Venn diagrams for groups' + title: Venn 1.39.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmothur_venn%2Fmothur_venn%2F1.39.5.0 homepage: http://mothur.org/ id: mothur @@ -11609,7 +12840,8 @@ to save and combine results from different queries, easy integration into larger workflows, and a comprehensive Web Services layer. galaxy: - - title: MouseMine 1.0.0 + - description: 'MouseMine: server' + title: MouseMine 1.0.0 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=mousemine homepage: http://www.mousemine.org/mousemine/begin.do id: mousemine @@ -11706,7 +12938,8 @@ companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. galaxy: - - title: msconvert 3.0.20287.2 + - 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 homepage: http://proteowizard.sourceforge.net/tools.shtml id: msconvert @@ -11727,7 +12960,8 @@ bunya: '' description: Tool for mass spectra metadata annotation. galaxy: - - title: MSMetaEnhancer 0.3.0+galaxy1 + - 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 homepage: https://github.com/RECETOX/MSMetaEnhancer id: msmetaenhancer @@ -11749,7 +12983,9 @@ bunya: '' description: Statistical tool for quantitative mass spectrometry-based proteomics. galaxy: - - title: MSstats 4.0.0+galaxy1 + - description: 'MSstats: statistical relative protein significance analysis in DDA, + SRM and DIA Mass Spectrometry' + title: MSstats 4.0.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmsstats%2Fmsstats%2F4.0.0%2Bgalaxy1 homepage: http://www.msstats.org/ id: msstats @@ -11773,7 +13009,9 @@ bunya: '' description: '' galaxy: - - title: MSstatsTMT 2.0.0+galaxy1 + - description: 'MSstatsTMT: protein significance analysis in shotgun mass spectrometry-based + proteomic experiments with tandem mass tag (TMT) labeling' + title: MSstatsTMT 2.0.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmsstatstmt%2Fmsstatstmt%2F2.0.0%2Bgalaxy1 homepage: '' id: bioconductor-msstatstmt @@ -11811,7 +13049,9 @@ logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. galaxy: - - title: MultiQC 1.11+galaxy1 + - description: 'MultiQC: aggregate results from bioinformatics analyses into a single + report' + title: MultiQC 1.11+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmultiqc%2Fmultiqc%2F1.11%2Bgalaxy1 homepage: http://multiqc.info/ id: multiqc @@ -11858,18 +13098,24 @@ finished or draft sequence. Basically it is a ultra-fast alignment of large-scale DNA and protein sequences galaxy: - - title: Delta-Filter 4.0.0rc1+galaxy2 + - description: 'Show-Coords: Parse delta file and report coordinates and other information' + title: Show-Coords 4.0.0rc1+galaxy3 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmummer_show_coords%2Fmummer_show_coords%2F4.0.0rc1%2Bgalaxy3 + - description: 'Nucmer: Align two or more sequences' + title: Nucmer 4.0.0rc1+galaxy3 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmummer_nucmer%2Fmummer_nucmer%2F4.0.0rc1%2Bgalaxy3 + - description: 'Mummerplot: Generate 2-D dotplot of aligned sequences' + title: Mummerplot 4.0.0rc1+galaxy3 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmummer_mummerplot%2Fmummer_mummerplot%2F4.0.0rc1%2Bgalaxy3 + - description: 'DNAdiff: Evaluate similarities/differences between two sequences' + title: DNAdiff 4.0.0rc1+galaxy3 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmummer_dnadiff%2Fmummer_dnadiff%2F4.0.0rc1%2Bgalaxy3 + - description: 'Delta-Filter: Filters alignment (delta) file from nucmer' + title: Delta-Filter 4.0.0rc1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmummer_delta_filter%2Fmummer_delta_filter%2F4.0.0rc1%2Bgalaxy2 - - title: DNAdiff 4.0.0rc1+galaxy2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmummer_dnadiff%2Fmummer_dnadiff%2F4.0.0rc1%2Bgalaxy2 - - title: Mummer 4.0.0rc1+galaxy2 + - description: 'Mummer: Align two or more sequences' + title: Mummer 4.0.0rc1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmummer_mummer%2Fmummer_mummer%2F4.0.0rc1%2Bgalaxy2 - - title: Mummerplot 4.0.0rc1+galaxy2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmummer_mummerplot%2Fmummer_mummerplot%2F4.0.0rc1%2Bgalaxy2 - - title: Nucmer 4.0.0rc1+galaxy2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmummer_nucmer%2Fmummer_nucmer%2F4.0.0rc1%2Bgalaxy2 - - title: Show-Coords 4.0.0rc1+galaxy2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmummer_show_coords%2Fmummer_show_coords%2F4.0.0rc1%2Bgalaxy2 homepage: http://mummer.sourceforge.net/ id: mummer license: Artistic-2.0 @@ -11923,11 +13169,17 @@ bunya: '' description: '' galaxy: - - title: Construct Expression Set Object 0.1.1+galaxy4 + - description: 'Construct Expression Set Object: Create an ExpressionSet object + from tabular and textual data' + title: Construct Expression Set Object 0.1.1+galaxy4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fmusic_construct_eset%2Fmusic_construct_eset%2F0.1.1%2Bgalaxy4 - - title: MuSiC Deconvolution 0.1.1+galaxy4 + - description: 'MuSiC Deconvolution: estimate cell type proportions in bulk RNA-seq + data' + title: MuSiC Deconvolution 0.1.1+galaxy4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fmusic_deconvolution%2Fmusic_deconvolution%2F0.1.1%2Bgalaxy4 - - title: Inspect Expression Set Object 0.1.1+galaxy4 + - description: 'Inspect Expression Set Object: Inspect an ExpressionSet object by + a variety of attributes' + title: Inspect Expression Set Object 0.1.1+galaxy4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fmusic_inspect_eset%2Fmusic_inspect_eset%2F0.1.1%2Bgalaxy4 homepage: '' id: music_deconvolution @@ -11944,7 +13196,9 @@ bunya: '' description: '' galaxy: - - title: mz to sqlite 2.1.1+galaxy0 + - description: 'mz to sqlite: Extract mzIdentML and associated proteomics datasets + into a SQLite DB' + title: mz to sqlite 2.1.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmz_to_sqlite%2Fmz_to_sqlite%2F2.1.1%2Bgalaxy0 homepage: '' id: mztosqlite @@ -12001,7 +13255,8 @@ knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro' galaxy: - - title: SampComp 1.0.0rc3.post2+galaxy1 + - description: 'SampComp: to compare Nanopolished datasets' + title: SampComp 1.0.0rc3.post2+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fnanocompore_sampcomp%2Fnanocompore_sampcomp%2F1.0.0rc3.post2%2Bgalaxy1 homepage: https://github.com/tleonardi/nanocompore id: nanocompore @@ -12025,7 +13280,8 @@ bunya: '' description: '' galaxy: - - title: NanoFilt 0.1.0 + - description: 'NanoFilt: Filtering and trimming of long read sequencing data' + title: NanoFilt 0.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fleomrtns%2Fnanofilt%2Fnanofilt%2F0.1.0 homepage: '' id: nanofilt @@ -12044,7 +13300,9 @@ bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences galaxy: - - title: NanoPlot 1.41.0+galaxy0 + - description: 'NanoPlot: Plotting suite for Oxford Nanopore sequencing data and + alignments' + title: NanoPlot 1.41.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fnanoplot%2Fnanoplot%2F1.41.0%2Bgalaxy0 homepage: https://github.com/wdecoster/NanoPlot id: nanoplot @@ -12066,13 +13324,20 @@ description: A package for detecting cytosine methylations and genetic variations from nanopore MinION sequencing data. galaxy: - - title: Nanopolish variants 0.14.0+galaxy0 + - description: 'Nanopolish variants: - Find SNPs of basecalled merged Nanopore reads + and polishes the consensus sequences' + title: Nanopolish variants 0.14.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fnanopolish_variants%2Fnanopolish_variants%2F0.14.0%2Bgalaxy0 - - title: Nanopolish polyA 0.14.0+galaxy0 + - description: 'Nanopolish polyA: - Estimate the length of the poly-A tail on direct + RNA reads.' + title: Nanopolish polyA 0.14.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fnanopolish_polya%2Fnanopolish_polya%2F0.14.0%2Bgalaxy0 - - title: Nanopolish methylation 0.14.0+galaxy0 + - description: 'Nanopolish methylation: - Classify nucleotides as methylated or + not.' + title: Nanopolish methylation 0.14.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fnanopolish_methylation%2Fnanopolish_methylation%2F0.14.0%2Bgalaxy0 - - title: Nanopolish eventalign 0.14.0+galaxy0 + - description: 'Nanopolish eventalign: - Align nanopore events to reference k-mers' + title: Nanopolish eventalign 0.14.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fnanopolish_eventalign%2Fnanopolish_eventalign%2F0.14.0%2Bgalaxy0 homepage: https://github.com/jts/nanopolish id: nanopolish @@ -12111,7 +13376,9 @@ bunya: '' description: '' galaxy: - - title: Natural Product likeness calculator 2.1 + - description: 'Natural Product likeness calculator: - calculates the similarity + of the molecule to the structure space covered by known natural products' + title: Natural Product likeness calculator 2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fnatural_product_likeness%2Fctb_np-likeness-calculator%2F2.1 homepage: '' id: natural_product_likeness_scorer @@ -12149,7 +13416,9 @@ bunya: '' description: '' galaxy: - - title: NCBI Accession Download 0.2.8+galaxy0 + - description: 'NCBI Accession Download: Download sequences from GenBank/RefSeq + by accession through the NCBI ENTREZ API' + title: NCBI Accession Download 0.2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fncbi_acc_download%2Fncbi_acc_download%2F0.2.8%2Bgalaxy0 homepage: '' id: ncbi_acc_download @@ -12328,7 +13597,8 @@ not require user interaction, which makes them suitable for automating phylogeny processing tasks. galaxy: - - title: Newick Display 1.6+galaxy1 + - description: 'Newick Display: visualize a phylogenetic tree' + title: Newick Display 1.6+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fnewick_utils%2Fnewick_display%2F1.6%2Bgalaxy1 homepage: https://www.ezlab.org/ id: newick_utils @@ -12350,7 +13620,9 @@ bunya: '' description: '' galaxy: - - title: Nextclade 2.7.0+galaxy0 + - description: 'Nextclade: Viral genome clade assignment, mutation calling, and + sequence quality checks' + title: Nextclade 2.7.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fnextclade%2Fnextclade%2F2.7.0%2Bgalaxy0 homepage: '' id: nextclade @@ -12495,7 +13767,8 @@ description: NGSUtils is a suite of software tools for working with next-generation sequencing datasets galaxy: - - title: BAM filter 0.5.9 + - description: 'BAM filter: Removes reads from a BAM file based on criteria' + title: BAM filter 0.5.9 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fngsutils_bam_filter%2Fngsutils_bam_filter%2F0.5.9 homepage: http://ngsutils.org id: ngsutils @@ -12536,7 +13809,8 @@ bunya: '' description: '' galaxy: - - title: NOVOplasty 4.3.1+galaxy0 + - description: 'NOVOplasty: de novo assembler for short circular genomes' + title: NOVOplasty 4.3.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fnovoplasty%2Fnovoplasty%2F4.3.1%2Bgalaxy0 homepage: https://github.com/ndierckx/NOVOPlasty id: NOVOPlasty @@ -12602,7 +13876,8 @@ bunya: '' description: '' galaxy: - - title: Naive Variant Caller (NVC) 0.0.4 + - description: 'Naive Variant Caller (NVC): - tabulate variable sites from BAM datasets' + title: Naive Variant Caller (NVC) 0.0.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fblankenberg%2Fnaive_variant_caller%2Fnaive_variant_caller%2F0.0.4 homepage: '' id: nvc @@ -12647,25 +13922,38 @@ files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. galaxy: - - title: obiannotate 1.2.13 + - description: 'obiannotate: Adds/Edits sequence record annotations' + title: obiannotate 1.2.13 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fobi_annotate%2Fobi_annotate%2F1.2.13 - - title: obiclean 1.2.13 + - description: 'obiclean: tags a set of sequences for PCR/sequencing errors identification' + title: obiclean 1.2.13 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fobi_clean%2Fobi_clean%2F1.2.13 - - title: obiconvert 1.2.13 + - description: 'obiconvert: converts sequence files to different output formats' + title: obiconvert 1.2.13 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fobi_convert%2Fobi_convert%2F1.2.13 - - title: obigrep 1.2.13 + - description: 'obigrep: Filters sequence file' + title: obigrep 1.2.13 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fobi_grep%2Fobi_grep%2F1.2.13 - - title: Illuminapairedend 1.2.13 + - description: 'Illuminapairedend: Construct consensus reads from Illumina pair-end + reads' + title: Illuminapairedend 1.2.13 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fobi_illumina_pairend%2Fobi_illumina_pairend%2F1.2.13 - - title: NGSfilter 1.2.13 + - description: 'NGSfilter: Assigns sequence records to the corresponding experiment/sample + based on DNA tags and primers' + title: NGSfilter 1.2.13 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fobi_ngsfilter%2Fobi_ngsfilter%2F1.2.13 - - title: obisort 1.2.13 + - description: 'obisort: sorts sequence records according to the value of a given + attribute' + title: obisort 1.2.13 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fobi_sort%2Fobi_sort%2F1.2.13 - - title: obistat 1.2.13 + - description: 'obistat: computes basic statistics for attribute values' + title: obistat 1.2.13 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fobi_stat%2Fobi_stat%2F1.2.13 - - title: obitab 1.2.13 + - description: 'obitab: converts sequence file to a tabular file' + title: obitab 1.2.13 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fobi_tab%2Fobi_tab%2F1.2.13 - - title: obiuniq 1.2.13 + - description: 'obiuniq: ' + title: obiuniq 1.2.13 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fobi_uniq%2Fobi_uniq%2F1.2.13 homepage: https://git.metabarcoding.org/obitools/obitools/wikis/home id: obitools @@ -12707,75 +13995,135 @@ Raw and intermediate mass spectrometry data can be visualised with the included viewer TOPPView. galaxy: - - title: XTandemAdapter 2.8+galaxy0 + - 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 - - title: XMLValidator 2.8+galaxy0 + - description: 'XMLValidator: Validates XML files against an XSD schema.' + title: XMLValidator 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_xmlvalidator%2FXMLValidator%2F2.8%2Bgalaxy0 - - title: TextExporter 2.8+galaxy0 + - 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 - - title: TargetedFileConverter 2.8+galaxy0 + - 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 - - title: ProteinQuantifier 2.8+galaxy0 + - 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 - - title: PeptideIndexer 2.8+galaxy0 + - description: 'PeptideIndexer: Refreshes the protein references for all peptide + hits.' + title: PeptideIndexer 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_peptideindexer%2FPeptideIndexer%2F2.8%2Bgalaxy0 - - title: PeakPickerHiRes 2.8+galaxy0 + - description: 'PeakPickerHiRes: Finds mass spectrometric peaks in profile mass + spectra.' + title: PeakPickerHiRes 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_peakpickerhires%2FPeakPickerHiRes%2F2.8%2Bgalaxy0 - - title: OpenSwathRTNormalizer 2.8+galaxy0 + - description: 'OpenSwathRTNormalizer: This tool will take a description of RT peptides + and their normalized retention time to write out a transformation file on how + to transform the RT space into the normalized space.' + title: OpenSwathRTNormalizer 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_openswathrtnormalizer%2FOpenSwathRTNormalizer%2F2.8%2Bgalaxy0 - - title: OpenSwathMzMLFileCacher 2.8+galaxy0 + - description: 'OpenSwathMzMLFileCacher: This tool caches the spectra and chromatogram + data of an mzML to disk.' + title: OpenSwathMzMLFileCacher 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_openswathmzmlfilecacher%2FOpenSwathMzMLFileCacher%2F2.8%2Bgalaxy0 - - title: OpenSwathFileSplitter 2.8+galaxy0 + - description: 'OpenSwathFileSplitter: Splits SWATH files into n files, each containing + one window.' + title: OpenSwathFileSplitter 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_openswathfilesplitter%2FOpenSwathFileSplitter%2F2.8%2Bgalaxy0 - - title: OpenSwathDIAPreScoring 2.8+galaxy0 + - description: 'OpenSwathDIAPreScoring: Scoring spectra using the DIA scores.' + title: OpenSwathDIAPreScoring 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_openswathdiaprescoring%2FOpenSwathDIAPreScoring%2F2.8%2Bgalaxy0 - - title: OpenSwathDecoyGenerator 2.8+galaxy0 + - description: 'OpenSwathDecoyGenerator: Generates decoys according to different + models for a specific TraML' + title: OpenSwathDecoyGenerator 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_openswathdecoygenerator%2FOpenSwathDecoyGenerator%2F2.8%2Bgalaxy0 - - title: OpenSwathAssayGenerator 2.8+galaxy0 + - description: 'OpenSwathAssayGenerator: Generates assays according to different + models for a specific TraML' + title: OpenSwathAssayGenerator 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_openswathassaygenerator%2FOpenSwathAssayGenerator%2F2.8%2Bgalaxy0 - - title: OpenSwathAnalyzer 2.8+galaxy0 + - description: 'OpenSwathAnalyzer: Picks peaks and finds features in an SWATH-MS + or SRM experiment.' + title: OpenSwathAnalyzer 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_openswathanalyzer%2FOpenSwathAnalyzer%2F2.8%2Bgalaxy0 - - title: MzTabExporter 2.8+galaxy0 + - description: 'MzTabExporter: Exports various XML formats to an mzTab file.' + title: MzTabExporter 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_mztabexporter%2FMzTabExporter%2F2.8%2Bgalaxy0 - - title: MultiplexResolver 2.8+galaxy0 + - description: 'MultiplexResolver: Completes peptide multiplets and resolves conflicts + within them.' + title: MultiplexResolver 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_multiplexresolver%2FMultiplexResolver%2F2.8%2Bgalaxy0 - - title: MSGFPlusAdapter 2.8+galaxy0 + - description: 'MSGFPlusAdapter: MS/MS database search using MS-GF+.' + title: MSGFPlusAdapter 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_msgfplusadapter%2FMSGFPlusAdapter%2F2.8%2Bgalaxy0 - - title: IDScoreSwitcher 2.8+galaxy0 + - description: 'IDScoreSwitcher: Switches between different scores of peptide or + protein hits in identification data' + title: IDScoreSwitcher 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_idscoreswitcher%2FIDScoreSwitcher%2F2.8%2Bgalaxy0 - - title: IDPosteriorErrorProbability 2.8+galaxy0 + - description: 'IDPosteriorErrorProbability: Estimates probabilities for incorrectly + assigned peptide sequences and a set of search engine scores using a mixture + model.' + title: IDPosteriorErrorProbability 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_idposteriorerrorprobability%2FIDPosteriorErrorProbability%2F2.8%2Bgalaxy0 - - title: IDMerger 2.8+galaxy0 + - description: 'IDMerger: Merges several protein/peptide identification files into + one file.' + title: IDMerger 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_idmerger%2FIDMerger%2F2.8%2Bgalaxy0 - - title: IDMapper 2.8+galaxy0 + - description: 'IDMapper: Assigns protein/peptide identifications to features or + consensus features.' + title: IDMapper 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_idmapper%2FIDMapper%2F2.8%2Bgalaxy0 - - title: IDFilter 2.8+galaxy0 + - description: 'IDFilter: Filters results from protein or peptide identification + engines based on different criteria.' + title: IDFilter 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_idfilter%2FIDFilter%2F2.8%2Bgalaxy0 - - title: IDConflictResolver 2.8+galaxy0 + - description: 'IDConflictResolver: Resolves ambiguous annotations of features with + peptide identifications' + title: IDConflictResolver 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_idconflictresolver%2FIDConflictResolver%2F2.8%2Bgalaxy0 - - title: HighResPrecursorMassCorrector 2.8+galaxy0 + - description: 'HighResPrecursorMassCorrector: Corrects the precursor mass and charge + determined by the instrument software.' + title: HighResPrecursorMassCorrector 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_highresprecursormasscorrector%2FHighResPrecursorMassCorrector%2F2.8%2Bgalaxy0 - - title: FileConverter 2.8+galaxy0 + - description: 'FileConverter: Converts between different MS file formats.' + title: FileConverter 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_fileconverter%2FFileConverter%2F2.8%2Bgalaxy0 - - title: FeatureFinderMultiplex 2.8+galaxy0 + - description: 'FeatureFinderMultiplex: Determination of peak ratios in LC-MS data' + title: FeatureFinderMultiplex 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_featurefindermultiplex%2FFeatureFinderMultiplex%2F2.8%2Bgalaxy0 - - title: FalseDiscoveryRate 2.8+galaxy0 + - description: 'FalseDiscoveryRate: Estimates the false discovery rate on peptide + and protein level using decoy searches.' + title: FalseDiscoveryRate 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_falsediscoveryrate%2FFalseDiscoveryRate%2F2.8%2Bgalaxy0 - - title: ConsensusID 2.8+galaxy0 + - description: 'ConsensusID: Computes a consensus of peptide identifications of + several identification engines.' + title: ConsensusID 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_consensusid%2FConsensusID%2F2.8%2Bgalaxy0 - - title: DecoyDatabase 2.8+galaxy0 + - description: 'DecoyDatabase: Create decoy sequence database from forward sequence + database.' + title: DecoyDatabase 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_decoydatabase%2FDecoyDatabase%2F2.8%2Bgalaxy0 - - title: FidoAdapter 2.8+galaxy0 + - description: 'FidoAdapter: Runs the protein inference engine Fido.' + title: FidoAdapter 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_fidoadapter%2FFidoAdapter%2F2.8%2Bgalaxy0 - - title: FileFilter 2.8+galaxy0 + - description: 'FileFilter: Extracts or manipulates portions of data from peak, + feature or consensus-feature files.' + title: FileFilter 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_filefilter%2FFileFilter%2F2.8%2Bgalaxy0 - - title: FileInfo 2.8+galaxy0 + - description: 'FileInfo: Shows basic information about the file, such as data ranges + and file type.' + title: FileInfo 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_fileinfo%2FFileInfo%2F2.8%2Bgalaxy0 - - title: FileMerger 2.8+galaxy0 + - description: 'FileMerger: Merges several MS files into one file.' + title: FileMerger 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_filemerger%2FFileMerger%2F2.8%2Bgalaxy0 - - title: OpenSwathConfidenceScoring 2.8+galaxy0 + - description: 'OpenSwathConfidenceScoring: Compute confidence scores for OpenSwath + results' + title: OpenSwathConfidenceScoring 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_openswathconfidencescoring%2FOpenSwathConfidenceScoring%2F2.8%2Bgalaxy0 - - title: OpenSwathWorkflow 2.8+galaxy0 + - description: 'OpenSwathWorkflow: Complete workflow to run OpenSWATH' + title: OpenSwathWorkflow 2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fopenms_openswathworkflow%2FOpenSwathWorkflow%2F2.8%2Bgalaxy0 homepage: http://www.openms.de id: openms @@ -12836,7 +14184,8 @@ gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. galaxy: - - title: OrthoFinder 2.5.5+galaxy0 + - description: 'OrthoFinder: finds orthogroups in a set of proteomes' + title: OrthoFinder 2.5.5+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Forthofinder_onlygroups%2Forthofinder_onlygroups%2F2.5.5%2Bgalaxy0 homepage: https://github.com/davidemms/OrthoFinder id: orthofinder @@ -12917,15 +14266,24 @@ bunya: '' description: '' galaxy: - - title: Calculate community metrics 0.0.2 + - description: 'Calculate community metrics: calculate community metrics from abundance + data' + title: Calculate community metrics 0.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fecology%2Fpampa_communitymetrics%2Fpampa_communitymetrics%2F0.0.2 - - title: Compute GLM on community data 0.0.2 + - description: 'Compute GLM on community data: Compute a GLM of your choice on community + data' + title: Compute GLM on community data 0.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fecology%2Fpampa_glmcomm%2Fpampa_glmcomm%2F0.0.2 - - title: Compute GLM on population data 0.0.2 + - description: 'Compute GLM on population data: Compute a GLM of your choice on + population data' + title: Compute GLM on population data 0.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fecology%2Fpampa_glmsp%2Fpampa_glmsp%2F0.0.2 - - title: Create a plot from GLM data 0.0.2 + - description: 'Create a plot from GLM data: as temporal trend' + title: Create a plot from GLM data 0.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fecology%2Fpampa_plotglm%2Fpampa_plotglm%2F0.0.2 - - title: Calculate presence absence table 0.0.2 + - description: 'Calculate presence absence table: calculate presence absence table + from observation data' + title: Calculate presence absence table 0.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fecology%2Fpampa_presabs%2Fpampa_presabs%2F0.0.2 homepage: https://github.com/ColineRoyaux/PAMPA-Galaxy id: pampa @@ -12963,7 +14321,8 @@ variant, and return a file of the same format. Pangolin's models can also be used with custom sequences. galaxy: - - title: Pangolin 4.3+galaxy1 + - description: 'Pangolin: Phylogenetic Assignment of Outbreak Lineages' + title: Pangolin 4.3+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpangolin%2Fpangolin%2F4.3%2Bgalaxy1 homepage: https://github.com/tkzeng/Pangolin id: pangolin @@ -12987,7 +14346,8 @@ bunya: '' description: '' galaxy: - - title: Parse parameter value 0.1.0 + - description: 'Parse parameter value: from dataset' + title: Parse parameter value 0.1.0 url: https://usegalaxy.org.au/root?tool_id=param_value_from_file homepage: '' id: param_value_from_file @@ -13035,7 +14395,9 @@ bunya: '' description: '' galaxy: - - title: Parse mitochondrial blast 1.0.2+galaxy0 + - description: 'Parse mitochondrial blast: overlap-conscious coverage calculation + between scaffold-accession number pairs from blast output' + title: Parse mitochondrial blast 1.0.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fparse_mito_blast%2Fparse_mito_blast%2F1.0.2%2Bgalaxy0 homepage: '' id: parse_mito_blast @@ -13093,7 +14455,8 @@ with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. galaxy: - - title: Pathview 1.34.0+galaxy0 + - description: 'Pathview: for pathway based data integration and visualization' + title: Pathview 1.34.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpathview%2Fpathview%2F1.34.0%2Bgalaxy0 homepage: http://bioconductor.org/packages/release/bioc/html/pathview.html id: pathview @@ -13121,7 +14484,8 @@ display and transform results from the Kraken and Centrifuge classifiers using interactive tables, heatmaps and flow diagrams. galaxy: - - title: Pavian 1.0 + - description: 'Pavian: Interactive analysis of metagenomics data' + title: Pavian 1.0 url: https://usegalaxy.org.au/root?tool_id=interactive_tool_pavian homepage: https://ccb.jhu.edu/software/pavian/ id: pavian @@ -13165,7 +14529,8 @@ description: Productive visualization of high-throughput sequencing data using the SeqCode open portable platform. galaxy: - - title: Paired-end histogram 1.0.1 + - description: 'Paired-end histogram: of insert size frequency' + title: Paired-end histogram 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpe_histogram%2Fpe_histogram%2F1.0.1 homepage: https://github.com/eblancoga/seqcode id: pe_histogram @@ -13193,7 +14558,8 @@ overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. galaxy: - - title: Pear 0.9.6.2 + - 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 homepage: http://sco.h-its.org/exelixis/web/software/pear/ id: pear @@ -13213,7 +14579,8 @@ bunya: '' description: '' galaxy: - - title: PepPointer 0.1.3+galaxy1 + - description: 'PepPointer: classify genomic location of peptides' + title: PepPointer 0.1.3+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fpep_pointer%2Fpep_pointer%2F0.1.3%2Bgalaxy1 homepage: '' id: PepPointer @@ -13235,13 +14602,20 @@ PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data galaxy: - - title: FastaCLI 4.0.41+galaxy1 + - description: 'FastaCLI: Appends decoy sequences to FASTA files' + title: FastaCLI 4.0.41+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fpeptideshaker%2Ffasta_cli%2F4.0.41%2Bgalaxy1 - - title: Identification Parameters 4.0.41+galaxy1 + - description: 'Identification Parameters: Sets the identification parameters to + be used in SearchGUI and PeptideShaker apps' + title: Identification Parameters 4.0.41+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fpeptideshaker%2Fident_params%2F4.0.41%2Bgalaxy1 - - title: Peptide Shaker 2.0.33+galaxy1 + - description: 'Peptide Shaker: Perform protein identification using various search + engines based on results from SearchGUI' + title: Peptide Shaker 2.0.33+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fpeptideshaker%2Fpeptide_shaker%2F2.0.33%2Bgalaxy1 - - title: Search GUI 4.0.41+galaxy1 + - description: 'Search GUI: Perform protein identification using various search + engines and prepare results for input to Peptide Shaker' + title: Search GUI 4.0.41+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fpeptideshaker%2Fsearch_gui%2F4.0.41%2Bgalaxy1 homepage: http://compomics.github.io/projects/peptide-shaker.html id: peptideshaker @@ -13264,7 +14638,9 @@ bunya: '' description: '' galaxy: - - title: Peptide Genomic Coordinate 1.0.0 + - description: 'Peptide Genomic Coordinate: Get Peptide''s genomic coordinate using + mzsqlite DB and genomic mapping sqlite DB' + title: Peptide Genomic Coordinate 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fpeptide_genomic_coordinate%2Fpeptide_genomic_coordinate%2F1.0.0 homepage: '' id: peptide_genomic_coordinate @@ -13281,13 +14657,18 @@ bunya: '' description: Semi-supervised learning for peptide identification from MS/MS data. galaxy: - - title: Search engine output to Pin converter 3.5+galaxy0 + - description: 'Search engine output to Pin converter: to create Percolator input + files' + title: Search engine output to Pin converter 3.5+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fpercolator%2Fpercolator_input_converters%2F3.5%2Bgalaxy0 - - title: Percolator 3.5+galaxy0 + - description: 'Percolator: accurate peptide identification' + title: Percolator 3.5+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fpercolator%2Fpercolator%2F3.5%2Bgalaxy0 - - title: Pout2mzid 0.3.03 + - description: 'Pout2mzid: add Percolator scoring to mzIdentML' + title: Pout2mzid 0.3.03 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fpercolator%2Fpout2mzid%2F0.3.03 - - title: Create nested list 3.3 + - description: 'Create nested list: based on filenames and batch sizes' + title: Create nested list 3.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fpercolator%2Fbatched_set_list_creator%2F3.3 homepage: http://noble.gs.washington.edu/proj/percolator/ id: percolator @@ -13328,7 +14709,8 @@ description: This tool is used to search a FASTA sequence against a library of Pfam HMM. galaxy: - - title: PfamScan 1.6+galaxy0 + - description: 'PfamScan: search a FASTA sequence against a library of Pfam HMM' + title: PfamScan 1.6+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fpfamscan%2Fpfamscan%2F1.6%2Bgalaxy0 homepage: https://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ id: pfamscan @@ -13347,7 +14729,9 @@ description: Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. galaxy: - - title: pharokka 1.3.2+galaxy0 + - description: 'pharokka: Rapid standardised annotation tool for bacteriophage genomes + and metagenomes' + title: pharokka 1.3.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpharokka%2Fpharokka%2F1.3.2%2Bgalaxy0 homepage: https://github.com/gbouras13/pharokka id: pharokka @@ -13370,7 +14754,8 @@ bunya: '' description: '' galaxy: - - title: Phinch Visualisation 0.1 + - description: 'Phinch Visualisation: ' + title: Phinch Visualisation 0.1 url: https://usegalaxy.org.au/root?tool_id=interactive_tool_phinch homepage: '' id: phinch @@ -13441,9 +14826,11 @@ description: Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. galaxy: - - title: Phyloseq Biom Filtering 1.22.3.2 + - description: 'Phyloseq Biom Filtering: biom file filter' + title: Phyloseq Biom Filtering 1.22.3.2 url: https://usegalaxy.org.au/root?tool_id=testtoolshed.g2.bx.psu.edu%2Frepos%2Fsimon-gladman%2Fphyloseq_filter%2Fbiom_filter%2F1.22.3.2 - - title: Phyloseq Ordination Plot 1.22.3.2 + - description: 'Phyloseq Ordination Plot: ordination plotting' + title: Phyloseq Ordination Plot 1.22.3.2 url: https://usegalaxy.org.au/root?tool_id=testtoolshed.g2.bx.psu.edu%2Frepos%2Fsimon-gladman%2Fphyloseq_ordination_plot%2Fphyloseq_ordinate%2F1.22.3.2 homepage: http://bioconductor.org/packages/release/bioc/html/phyloseq.html id: phyloseq @@ -13466,7 +14853,8 @@ bunya: '' description: Phylogenetic estimation software using Maximum Likelihood galaxy: - - title: PhyML 3.3.20220408+galaxy0 + - description: 'PhyML: Phylogeny software based on the maximum-likelihood method' + title: PhyML 3.3.20220408+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fphyml%2Fphyml%2F3.3.20220408%2Bgalaxy0 homepage: https://www.atgc-montpellier.fr/phyml/ id: phyml @@ -13499,67 +14887,114 @@ (HTS) data in formats such as SAM/BAM/CRAM and VCF. Available as a standalone program or within the GATK4 program. galaxy: - - title: ReplaceSamHeader 2.18.2.1 + - description: 'ReplaceSamHeader: replace header in a SAM/BAM dataset' + title: ReplaceSamHeader 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_ReplaceSamHeader%2F2.18.2.1 - - title: FilterSamReads 2.18.2.1 + - description: 'FilterSamReads: include or exclude aligned and unaligned reads and + read lists' + title: FilterSamReads 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_FilterSamReads%2F2.18.2.1 - - title: CollectHsMetrics 2.18.2 + - description: 'CollectHsMetrics: compute metrics about datasets generated through + hybrid-selection (e.g. exome)' + title: CollectHsMetrics 2.18.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_CollectHsMetrics%2F2.18.2 - - title: RevertOriginalBaseQualitiesAndAddMateCigar 2.18.2.1 + - description: 'RevertOriginalBaseQualitiesAndAddMateCigar: revert the original + base qualities and add the mate cigar tag' + title: RevertOriginalBaseQualitiesAndAddMateCigar 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_RevertOriginalBaseQualitiesAndAddMateCigar%2F2.18.2.1 - - title: MergeBamAlignment 2.18.2.2 + - description: 'MergeBamAlignment: merge alignment data with additional info stored + in an unmapped BAM dataset' + title: MergeBamAlignment 2.18.2.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_MergeBamAlignment%2F2.18.2.2 - - title: AddOrReplaceReadGroups 2.18.2.1 + - description: 'AddOrReplaceReadGroups: add or replaces read group information' + title: AddOrReplaceReadGroups 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_AddOrReplaceReadGroups%2F2.18.2.1 - - title: MergeSamFiles 2.18.2.1 + - description: 'MergeSamFiles: merges multiple SAM/BAM datasets into one' + title: MergeSamFiles 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_MergeSamFiles%2F2.18.2.1 - - title: FixMateInformation 2.18.2.1 + - description: 'FixMateInformation: ensure that all mate-pair information is in + sync between each read and it''s mate pair' + title: FixMateInformation 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_FixMateInformation%2F2.18.2.1 - - title: ReorderSam 2.18.2.1 + - description: 'ReorderSam: reorder reads to match ordering in reference sequences' + title: ReorderSam 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_ReorderSam%2F2.18.2.1 - - title: CollectGcBiasMetrics 2.18.2.1 + - description: 'CollectGcBiasMetrics: charts the GC bias metrics' + title: CollectGcBiasMetrics 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_CollectGcBiasMetrics%2F2.18.2.1 - - title: EstimateLibraryComplexity 2.18.2.1 + - description: 'EstimateLibraryComplexity: assess sequence library complexity from + read sequences' + title: EstimateLibraryComplexity 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_EstimateLibraryComplexity%2F2.18.2.1 - - title: MarkDuplicatesWithMateCigar 2.18.2.3 + - description: 'MarkDuplicatesWithMateCigar: examine aligned records in BAM datasets + to locate duplicate molecules' + title: MarkDuplicatesWithMateCigar 2.18.2.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_MarkDuplicatesWithMateCigar%2F2.18.2.3 - - title: CollectBaseDistributionByCycle 2.18.2.2 + - description: 'CollectBaseDistributionByCycle: charts the nucleotide distribution + per cycle in a SAM or BAM dataset' + title: CollectBaseDistributionByCycle 2.18.2.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_CollectBaseDistributionByCycle%2F2.18.2.2 - - title: BedToIntervalList 2.18.2.1 + - description: 'BedToIntervalList: convert coordinate data into picard interval + list format' + title: BedToIntervalList 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_BedToIntervalList%2F2.18.2.1 - - title: CleanSam 2.18.2.1 + - description: 'CleanSam: perform SAM/BAM grooming' + title: CleanSam 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_CleanSam%2F2.18.2.1 - - title: SamToFastq 2.18.2.3 + - description: 'SamToFastq: extract reads and qualities from SAM/BAM dataset and + convert to fastq' + title: SamToFastq 2.18.2.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_SamToFastq%2F2.18.2.3 - - title: FastqToSam 2.18.2.2 + - description: 'FastqToSam: convert Fastq data into unaligned BAM' + title: FastqToSam 2.18.2.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_FastqToSam%2F2.18.2.2 - - title: MarkDuplicates 2.18.2.4 + - description: 'MarkDuplicates: examine aligned records in BAM datasets to locate + duplicate molecules' + title: MarkDuplicates 2.18.2.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_MarkDuplicates%2F2.18.2.4 - - title: MeanQualityByCycle 2.18.2.1 + - description: 'MeanQualityByCycle: chart distribution of base qualities' + title: MeanQualityByCycle 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_MeanQualityByCycle%2F2.18.2.1 - - title: NormalizeFasta 2.18.2.1 + - description: 'NormalizeFasta: normalize fasta datasets' + title: NormalizeFasta 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_NormalizeFasta%2F2.18.2.1 - - title: AddCommentsToBam 2.18.2.1 + - description: 'AddCommentsToBam: add comments to BAM dataset' + title: AddCommentsToBam 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_AddCommentsToBam%2F2.18.2.1 - - title: CollectInsertSizeMetrics 2.18.2.2 + - description: 'CollectInsertSizeMetrics: plots distribution of insert sizes' + title: CollectInsertSizeMetrics 2.18.2.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_CollectInsertSizeMetrics%2F2.18.2.2 - - title: QualityScoreDistribution 2.18.2.1 + - description: 'QualityScoreDistribution: chart quality score distribution' + title: QualityScoreDistribution 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_QualityScoreDistribution%2F2.18.2.1 - - title: SortSam 2.18.2.1 + - description: 'SortSam: sort SAM/BAM dataset' + title: SortSam 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_SortSam%2F2.18.2.1 - - title: RevertSam 2.18.2.1 + - description: 'RevertSam: revert SAM/BAM datasets to a previous state' + title: RevertSam 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_RevertSam%2F2.18.2.1 - - title: CollectWgsMetrics 2.18.2.1 + - description: 'CollectWgsMetrics: compute metrics for evaluating of whole genome + sequencing experiments' + title: CollectWgsMetrics 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_CollectWgsMetrics%2F2.18.2.1 - - title: CollectRnaSeqMetrics 2.18.2.2 + - description: 'CollectRnaSeqMetrics: collect metrics about the alignment of RNA + to various functional classes of loci in the genome' + title: CollectRnaSeqMetrics 2.18.2.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_CollectRnaSeqMetrics%2F2.18.2.2 - - title: ValidateSamFile 2.18.2.2 + - description: 'ValidateSamFile: assess validity of SAM/BAM dataset' + title: ValidateSamFile 2.18.2.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_ValidateSamFile%2F2.18.2.2 - - title: Picard Collect Sequencing Artifact Metrics 2.18.2.2 + - description: 'Picard Collect Sequencing Artifact Metrics: Collect metrics to quantify + single-base sequencing artifacts' + title: Picard Collect Sequencing Artifact Metrics 2.18.2.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_artifact_metrics%2F2.18.2.2 - - title: Downsample SAM/BAM 2.18.2.1 + - description: 'Downsample SAM/BAM: Downsample a file to retain a subset of the + reads' + title: Downsample SAM/BAM 2.18.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_DownsampleSam%2F2.18.2.1 - - title: Collect Alignment Summary Metrics 2.18.2.2 + - description: 'Collect Alignment Summary Metrics: writes a file containing summary + alignment metrics' + title: Collect Alignment Summary Metrics 2.18.2.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_CASM%2F2.18.2.2 homepage: https://github.com/broadinstitute/picard id: picard @@ -13582,17 +15017,27 @@ metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. galaxy: - - title: Categorize 1.1.1.0 + - description: 'Categorize: by collapsing hierarchical data to a specified functional + level' + title: Categorize 1.1.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust_categorize%2Fpicrust_categorize%2F1.1.1.0 - - title: Compare BIOM tables 1.1.1.1 + - description: 'Compare BIOM tables: Compare the accuracy of biom files (expected + and observed) either by observations (default) or by samples.' + title: Compare BIOM tables 1.1.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust_compare_biom%2Fpicrust_compare_biom%2F1.1.1.1 - - title: Format 1.1.1.0 + - description: 'Format: tree and trait tables' + title: Format 1.1.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust_format_tree_and_trait_table%2Fpicrust_format_tree_and_trait_table%2F1.1.1.0 - - title: Metagenome Contributions 1.1.1.0 + - description: 'Metagenome Contributions: of OTUs to user-specified functions' + title: Metagenome Contributions 1.1.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust_metagenome_contributions%2Fpicrust_metagenome_contributions%2F1.1.1.0 - - title: Normalize 1.1.1.1 + - description: 'Normalize: the relative abundance of each OTU by the predicted number + of 16S copies' + title: Normalize 1.1.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust_normalize_by_copy_number%2Fpicrust_normalize_by_copy_number%2F1.1.1.1 - - title: Predict Metagenome 1.1.1.0 + - description: 'Predict Metagenome: based on the abundance of OTUs and a functional + database' + title: Predict Metagenome 1.1.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust_predict_metagenomes%2Fpicrust_predict_metagenomes%2F1.1.1.0 homepage: http://picrust.github.io/picrust/ id: picrust @@ -13618,19 +15063,28 @@ of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. galaxy: - - title: PICRUSt2 Add descriptions 2.5.1+galaxy0 + - 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 - - title: PICRUSt2 Hidden state prediction (HSP) 2.5.1+galaxy0 + - 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 - - title: PICRUSt2 Metagenome prediction 2.5.1+galaxy0 + - 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 - - title: PICRUSt2 Pathway abundance inference 2.5.1+galaxy0 + - 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 Full pipeline 2.5.1+galaxy0 + - 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 - - title: PICRUSt2 Sequence placement 2.5.1+galaxy0 + - 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 - - title: PICRUSt2 Generation of shuffled predictions 2.5.1+galaxy0 + - 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 homepage: https://github.com/picrust/picrust2 id: picrust2 @@ -13653,7 +15107,8 @@ bunya: '' description: '' galaxy: - - title: Pileup-to-Interval 1.0.3 + - description: 'Pileup-to-Interval: condenses pileup format into ranges of bases' + title: Pileup-to-Interval 1.0.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpileup_interval%2Fpileup_interval%2F1.0.3 homepage: '' id: pileup_interval @@ -13670,7 +15125,8 @@ bunya: '' description: '' galaxy: - - title: Filter pileup 1.0.2 + - description: 'Filter pileup: on coverage and SNPs' + title: Filter pileup 1.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpileup_parser%2Fpileup_parser%2F1.0.2 homepage: '' id: pileup_parser @@ -13688,7 +15144,9 @@ description: Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. galaxy: - - title: pilon 1.20.1 + - description: 'pilon: An automated genome assembly improvement and variant detection + tool' + title: pilon 1.20.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpilon%2Fpilon%2F1.20.1 homepage: http://www.broadinstitute.org/software/pilon/ id: pilon @@ -13718,7 +15176,8 @@ analysis in a simple to use, transparent, accessible, reproducible, and user-friendly environment' galaxy: - - title: PIPE-T 1.0 + - description: 'PIPE-T: A tool for analyzing RTqPCR expression data' + title: PIPE-T 1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdavidecangelosi%2Fpipe_t%2Fpipe-t%2F1.0 homepage: https://github.com/igg-molecular-biology-lab/pipe-t id: pipe_t @@ -13741,7 +15200,8 @@ bunya: '' description: '' galaxy: - - title: PlasFlow 1.1.0+galaxy0 + - description: 'PlasFlow: Prediction of plasmid sequences in metagenomic contigs' + title: PlasFlow 1.1.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fplasflow%2FPlasFlow%2F1.1.0%2Bgalaxy0 homepage: '' id: PlasFlow @@ -13816,11 +15276,15 @@ bunya: '' description: '' galaxy: - - title: Plot confusion matrix, precision, recall and ROC and AUC curves 0.2 + - 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 0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fplotly_ml_performance_plots%2Fplotly_ml_performance_plots%2F0.2 - - title: Parallel Coordinates Plot 0.2 + - 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 - - title: Plot actual vs predicted curves and residual plots 0.1 + - description: 'Plot actual vs predicted curves and residual plots: of tabular data' + title: Plot actual vs predicted curves and residual plots 0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fplotly_regression_performance_plots%2Fplotly_regression_performance_plots%2F0.1 homepage: '' id: plotly @@ -13856,7 +15320,8 @@ bunya: '' description: '' galaxy: - - title: Poisson two-sample test 1.0.0 + - description: 'Poisson two-sample test: ' + title: Poisson two-sample test 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpoisson2test%2Fpoisson2test%2F1.0.0 homepage: '' id: poisson2test @@ -13873,7 +15338,8 @@ bunya: '' description: '' galaxy: - - title: Porechop 0.2.4+galaxy0 + - description: 'Porechop: adapter trimmer for Oxford Nanopore reads' + title: Porechop 0.2.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fporechop%2Fporechop%2F0.2.4%2Bgalaxy0 homepage: '' id: porechop @@ -13891,31 +15357,45 @@ description: Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. galaxy: - - title: Extract nanopore events 0.6.1a1.1 + - description: 'Extract nanopore events: from a set of sequencing reads' + title: Extract nanopore events 0.6.1a1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fporetools_events%2Fporetools_events%2F0.6.1a1.1 - - title: Extract reads 0.6.1a1.0 + - description: 'Extract reads: in FASTA or FASTQ format from nanopore files' + title: Extract reads 0.6.1a1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fporetools_extract%2Fporetools_extract%2F0.6.1a1.0 - - title: Generate histogram 0.6.1a1.1 + - description: 'Generate histogram: of nanopore read lengths' + title: Generate histogram 0.6.1a1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fporetools_hist%2Fporetools_hist%2F0.6.1a1.1 - - title: Show nucleotide 0.6.1a1.0 + - description: 'Show nucleotide: distribution in nanopore sequencing reads' + title: Show nucleotide 0.6.1a1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fporetools_nucdist%2Fporetools_nucdist%2F0.6.1a1.0 - - title: Plot performance 0.6.1a1.1 + - description: 'Plot performance: per cell in nanopore reads' + title: Plot performance 0.6.1a1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fporetools_occupancy%2Fporetools_occupancy%2F0.6.1a1.1 - - title: Show quality 0.6.1a1.0 + - description: 'Show quality: score distribution in nanopore sequencing reads' + title: Show quality 0.6.1a1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fporetools_qualdist%2Fporetools_qualdist%2F0.6.1a1.0 - - title: Generate box-whisker 0.6.1a1.1 + - description: 'Generate box-whisker: plot of quality score distribution over positions + in nanopore reads' + title: Generate box-whisker 0.6.1a1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fporetools_qualpos%2Fporetools_qualpos%2F0.6.1a1.1 - - title: Plot signals 0.6.1a1.1 + - description: 'Plot signals: for nanopore reads' + title: Plot signals 0.6.1a1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fporetools_squiggle%2Fporetools_squiggle%2F0.6.1a1.1 - - title: Read length statistics 0.6.1a1.0 + - description: 'Read length statistics: from a set of FAST5 files' + title: Read length statistics 0.6.1a1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fporetools_stats%2Fporetools_stats%2F0.6.1a1.0 - - title: Extract FASTQ 0.6.1a1.0 + - description: 'Extract FASTQ: in tabular format from a set of FAST5 files' + title: Extract FASTQ 0.6.1a1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fporetools_tabular%2Fporetools_tabular%2F0.6.1a1.0 - - title: Extract time 0.6.1a1.0 + - description: 'Extract time: and channel information from a set of FAST5 files' + title: Extract time 0.6.1a1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fporetools_times%2Fporetools_times%2F0.6.1a1.0 - - title: Get longest read 0.6.1a1.0 + - description: 'Get longest read: from a set of FAST5 files.' + title: Get longest read 0.6.1a1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fporetools_winner%2Fporetools_winner%2F0.6.1a1.0 - - title: "Collector\u2019s curve 0.6.1a1.1" + - description: "Collector\u2019s curve: of sequencing yield over time" + title: "Collector\u2019s curve 0.6.1a1.1" url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fporetools_yield_plot%2Fporetools_yield_plot%2F0.6.1a1.1 homepage: https://github.com/arq5x/poretools id: poretools @@ -13956,7 +15436,8 @@ bunya: '' description: '' galaxy: - - title: PretextMap 0.1.9+galaxy1 + - description: 'PretextMap: converts SAM or BAM files into genome contact maps' + title: PretextMap 0.1.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpretext_map%2Fpretext_map%2F0.1.9%2Bgalaxy1 homepage: '' id: pretext_map @@ -13973,7 +15454,8 @@ bunya: '' description: Pretext is an OpenGL-powered pretext contact map viewer. galaxy: - - title: Pretext Snapshot 0.0.3+galaxy2 + - description: 'Pretext Snapshot: image generator for Pretext contact maps' + title: Pretext Snapshot 0.0.3+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpretext_snapshot%2Fpretext_snapshot%2F0.0.3%2Bgalaxy2 homepage: https://github.com/wtsi-hpag/PretextView id: pretextview @@ -14040,7 +15522,8 @@ implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) and generates the peak table. galaxy: - - title: proFIA 3.1.0 + - description: 'proFIA: Preprocessing of FIA-HRMS data' + title: proFIA 3.1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fethevenot%2Fprofia%2Fprofia%2F3.1.0 homepage: http://bioconductor.org/packages/release/bioc/html/proFIA.html id: profia @@ -14079,7 +15562,8 @@ description: Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. galaxy: - - title: Prokka 1.14.6+galaxy1 + - description: 'Prokka: Prokaryotic genome annotation' + title: Prokka 1.14.6+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fcrs4%2Fprokka%2Fprokka%2F1.14.6%2Bgalaxy1 homepage: https://github.com/tseemann/prokka id: prokka @@ -14124,7 +15608,8 @@ bunya: '' description: '' galaxy: - - title: proportional venn 0.5 + - description: 'proportional venn: from 2-3 sets' + title: proportional venn 0.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fidot%2Fprop_venn%2Fprop_venn%2F0.5 homepage: '' id: prop_venn @@ -14165,7 +15650,9 @@ recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences' galaxy: - - title: Purge overlaps 1.2.6+galaxy0 + - description: 'Purge overlaps: and haplotigs in an assembly based on read depth + (purge_dups)' + title: Purge overlaps 1.2.6+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpurge_dups%2Fpurge_dups%2F1.2.6%2Bgalaxy0 homepage: https://github.com/dfguan/purge_dups id: purge_dups @@ -14204,7 +15691,8 @@ description: PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. galaxy: - - title: Pycoqc 2.5.2+galaxy0 + - description: 'Pycoqc: quality control for Nanopore sequencing data' + title: Pycoqc 2.5.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpycoqc%2Fpycoqc%2F2.5.2%2Bgalaxy0 homepage: https://a-slide.github.io/pycoQC/ id: pycoqc @@ -14231,7 +15719,8 @@ pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.' galaxy: - - title: pyGenomeTracks 3.8+galaxy2 + - description: 'pyGenomeTracks: plot genomic data tracks' + title: pyGenomeTracks 3.8+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpygenometracks%2FpygenomeTracks%2F3.8%2Bgalaxy2 homepage: https://github.com/deeptools/pyGenomeTracks id: pygenometracks @@ -14253,13 +15742,18 @@ bunya: '' description: '' galaxy: - - title: PyProphet merge 2.1.4.0 + - description: 'PyProphet merge: Merge multiple osw files' + title: PyProphet merge 2.1.4.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fpyprophet_merge%2Fpyprophet_merge%2F2.1.4.0 - - title: PyProphet peptide 2.1.4.0 + - description: 'PyProphet peptide: Peptide error-rate estimation' + title: PyProphet peptide 2.1.4.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fpyprophet_peptide%2Fpyprophet_peptide%2F2.1.4.0 - - title: PyProphet protein 2.1.4.0 + - description: 'PyProphet protein: Protein error-rate estimation' + title: PyProphet protein 2.1.4.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fpyprophet_protein%2Fpyprophet_protein%2F2.1.4.0 - - title: PyProphet score 2.1.4.2 + - description: 'PyProphet score: Error-rate estimation for MS1, MS2 and transition-level + data' + title: PyProphet score 2.1.4.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fpyprophet_score%2Fpyprophet_score%2F2.1.4.2 homepage: '' id: pyprophet @@ -14366,327 +15860,584 @@ description: "QIIME 2\u2122 is a next-generation microbiome bioinformatics platform\ \ that is extensible, free, open source, and community developed." galaxy: - - title: qiime2 tools import 2023.5.0+dist.h193f7cc9.3 + - description: 'qiime2 tools import: Import data into a QIIME 2 artifact' + title: qiime2 tools import 2023.5.0+dist.h193f7cc9.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2_core__tools__import%2Fqiime2_core__tools__import%2F2023.5.0%2Bdist.h193f7cc9.3 - - title: qiime2 alignment mafft-add 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 alignment mafft-add: Add sequences to multiple sequence alignment + with MAFFT.' + title: qiime2 alignment mafft-add 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__alignment__mafft_add%2Fqiime2__alignment__mafft_add%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 alignment mafft 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 alignment mafft: De novo multiple sequence alignment with + MAFFT' + title: qiime2 alignment mafft 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__alignment__mafft%2Fqiime2__alignment__mafft%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 alignment mask 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 alignment mask: Positional conservation and gap filtering.' + title: qiime2 alignment mask 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__alignment__mask%2Fqiime2__alignment__mask%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 composition add-pseudocount 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 composition add-pseudocount: Add pseudocount to table.' + title: qiime2 composition add-pseudocount 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__composition__add_pseudocount%2Fqiime2__composition__add_pseudocount%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 composition ancom 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 composition ancom: Apply ANCOM to identify features that + differ in abundance.' + title: qiime2 composition ancom 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__composition__ancom%2Fqiime2__composition__ancom%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 composition tabulate 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 composition tabulate: View tabular output from ANCOM-BC.' + title: qiime2 composition tabulate 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__composition__tabulate%2Fqiime2__composition__tabulate%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 tools export 2023.5.0+dist.h193f7cc9.2 + - description: 'qiime2 tools export: Export data from a QIIME 2 artifact' + title: qiime2 tools export 2023.5.0+dist.h193f7cc9.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2_core__tools__export%2Fqiime2_core__tools__export%2F2023.5.0%2Bdist.h193f7cc9.2 - - title: qiime2 cutadapt demux-paired 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 cutadapt demux-paired: Demultiplex paired-end sequence data + with barcodes in-sequence.' + title: qiime2 cutadapt demux-paired 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__cutadapt__demux_paired%2Fqiime2__cutadapt__demux_paired%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 cutadapt demux-single 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 cutadapt demux-single: Demultiplex single-end sequence data + with barcodes in-sequence.' + title: qiime2 cutadapt demux-single 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__cutadapt__demux_single%2Fqiime2__cutadapt__demux_single%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 cutadapt trim-paired 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 cutadapt trim-paired: Find and remove adapters in demultiplexed + paired-end sequences.' + title: qiime2 cutadapt trim-paired 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__cutadapt__trim_paired%2Fqiime2__cutadapt__trim_paired%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 cutadapt trim-single 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 cutadapt trim-single: Find and remove adapters in demultiplexed + single-end sequences.' + title: qiime2 cutadapt trim-single 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__cutadapt__trim_single%2Fqiime2__cutadapt__trim_single%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 dada2 denoise-ccs 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 dada2 denoise-ccs: Denoise and dereplicate single-end Pacbio + CCS' + title: qiime2 dada2 denoise-ccs 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__dada2__denoise_ccs%2Fqiime2__dada2__denoise_ccs%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 dada2 denoise-paired 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 dada2 denoise-paired: Denoise and dereplicate paired-end + sequences' + title: qiime2 dada2 denoise-paired 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__dada2__denoise_paired%2Fqiime2__dada2__denoise_paired%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 dada2 denoise-pyro 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 dada2 denoise-pyro: Denoise and dereplicate single-end pyrosequences' + title: qiime2 dada2 denoise-pyro 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__dada2__denoise_pyro%2Fqiime2__dada2__denoise_pyro%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 dada2 denoise-single 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 dada2 denoise-single: Denoise and dereplicate single-end + sequences' + title: qiime2 dada2 denoise-single 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__dada2__denoise_single%2Fqiime2__dada2__denoise_single%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 deblur denoise-16S 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 deblur denoise-16S: Deblur sequences using a 16S positive + filter.' + title: qiime2 deblur denoise-16S 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__deblur__denoise_16s%2Fqiime2__deblur__denoise_16S%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 deblur denoise-other 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 deblur denoise-other: Deblur sequences using a user-specified + positive filter.' + title: qiime2 deblur denoise-other 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__deblur__denoise_other%2Fqiime2__deblur__denoise_other%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 deblur visualize-stats 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 deblur visualize-stats: Visualize Deblur stats per sample.' + title: qiime2 deblur visualize-stats 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__deblur__visualize_stats%2Fqiime2__deblur__visualize_stats%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 demux emp-paired 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 demux emp-paired: Demultiplex paired-end sequence data generated + with the EMP protocol.' + title: qiime2 demux emp-paired 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__demux__emp_paired%2Fqiime2__demux__emp_paired%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 demux emp-single 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 demux emp-single: Demultiplex sequence data generated with + the EMP protocol.' + title: qiime2 demux emp-single 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__demux__emp_single%2Fqiime2__demux__emp_single%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 demux filter-samples 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 demux filter-samples: Filter samples out of demultiplexed + data.' + title: qiime2 demux filter-samples 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__demux__filter_samples%2Fqiime2__demux__filter_samples%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 demux subsample-paired 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 demux subsample-paired: Subsample paired-end sequences without + replacement.' + title: qiime2 demux subsample-paired 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__demux__subsample_paired%2Fqiime2__demux__subsample_paired%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 demux subsample-single 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 demux subsample-single: Subsample single-end sequences without + replacement.' + title: qiime2 demux subsample-single 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__demux__subsample_single%2Fqiime2__demux__subsample_single%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 demux summarize 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 demux summarize: Summarize counts per sample.' + title: qiime2 demux summarize 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__demux__summarize%2Fqiime2__demux__summarize%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity adonis 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity adonis: adonis PERMANOVA test for beta group significance' + title: qiime2 diversity adonis 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__adonis%2Fqiime2__diversity__adonis%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity alpha-correlation 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity alpha-correlation: Alpha diversity correlation' + title: qiime2 diversity alpha-correlation 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_correlation%2Fqiime2__diversity__alpha_correlation%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity alpha-group-significance 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity alpha-group-significance: Alpha diversity comparisons' + title: qiime2 diversity alpha-group-significance 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_group_significance%2Fqiime2__diversity__alpha_group_significance%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity alpha 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity alpha: Alpha diversity' + title: qiime2 diversity alpha 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha%2Fqiime2__diversity__alpha%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity alpha-phylogenetic 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity alpha-phylogenetic: Alpha diversity (phylogenetic)' + title: qiime2 diversity alpha-phylogenetic 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_phylogenetic%2Fqiime2__diversity__alpha_phylogenetic%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity alpha-rarefaction 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity alpha-rarefaction: Alpha rarefaction curves' + title: qiime2 diversity alpha-rarefaction 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_rarefaction%2Fqiime2__diversity__alpha_rarefaction%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity beta-correlation 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity beta-correlation: Beta diversity correlation' + title: qiime2 diversity beta-correlation 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__beta_correlation%2Fqiime2__diversity__beta_correlation%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity beta-group-significance 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity beta-group-significance: Beta diversity group significance' + title: qiime2 diversity beta-group-significance 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__beta_group_significance%2Fqiime2__diversity__beta_group_significance%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity beta 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity beta: Beta diversity' + title: qiime2 diversity beta 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__beta%2Fqiime2__diversity__beta%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity beta-phylogenetic 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity beta-phylogenetic: Beta diversity (phylogenetic)' + title: qiime2 diversity beta-phylogenetic 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__beta_phylogenetic%2Fqiime2__diversity__beta_phylogenetic%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity beta-rarefaction 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity beta-rarefaction: Beta diversity rarefaction' + title: qiime2 diversity beta-rarefaction 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__beta_rarefaction%2Fqiime2__diversity__beta_rarefaction%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity bioenv 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity bioenv: bioenv' + title: qiime2 diversity bioenv 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__bioenv%2Fqiime2__diversity__bioenv%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity core-metrics 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity core-metrics: Core diversity metrics (non-phylogenetic)' + title: qiime2 diversity core-metrics 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__core_metrics%2Fqiime2__diversity__core_metrics%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity core-metrics-phylogenetic 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity core-metrics-phylogenetic: Core diversity metrics + (phylogenetic and non-phylogenetic)' + title: qiime2 diversity core-metrics-phylogenetic 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__core_metrics_phylogenetic%2Fqiime2__diversity__core_metrics_phylogenetic%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity filter-distance-matrix 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity filter-distance-matrix: Filter samples from a distance + matrix.' + title: qiime2 diversity filter-distance-matrix 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__filter_distance_matrix%2Fqiime2__diversity__filter_distance_matrix%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity-lib alpha-passthrough 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity-lib alpha-passthrough: Alpha Passthrough (non-phylogenetic)' + title: qiime2 diversity-lib alpha-passthrough 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity_lib__alpha_passthrough%2Fqiime2__diversity_lib__alpha_passthrough%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity-lib beta-passthrough 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity-lib beta-passthrough: Beta Passthrough (non-phylogenetic)' + title: qiime2 diversity-lib beta-passthrough 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity_lib__beta_passthrough%2Fqiime2__diversity_lib__beta_passthrough%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity-lib beta-phylogenetic-meta-passthrough 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity-lib beta-phylogenetic-meta-passthrough: Beta Phylogenetic + Meta Passthrough' + title: qiime2 diversity-lib beta-phylogenetic-meta-passthrough 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity_lib__beta_phylogenetic_meta_passthrough%2Fqiime2__diversity_lib__beta_phylogenetic_meta_passthrough%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity-lib beta-phylogenetic-passthrough 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity-lib beta-phylogenetic-passthrough: Beta Phylogenetic + Passthrough' + title: qiime2 diversity-lib beta-phylogenetic-passthrough 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity_lib__beta_phylogenetic_passthrough%2Fqiime2__diversity_lib__beta_phylogenetic_passthrough%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity-lib faith-pd 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity-lib faith-pd: Faith''s Phylogenetic Diversity' + title: qiime2 diversity-lib faith-pd 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity_lib__faith_pd%2Fqiime2__diversity_lib__faith_pd%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity-lib jaccard 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity-lib jaccard: Jaccard Distance' + title: qiime2 diversity-lib jaccard 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity_lib__jaccard%2Fqiime2__diversity_lib__jaccard%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity-lib observed-features 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity-lib observed-features: Observed Features' + title: qiime2 diversity-lib observed-features 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity_lib__observed_features%2Fqiime2__diversity_lib__observed_features%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity-lib pielou-evenness 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity-lib pielou-evenness: Pielou''s Evenness' + title: qiime2 diversity-lib pielou-evenness 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity_lib__pielou_evenness%2Fqiime2__diversity_lib__pielou_evenness%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity-lib shannon-entropy 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity-lib shannon-entropy: Shannon''s Entropy' + title: qiime2 diversity-lib shannon-entropy 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity_lib__shannon_entropy%2Fqiime2__diversity_lib__shannon_entropy%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity-lib unweighted-unifrac 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity-lib unweighted-unifrac: Unweighted Unifrac' + title: qiime2 diversity-lib unweighted-unifrac 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity_lib__unweighted_unifrac%2Fqiime2__diversity_lib__unweighted_unifrac%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity-lib weighted-unifrac 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity-lib weighted-unifrac: Weighted Unifrac' + title: qiime2 diversity-lib weighted-unifrac 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity_lib__weighted_unifrac%2Fqiime2__diversity_lib__weighted_unifrac%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity mantel 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity mantel: Apply the Mantel test to two distance matrices' + title: qiime2 diversity mantel 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__mantel%2Fqiime2__diversity__mantel%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity pcoa-biplot 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity pcoa-biplot: Principal Coordinate Analysis Biplot' + title: qiime2 diversity pcoa-biplot 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__pcoa_biplot%2Fqiime2__diversity__pcoa_biplot%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity pcoa 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity pcoa: Principal Coordinate Analysis' + title: qiime2 diversity pcoa 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__pcoa%2Fqiime2__diversity__pcoa%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity procrustes-analysis 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity procrustes-analysis: Procrustes Analysis' + title: qiime2 diversity procrustes-analysis 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__procrustes_analysis%2Fqiime2__diversity__procrustes_analysis%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity tsne 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity tsne: t-distributed stochastic neighbor embedding' + title: qiime2 diversity tsne 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__tsne%2Fqiime2__diversity__tsne%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity umap 2023.5.1+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity umap: Uniform Manifold Approximation and Projection' + title: qiime2 diversity umap 2023.5.1+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__umap%2Fqiime2__diversity__umap%2F2023.5.1%2Bq2galaxy.2023.5.0.2 - - title: qiime2 emperor biplot 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 emperor biplot: Visualize and Interact with Principal Coordinates + Analysis Biplot' + title: qiime2 emperor biplot 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__emperor__biplot%2Fqiime2__emperor__biplot%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 emperor plot 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 emperor plot: Visualize and Interact with Principal Coordinates + Analysis Plots' + title: qiime2 emperor plot 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__emperor__plot%2Fqiime2__emperor__plot%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 emperor procrustes-plot 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 emperor procrustes-plot: Visualize and Interact with a procrustes + plot' + title: qiime2 emperor procrustes-plot 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__emperor__procrustes_plot%2Fqiime2__emperor__procrustes_plot%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-classifier blast 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-classifier blast: BLAST+ local alignment search.' + title: qiime2 feature-classifier blast 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_classifier__blast%2Fqiime2__feature_classifier__blast%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-classifier classify-consensus-blast 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-classifier classify-consensus-blast: BLAST+ consensus + taxonomy classifier' + title: qiime2 feature-classifier classify-consensus-blast 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_classifier__classify_consensus_blast%2Fqiime2__feature_classifier__classify_consensus_blast%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-classifier classify-consensus-vsearch 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-classifier classify-consensus-vsearch: VSEARCH-based + consensus taxonomy classifier' + title: qiime2 feature-classifier classify-consensus-vsearch 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_classifier__classify_consensus_vsearch%2Fqiime2__feature_classifier__classify_consensus_vsearch%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-classifier classify-hybrid-vsearch-sklearn 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-classifier classify-hybrid-vsearch-sklearn: ALPHA + Hybrid classifier: VSEARCH exact match + sklearn classifier' + title: qiime2 feature-classifier classify-hybrid-vsearch-sklearn 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_classifier__classify_hybrid_vsearch_sklearn%2Fqiime2__feature_classifier__classify_hybrid_vsearch_sklearn%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-classifier classify-sklearn 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-classifier classify-sklearn: Pre-fitted sklearn-based + taxonomy classifier' + title: qiime2 feature-classifier classify-sklearn 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_classifier__classify_sklearn%2Fqiime2__feature_classifier__classify_sklearn%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-classifier extract-reads 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-classifier extract-reads: Extract reads from reference + sequences.' + title: qiime2 feature-classifier extract-reads 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_classifier__extract_reads%2Fqiime2__feature_classifier__extract_reads%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-classifier find-consensus-annotation 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-classifier find-consensus-annotation: Find consensus + among multiple annotations.' + title: qiime2 feature-classifier find-consensus-annotation 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_classifier__find_consensus_annotation%2Fqiime2__feature_classifier__find_consensus_annotation%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-classifier fit-classifier-naive-bayes 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-classifier fit-classifier-naive-bayes: Train the + naive_bayes classifier' + title: qiime2 feature-classifier fit-classifier-naive-bayes 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_classifier__fit_classifier_naive_bayes%2Fqiime2__feature_classifier__fit_classifier_naive_bayes%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-classifier fit-classifier-sklearn 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-classifier fit-classifier-sklearn: Train an almost + arbitrary scikit-learn classifier' + title: qiime2 feature-classifier fit-classifier-sklearn 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_classifier__fit_classifier_sklearn%2Fqiime2__feature_classifier__fit_classifier_sklearn%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-classifier vsearch-global 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-classifier vsearch-global: VSEARCH global alignment + search' + title: qiime2 feature-classifier vsearch-global 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_classifier__vsearch_global%2Fqiime2__feature_classifier__vsearch_global%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-table core-features 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-table core-features: Identify core features in table' + title: qiime2 feature-table core-features 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__core_features%2Fqiime2__feature_table__core_features%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-table filter-features-conditionally 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-table filter-features-conditionally: Filter features + from a table based on abundance and prevalence' + title: qiime2 feature-table filter-features-conditionally 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__filter_features_conditionally%2Fqiime2__feature_table__filter_features_conditionally%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-table filter-samples 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-table filter-samples: Filter samples from table' + title: qiime2 feature-table filter-samples 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__filter_samples%2Fqiime2__feature_table__filter_samples%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-table filter-seqs 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-table filter-seqs: Filter features from sequences' + title: qiime2 feature-table filter-seqs 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__filter_seqs%2Fqiime2__feature_table__filter_seqs%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-table group 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-table group: Group samples or features by a metadata + column' + title: qiime2 feature-table group 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__group%2Fqiime2__feature_table__group%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-table heatmap 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-table heatmap: Generate a heatmap representation + of a feature table' + title: qiime2 feature-table heatmap 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__heatmap%2Fqiime2__feature_table__heatmap%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-table merge 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-table merge: Combine multiple tables' + title: qiime2 feature-table merge 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__merge%2Fqiime2__feature_table__merge%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-table merge-seqs 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-table merge-seqs: Combine collections of feature + sequences' + title: qiime2 feature-table merge-seqs 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__merge_seqs%2Fqiime2__feature_table__merge_seqs%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-table merge-taxa 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-table merge-taxa: Combine collections of feature + taxonomies' + title: qiime2 feature-table merge-taxa 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__merge_taxa%2Fqiime2__feature_table__merge_taxa%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-table presence-absence 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-table presence-absence: Convert to presence/absence' + title: qiime2 feature-table presence-absence 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__presence_absence%2Fqiime2__feature_table__presence_absence%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-table rarefy 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-table rarefy: Rarefy table' + title: qiime2 feature-table rarefy 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__rarefy%2Fqiime2__feature_table__rarefy%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-table relative-frequency 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-table relative-frequency: Convert to relative frequencies' + title: qiime2 feature-table relative-frequency 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__relative_frequency%2Fqiime2__feature_table__relative_frequency%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-table rename-ids 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-table rename-ids: Renames sample or feature ids in + a table' + title: qiime2 feature-table rename-ids 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__rename_ids%2Fqiime2__feature_table__rename_ids%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-table subsample 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-table subsample: Subsample table' + title: qiime2 feature-table subsample 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__subsample%2Fqiime2__feature_table__subsample%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-table summarize 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-table summarize: Summarize table' + title: qiime2 feature-table summarize 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__summarize%2Fqiime2__feature_table__summarize%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-table tabulate-seqs 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-table tabulate-seqs: View sequence associated with + each feature' + title: qiime2 feature-table tabulate-seqs 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__tabulate_seqs%2Fqiime2__feature_table__tabulate_seqs%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-table transpose 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-table transpose: Transpose a feature table.' + title: qiime2 feature-table transpose 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__transpose%2Fqiime2__feature_table__transpose%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 fragment-insertion classify-otus-experimental 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 fragment-insertion classify-otus-experimental: Experimental: + Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.' + title: qiime2 fragment-insertion classify-otus-experimental 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__fragment_insertion__classify_otus_experimental%2Fqiime2__fragment_insertion__classify_otus_experimental%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 fragment-insertion filter-features 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 fragment-insertion filter-features: Filter fragments in tree + from table.' + title: qiime2 fragment-insertion filter-features 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__fragment_insertion__filter_features%2Fqiime2__fragment_insertion__filter_features%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 fragment-insertion sepp 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 fragment-insertion sepp: Insert fragment sequences using + SEPP into reference phylogenies.' + title: qiime2 fragment-insertion sepp 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__fragment_insertion__sepp%2Fqiime2__fragment_insertion__sepp%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 gneiss assign-ids 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 gneiss assign-ids: Assigns ids on internal nodes in the tree, + and makes sure that they are consistent with the table columns.' + title: qiime2 gneiss assign-ids 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__gneiss__assign_ids%2Fqiime2__gneiss__assign_ids%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 gneiss correlation-clustering 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 gneiss correlation-clustering: Hierarchical clustering using + feature correlation.' + title: qiime2 gneiss correlation-clustering 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__gneiss__correlation_clustering%2Fqiime2__gneiss__correlation_clustering%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 gneiss dendrogram-heatmap 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 gneiss dendrogram-heatmap: Dendrogram heatmap.' + title: qiime2 gneiss dendrogram-heatmap 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__gneiss__dendrogram_heatmap%2Fqiime2__gneiss__dendrogram_heatmap%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 gneiss gradient-clustering 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 gneiss gradient-clustering: Hierarchical clustering using + gradient information.' + title: qiime2 gneiss gradient-clustering 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__gneiss__gradient_clustering%2Fqiime2__gneiss__gradient_clustering%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 gneiss ilr-hierarchical 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 gneiss ilr-hierarchical: Isometric Log-ratio Transform applied + to a hierarchical clustering' + title: qiime2 gneiss ilr-hierarchical 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__gneiss__ilr_hierarchical%2Fqiime2__gneiss__ilr_hierarchical%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 gneiss ilr-phylogenetic-differential 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 gneiss ilr-phylogenetic-differential: Differentially abundant + Phylogenetic Log Ratios.' + title: qiime2 gneiss ilr-phylogenetic-differential 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__gneiss__ilr_phylogenetic_differential%2Fqiime2__gneiss__ilr_phylogenetic_differential%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 gneiss ilr-phylogenetic 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 gneiss ilr-phylogenetic: Isometric Log-ratio Transform applied + to a phylogenetic tree' + title: qiime2 gneiss ilr-phylogenetic 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__gneiss__ilr_phylogenetic%2Fqiime2__gneiss__ilr_phylogenetic%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 gneiss ilr-phylogenetic-ordination 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 gneiss ilr-phylogenetic-ordination: Ordination through a + phylogenetic Isometric Log Ratio transform.' + title: qiime2 gneiss ilr-phylogenetic-ordination 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__gneiss__ilr_phylogenetic_ordination%2Fqiime2__gneiss__ilr_phylogenetic_ordination%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 longitudinal anova 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 longitudinal anova: ANOVA test' + title: qiime2 longitudinal anova 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__longitudinal__anova%2Fqiime2__longitudinal__anova%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 longitudinal feature-volatility 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 longitudinal feature-volatility: Feature volatility analysis' + title: qiime2 longitudinal feature-volatility 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__longitudinal__feature_volatility%2Fqiime2__longitudinal__feature_volatility%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 longitudinal first-differences 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 longitudinal first-differences: Compute first differences + or difference from baseline between sequential states' + title: qiime2 longitudinal first-differences 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__longitudinal__first_differences%2Fqiime2__longitudinal__first_differences%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 longitudinal first-distances 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 longitudinal first-distances: Compute first distances or + distance from baseline between sequential states' + title: qiime2 longitudinal first-distances 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__longitudinal__first_distances%2Fqiime2__longitudinal__first_distances%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 longitudinal linear-mixed-effects 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 longitudinal linear-mixed-effects: Linear mixed effects modeling' + title: qiime2 longitudinal linear-mixed-effects 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__longitudinal__linear_mixed_effects%2Fqiime2__longitudinal__linear_mixed_effects%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 longitudinal maturity-index 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 longitudinal maturity-index: Microbial maturity index prediction.' + title: qiime2 longitudinal maturity-index 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__longitudinal__maturity_index%2Fqiime2__longitudinal__maturity_index%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 longitudinal nmit 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 longitudinal nmit: Nonparametric microbial interdependence + test' + title: qiime2 longitudinal nmit 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__longitudinal__nmit%2Fqiime2__longitudinal__nmit%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 longitudinal pairwise-differences 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 longitudinal pairwise-differences: Paired difference testing + and boxplots' + title: qiime2 longitudinal pairwise-differences 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__longitudinal__pairwise_differences%2Fqiime2__longitudinal__pairwise_differences%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 longitudinal pairwise-distances 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 longitudinal pairwise-distances: Paired pairwise distance + testing and boxplots' + title: qiime2 longitudinal pairwise-distances 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__longitudinal__pairwise_distances%2Fqiime2__longitudinal__pairwise_distances%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 longitudinal plot-feature-volatility 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 longitudinal plot-feature-volatility: Plot longitudinal feature + volatility and importances' + title: qiime2 longitudinal plot-feature-volatility 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__longitudinal__plot_feature_volatility%2Fqiime2__longitudinal__plot_feature_volatility%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 longitudinal volatility 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 longitudinal volatility: Generate interactive volatility + plot' + title: qiime2 longitudinal volatility 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__longitudinal__volatility%2Fqiime2__longitudinal__volatility%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 metadata distance-matrix 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 metadata distance-matrix: Create a distance matrix from a + numeric Metadata column' + title: qiime2 metadata distance-matrix 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__metadata__distance_matrix%2Fqiime2__metadata__distance_matrix%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 metadata shuffle-groups 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 metadata shuffle-groups: Shuffle values in a categorical + sample metadata column.' + title: qiime2 metadata shuffle-groups 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__metadata__shuffle_groups%2Fqiime2__metadata__shuffle_groups%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 metadata tabulate 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 metadata tabulate: Interactively explore Metadata in an HTML + table' + title: qiime2 metadata tabulate 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__metadata__tabulate%2Fqiime2__metadata__tabulate%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 phylogeny align-to-tree-mafft-fasttree 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 phylogeny align-to-tree-mafft-fasttree: Build a phylogenetic + tree using fasttree and mafft alignment' + title: qiime2 phylogeny align-to-tree-mafft-fasttree 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__phylogeny__align_to_tree_mafft_fasttree%2Fqiime2__phylogeny__align_to_tree_mafft_fasttree%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 phylogeny align-to-tree-mafft-iqtree 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 phylogeny align-to-tree-mafft-iqtree: Build a phylogenetic + tree using iqtree and mafft alignment.' + title: qiime2 phylogeny align-to-tree-mafft-iqtree 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__phylogeny__align_to_tree_mafft_iqtree%2Fqiime2__phylogeny__align_to_tree_mafft_iqtree%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 phylogeny align-to-tree-mafft-raxml 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 phylogeny align-to-tree-mafft-raxml: Build a phylogenetic + tree using raxml and mafft alignment.' + title: qiime2 phylogeny align-to-tree-mafft-raxml 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__phylogeny__align_to_tree_mafft_raxml%2Fqiime2__phylogeny__align_to_tree_mafft_raxml%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 phylogeny fasttree 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 phylogeny fasttree: Construct a phylogenetic tree with FastTree.' + title: qiime2 phylogeny fasttree 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__phylogeny__fasttree%2Fqiime2__phylogeny__fasttree%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 phylogeny filter-table 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 phylogeny filter-table: Remove features from table if they''re + not present in tree.' + title: qiime2 phylogeny filter-table 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__phylogeny__filter_table%2Fqiime2__phylogeny__filter_table%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 phylogeny filter-tree 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 phylogeny filter-tree: Remove features from tree based on + metadata' + title: qiime2 phylogeny filter-tree 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__phylogeny__filter_tree%2Fqiime2__phylogeny__filter_tree%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 phylogeny iqtree 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 phylogeny iqtree: Construct a phylogenetic tree with IQ-TREE.' + title: qiime2 phylogeny iqtree 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__phylogeny__iqtree%2Fqiime2__phylogeny__iqtree%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 phylogeny iqtree-ultrafast-bootstrap 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 phylogeny iqtree-ultrafast-bootstrap: Construct a phylogenetic + tree with IQ-TREE with bootstrap supports.' + title: qiime2 phylogeny iqtree-ultrafast-bootstrap 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__phylogeny__iqtree_ultrafast_bootstrap%2Fqiime2__phylogeny__iqtree_ultrafast_bootstrap%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 phylogeny midpoint-root 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 phylogeny midpoint-root: Midpoint root an unrooted phylogenetic + tree.' + title: qiime2 phylogeny midpoint-root 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__phylogeny__midpoint_root%2Fqiime2__phylogeny__midpoint_root%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 phylogeny raxml 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 phylogeny raxml: Construct a phylogenetic tree with RAxML.' + title: qiime2 phylogeny raxml 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__phylogeny__raxml%2Fqiime2__phylogeny__raxml%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 phylogeny raxml-rapid-bootstrap 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 phylogeny raxml-rapid-bootstrap: Construct a phylogenetic + tree with bootstrap supports using RAxML.' + title: qiime2 phylogeny raxml-rapid-bootstrap 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__phylogeny__raxml_rapid_bootstrap%2Fqiime2__phylogeny__raxml_rapid_bootstrap%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 phylogeny robinson-foulds 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 phylogeny robinson-foulds: Calculate Robinson-Foulds distance + between phylogenetic trees.' + title: qiime2 phylogeny robinson-foulds 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__phylogeny__robinson_foulds%2Fqiime2__phylogeny__robinson_foulds%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 quality-control bowtie2-build 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 quality-control bowtie2-build: Build bowtie2 index from reference + sequences.' + title: qiime2 quality-control bowtie2-build 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__quality_control__bowtie2_build%2Fqiime2__quality_control__bowtie2_build%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 quality-control evaluate-composition 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 quality-control evaluate-composition: Evaluate expected vs. + observed taxonomic composition of samples' + title: qiime2 quality-control evaluate-composition 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__quality_control__evaluate_composition%2Fqiime2__quality_control__evaluate_composition%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 quality-control evaluate-seqs 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 quality-control evaluate-seqs: Compare query (observed) vs. + reference (expected) sequences.' + title: qiime2 quality-control evaluate-seqs 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__quality_control__evaluate_seqs%2Fqiime2__quality_control__evaluate_seqs%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 quality-control evaluate-taxonomy 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 quality-control evaluate-taxonomy: Evaluate expected vs. + observed taxonomic assignments' + title: qiime2 quality-control evaluate-taxonomy 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__quality_control__evaluate_taxonomy%2Fqiime2__quality_control__evaluate_taxonomy%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 quality-control exclude-seqs 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 quality-control exclude-seqs: Exclude sequences by alignment' + title: qiime2 quality-control exclude-seqs 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__quality_control__exclude_seqs%2Fqiime2__quality_control__exclude_seqs%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 quality-control filter-reads 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 quality-control filter-reads: Filter demultiplexed sequences + by alignment to reference database.' + title: qiime2 quality-control filter-reads 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__quality_control__filter_reads%2Fqiime2__quality_control__filter_reads%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 quality-filter q-score 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 quality-filter q-score: Quality filter based on sequence + quality scores.' + title: qiime2 quality-filter q-score 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__quality_filter__q_score%2Fqiime2__quality_filter__q_score%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 sample-classifier classify-samples-from-dist 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 sample-classifier classify-samples-from-dist: Run k-nearest-neighbors + on a labeled distance matrix.' + title: qiime2 sample-classifier classify-samples-from-dist 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__sample_classifier__classify_samples_from_dist%2Fqiime2__sample_classifier__classify_samples_from_dist%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 sample-classifier classify-samples 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 sample-classifier classify-samples: Train and test a cross-validated + supervised learning classifier.' + title: qiime2 sample-classifier classify-samples 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__sample_classifier__classify_samples%2Fqiime2__sample_classifier__classify_samples%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 sample-classifier classify-samples-ncv 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 sample-classifier classify-samples-ncv: Nested cross-validated + supervised learning classifier.' + title: qiime2 sample-classifier classify-samples-ncv 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__sample_classifier__classify_samples_ncv%2Fqiime2__sample_classifier__classify_samples_ncv%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 sample-classifier confusion-matrix 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 sample-classifier confusion-matrix: Make a confusion matrix + from sample classifier predictions.' + title: qiime2 sample-classifier confusion-matrix 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__sample_classifier__confusion_matrix%2Fqiime2__sample_classifier__confusion_matrix%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 sample-classifier fit-classifier 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 sample-classifier fit-classifier: Fit a supervised learning + classifier.' + title: qiime2 sample-classifier fit-classifier 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__sample_classifier__fit_classifier%2Fqiime2__sample_classifier__fit_classifier%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 sample-classifier fit-regressor 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 sample-classifier fit-regressor: Fit a supervised learning + regressor.' + title: qiime2 sample-classifier fit-regressor 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__sample_classifier__fit_regressor%2Fqiime2__sample_classifier__fit_regressor%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 sample-classifier heatmap 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 sample-classifier heatmap: Generate heatmap of important + features.' + title: qiime2 sample-classifier heatmap 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__sample_classifier__heatmap%2Fqiime2__sample_classifier__heatmap%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 sample-classifier metatable 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 sample-classifier metatable: Convert (and merge) positive + numeric metadata (in)to feature table.' + title: qiime2 sample-classifier metatable 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__sample_classifier__metatable%2Fqiime2__sample_classifier__metatable%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 sample-classifier predict-classification 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 sample-classifier predict-classification: Use trained classifier + to predict target values for new samples.' + title: qiime2 sample-classifier predict-classification 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__sample_classifier__predict_classification%2Fqiime2__sample_classifier__predict_classification%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 sample-classifier predict-regression 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 sample-classifier predict-regression: Use trained regressor + to predict target values for new samples.' + title: qiime2 sample-classifier predict-regression 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__sample_classifier__predict_regression%2Fqiime2__sample_classifier__predict_regression%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 sample-classifier regress-samples 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 sample-classifier regress-samples: Train and test a cross-validated + supervised learning regressor.' + title: qiime2 sample-classifier regress-samples 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__sample_classifier__regress_samples%2Fqiime2__sample_classifier__regress_samples%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 sample-classifier regress-samples-ncv 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 sample-classifier regress-samples-ncv: Nested cross-validated + supervised learning regressor.' + title: qiime2 sample-classifier regress-samples-ncv 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__sample_classifier__regress_samples_ncv%2Fqiime2__sample_classifier__regress_samples_ncv%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 sample-classifier scatterplot 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 sample-classifier scatterplot: Make 2D scatterplot and linear + regression of regressor predictions.' + title: qiime2 sample-classifier scatterplot 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__sample_classifier__scatterplot%2Fqiime2__sample_classifier__scatterplot%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 sample-classifier split-table 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 sample-classifier split-table: Split a feature table into + training and testing sets.' + title: qiime2 sample-classifier split-table 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__sample_classifier__split_table%2Fqiime2__sample_classifier__split_table%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 sample-classifier summarize 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 sample-classifier summarize: Summarize parameter and feature + extraction information for a trained estimator.' + title: qiime2 sample-classifier summarize 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__sample_classifier__summarize%2Fqiime2__sample_classifier__summarize%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 taxa barplot 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 taxa barplot: Visualize taxonomy with an interactive bar + plot' + title: qiime2 taxa barplot 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__taxa__barplot%2Fqiime2__taxa__barplot%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 taxa collapse 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 taxa collapse: Collapse features by their taxonomy at the + specified level' + title: qiime2 taxa collapse 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__taxa__collapse%2Fqiime2__taxa__collapse%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 taxa filter-seqs 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 taxa filter-seqs: Taxonomy-based feature sequence filter.' + title: qiime2 taxa filter-seqs 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__taxa__filter_seqs%2Fqiime2__taxa__filter_seqs%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 taxa filter-table 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 taxa filter-table: Taxonomy-based feature table filter.' + title: qiime2 taxa filter-table 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__taxa__filter_table%2Fqiime2__taxa__filter_table%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 vsearch cluster-features-closed-reference 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 vsearch cluster-features-closed-reference: Closed-reference + clustering of features.' + title: qiime2 vsearch cluster-features-closed-reference 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__vsearch__cluster_features_closed_reference%2Fqiime2__vsearch__cluster_features_closed_reference%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 vsearch cluster-features-de-novo 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 vsearch cluster-features-de-novo: De novo clustering of features.' + title: qiime2 vsearch cluster-features-de-novo 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__vsearch__cluster_features_de_novo%2Fqiime2__vsearch__cluster_features_de_novo%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 vsearch cluster-features-open-reference 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 vsearch cluster-features-open-reference: Open-reference clustering + of features.' + title: qiime2 vsearch cluster-features-open-reference 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__vsearch__cluster_features_open_reference%2Fqiime2__vsearch__cluster_features_open_reference%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 vsearch dereplicate-sequences 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 vsearch dereplicate-sequences: Dereplicate sequences.' + title: qiime2 vsearch dereplicate-sequences 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__vsearch__dereplicate_sequences%2Fqiime2__vsearch__dereplicate_sequences%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 vsearch fastq-stats 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 vsearch fastq-stats: Fastq stats with vsearch.' + title: qiime2 vsearch fastq-stats 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__vsearch__fastq_stats%2Fqiime2__vsearch__fastq_stats%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 vsearch merge-pairs 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 vsearch merge-pairs: Merge paired-end reads.' + title: qiime2 vsearch merge-pairs 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__vsearch__merge_pairs%2Fqiime2__vsearch__merge_pairs%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 vsearch uchime-denovo 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 vsearch uchime-denovo: De novo chimera filtering with vsearch.' + title: qiime2 vsearch uchime-denovo 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__vsearch__uchime_denovo%2Fqiime2__vsearch__uchime_denovo%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 vsearch uchime-ref 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 vsearch uchime-ref: Reference-based chimera filtering with + vsearch.' + title: qiime2 vsearch uchime-ref 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__vsearch__uchime_ref%2Fqiime2__vsearch__uchime_ref%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 composition ancombc 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 composition ancombc: Analysis of Composition of Microbiomes + with Bias Correction' + title: qiime2 composition ancombc 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__composition__ancombc%2Fqiime2__composition__ancombc%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 diversity-lib bray-curtis 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 diversity-lib bray-curtis: Bray-Curtis Dissimilarity' + title: qiime2 diversity-lib bray-curtis 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity_lib__bray_curtis%2Fqiime2__diversity_lib__bray_curtis%2F2023.5.0%2Bq2galaxy.2023.5.0.2 - - title: qiime2 feature-table filter-features 2023.5.0+q2galaxy.2023.5.0.2 + - description: 'qiime2 feature-table filter-features: Filter features from table' + title: qiime2 feature-table filter-features 2023.5.0+q2galaxy.2023.5.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__filter_features%2Fqiime2__feature_table__filter_features%2F2023.5.0%2Bq2galaxy.2023.5.0.2 homepage: https://qiime2.org id: qiime2 @@ -14710,7 +16461,8 @@ bunya: '' description: '' galaxy: - - title: Boxplot 1.0.1 + - description: 'Boxplot: of quality statistics' + title: Boxplot 1.0.1 url: https://usegalaxy.org.au/root?tool_id=qual_stats_boxplot homepage: '' id: qual_stats_boxplot @@ -14729,13 +16481,17 @@ both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. galaxy: - - title: QualiMap BamQC 2.2.2d+galaxy3 + - 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 - - title: QualiMap Multi-Sample BamQC 2.2.2d + - 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 Counts QC 2.2.2d + - 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 RNA-Seq QC 2.2.2d+galaxy1 + - 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 homepage: https://qualimap.bioinfo.cipf.es/ id: qualimap @@ -14764,29 +16520,44 @@ and file specifications are available at: https: phac-nml.github.io quasitools Contact gary.vandomselaar@canada.ca' galaxy: - - title: Consensus Sequence 0.7.0+galaxy1 + - description: 'Consensus Sequence: Generate a consensus sequence from a BAM file' + title: Consensus Sequence 0.7.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fquasitools%2Fconsensus%2F0.7.0%2Bgalaxy1 - - title: Complexity BAM 0.7.0+galaxy1 + - description: 'Complexity BAM: ' + title: Complexity BAM 0.7.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fquasitools%2Fcomplexity_bam%2F0.7.0%2Bgalaxy1 - - title: Quasispecies Distance 0.7.0+galaxy1 + - description: 'Quasispecies Distance: Calculate the evolutionary distance between + viral quasispecies.' + title: Quasispecies Distance 0.7.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fquasitools%2Fdistance%2F0.7.0%2Bgalaxy1 - - title: Complexity FASTA 0.7.0+galaxy1 + - description: 'Complexity FASTA: ' + title: Complexity FASTA 0.7.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fquasitools%2Fcomplexity_fasta%2F0.7.0%2Bgalaxy1 - - title: Nucleotide Variants 0.7.0+galaxy1 + - description: 'Nucleotide Variants: Identifies nucleotide variants' + title: Nucleotide Variants 0.7.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fquasitools%2Fcallntvar%2F0.7.0%2Bgalaxy1 - - title: Quality control 0.7.0+galaxy1 + - description: 'Quality control: Performs quality control on FASTQ reads.' + title: Quality control 0.7.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fquasitools%2Fquality%2F0.7.0%2Bgalaxy1 - - title: Amino Acid Variants 0.7.0+galaxy1 + - description: 'Amino Acid Variants: Identifies amino acid mutations' + title: Amino Acid Variants 0.7.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fquasitools%2Faavariants%2F0.7.0%2Bgalaxy1 - - title: Hydra pipeline 0.7.0+galaxy1 + - description: 'Hydra pipeline: Identifies drug resistance within an NGS dataset' + title: Hydra pipeline 0.7.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fquasitools%2Fhydra%2F0.7.0%2Bgalaxy1 - - title: Codon Variants 0.7.0+galaxy1 + - description: 'Codon Variants: Identifies codon variants and non-synonymous/synonymous + mutations' + title: Codon Variants 0.7.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fquasitools%2Fcallcodonvar%2F0.7.0%2Bgalaxy1 - - title: dNdS Report 0.7.0+galaxy1 + - description: 'dNdS Report: Calculate the dN/dS value for each region in a bed + file' + title: dNdS Report 0.7.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fquasitools%2Fdnds%2F0.7.0%2Bgalaxy1 - - title: Amino Acid Coverage 0.7.0+galaxy1 + - description: 'Amino Acid Coverage: Builds an aa census and returns its coverage' + title: Amino Acid Coverage 0.7.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fquasitools%2Faacoverage%2F0.7.0%2Bgalaxy1 - - title: Drug Resistance Mutations 0.7.0+galaxy1 + - description: 'Drug Resistance Mutations: ' + title: Drug Resistance Mutations 0.7.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fquasitools%2Fdrmutations%2F0.7.0%2Bgalaxy1 homepage: https://phac-nml.github.io/quasitools/ id: quasitools @@ -14811,7 +16582,8 @@ description: "QUAST stands for QUality ASsessment Tool. \nIt evaluates a quality\ \ of genome assemblies by computing various metrics and providing nice reports." galaxy: - - title: Quast 5.2.0+galaxy1 + - description: 'Quast: Genome assembly Quality' + title: Quast 5.2.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fquast%2Fquast%2F5.2.0%2Bgalaxy1 homepage: http://quast.sourceforge.net/quast id: quast @@ -14836,7 +16608,8 @@ further process to generate tabular outputs containing desired information and formatting. galaxy: - - title: Query Tabular 3.3.1 + - 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 homepage: https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular id: query_tabular @@ -14884,15 +16657,25 @@ bunya: '' description: '' galaxy: - - title: Initial processing using RaceID 0.2.3+galaxy3 + - 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: Clustering using RaceID 0.2.3+galaxy3 + - 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 - - title: Cluster Inspection using RaceID 0.2.3+galaxy3 + - 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: Lineage Branch Analysis using StemID 0.2.3+galaxy3 + - 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 - - title: Lineage computation using StemID 0.2.3+galaxy3 + - 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 homepage: '' id: r-raceid @@ -14907,15 +16690,21 @@ topics: '' - biocontainers: Racon bunya: '' - description: 'The Possibility to Use Oxford Nanopore Technology | Ultrafast consensus - module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 - Note: This was the original repository which will no longer be officially maintained. - Please use the new official repository here: https://github.com/isovic/racon| + description: 'Consensus module for raw de novo DNA assembly of long uncorrected + reads + + Racon is intended as a standalone consensus module to correct raw contigs generated - by rapid assembly methods which do not include a consensus step | Consensus module - for raw de novo DNA assembly of long uncorrected reads' - galaxy: - - title: Racon 1.5.0+galaxy1 + by rapid assembly methods which do not include a consensus step. The goal of Racon + is to generate genomic consensus which is of similar or better quality compared + to the output generated by assembly methods which employ both error correction + and consensus steps, while providing a speedup of several times compared to those + methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore + Technologies.' + galaxy: + - description: 'Racon: Consensus module for raw de novo DNA assembly of long uncorrected + reads' + title: Racon 1.5.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fracon%2Fracon%2F1.5.0%2Bgalaxy1 homepage: https://github.com/isovic/racon id: racon @@ -14926,22 +16715,26 @@ - 1.4.3 pawsey: '' publications: - - title: 10.3390/PLANTS8080270 + - title: 'Constructing a reference genome in a single lab: The possibility to use + oxford nanopore technology' url: https://doi.org/10.3390/PLANTS8080270 registry-link: Racon resource-documentation: .nan topics: - Whole genome sequencing - Sequence assembly - - Plant biology - biocontainers: ramclustr bunya: '' description: A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. galaxy: - - title: RAMClustR define experiment 1.0.2+galaxy0 + - 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 1.3.0+galaxy1 + - 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 homepage: https://github.com/cbroeckl/RAMClustR id: ramclustr @@ -15021,7 +16814,8 @@ bunya: '' description: '' galaxy: - - title: Ratmine 1.0.0 + - description: 'Ratmine: server' + title: Ratmine 1.0.0 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=ratmine homepage: '' id: ratmine @@ -15059,7 +16853,8 @@ Raven is a de novo genome assembler for long uncorrected reads.' galaxy: - - title: Raven 1.8.0+galaxy0 + - description: 'Raven: De novo assembly of Oxford Nanopore Technologies data' + title: Raven 1.8.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fraven%2Fraven%2F1.8.0%2Bgalaxy0 homepage: https://github.com/lbcb-sci/raven id: raven @@ -15082,7 +16877,9 @@ description: A standalone tool for extracting data directly from raw files generated by Thermo Orbitrap family instruments. galaxy: - - title: Raw Tools 1.4.2.0 + - description: 'Raw Tools: Perform scan data parsing, quantification and quality + control analysis of Thermo Orbitrap raw mass spectrometer files.' + title: Raw Tools 1.4.2.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Frawtools%2Frawtools%2F1.4.2.0 homepage: https://github.com/kevinkovalchik/RawTools id: rawtools @@ -15105,7 +16902,9 @@ - 8.2.12 description: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. galaxy: - - title: RAxML 8.2.12+galaxy1 + - description: 'RAxML: Maximum Likelihood based inference of large phylogenetic + trees' + title: RAxML 8.2.12+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fraxml%2Fraxml%2F8.2.12%2Bgalaxy1 homepage: https://sco.h-its.org/exelixis/web/software/raxml/ id: raxml @@ -15144,9 +16943,12 @@ description: RDKit is an Open-Source Cheminformatics Software. Fast, Efficient Fragment-Based Coordinate Generation for Open Babel. galaxy: - - title: Enumerate changes 2020.03.4+galaxy0 + - description: 'Enumerate changes: calculated with Dimorphite DL and RDKit' + title: Enumerate changes 2020.03.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fenumerate_charges%2Fenumerate_charges%2F2020.03.4%2Bgalaxy0 - - title: Max SuCOS score 2020.03.4+galaxy0 + - description: 'Max SuCOS score: - determine maximum SuCOS score of ligands against + clustered fragment hits' + title: Max SuCOS score 2020.03.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsucos_max_score%2Fsucos_max_score%2F2020.03.4%2Bgalaxy0 homepage: http://www.rdkit.org id: rdkit @@ -15168,7 +16970,8 @@ bunya: '' description: '' galaxy: - - title: Create Frankenstein ligand 2013.1-0+galaxy0 + - description: 'Create Frankenstein ligand: for docking active site definition' + title: Create Frankenstein ligand 2013.1-0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fctb_frankenstein_ligand%2Fctb_frankenstein_ligand%2F2013.1-0%2Bgalaxy0 homepage: '' id: rdock @@ -15212,21 +17015,36 @@ correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. galaxy: - - title: recetox-aplcms - align features 0.12.0+galaxy1 + - 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 - - title: recetox-aplcms - compute clusters 0.12.0+galaxy2 + - 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 template 0.12.0+galaxy1 + - 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 - - title: recetox-aplcms - correct time 0.12.0+galaxy2 + - 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 - - title: recetox-aplcms - generate feature table 0.12.0+galaxy2 + - 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 - - title: recetox-aplcms - merge known table 0.12.0+galaxy1 + - 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 - recover weaker signals 0.12.0+galaxy2 + - 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 - - title: recetox-aplcms - remove noise 0.12.0+galaxy2 + - 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 homepage: https://github.com/RECETOX/recetox-aplcms id: recetox-aplcms @@ -15245,7 +17063,8 @@ description: This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. galaxy: - - title: Red 2018.09.10+galaxy1 + - description: 'Red: repeat masking' + title: Red 2018.09.10+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fred%2Fred%2F2018.09.10%2Bgalaxy1 homepage: https://github.com/REDetector/RED id: red @@ -15343,7 +17162,9 @@ of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).' galaxy: - - title: RepeatMasker 4.1.5+galaxy0 + - description: 'RepeatMasker: screen DNA sequences for interspersed repeats and + low complexity regions' + title: RepeatMasker 4.1.5+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Frepeat_masker%2Frepeatmasker_wrapper%2F4.1.5%2Bgalaxy0 homepage: http://www.repeatmasker.org/ id: repeatmasker @@ -15369,7 +17190,8 @@ computational methods for identifying repeat element boundaries and family relationships from sequence data. galaxy: - - title: RepeatModeler 2.0.4+galaxy1 + - description: 'RepeatModeler: Model repetitive DNA' + title: RepeatModeler 2.0.4+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fcsbl%2Frepeatmodeler%2Frepeatmodeler%2F2.0.4%2Bgalaxy1 homepage: https://github.com/Dfam-consortium/RepeatModeler id: repeatmodeler @@ -15415,7 +17237,8 @@ bunya: '' description: '' galaxy: - - title: RepEnrich 1.6.1 + - description: 'RepEnrich: Repeat Element Profiling' + title: RepEnrich 1.6.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fartbio%2Frepenrich%2Frepenrich%2F1.6.1 homepage: '' id: repenrich @@ -15432,7 +17255,8 @@ bunya: '' description: '' galaxy: - - title: Replace column 0.2 + - 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 homepage: '' id: replace_column_with_key_value_file @@ -15474,7 +17298,8 @@ cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records. galaxy: - - title: RMassBank 3.0.0+galaxy2 + - 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 homepage: http://bioconductor.org/packages/release/bioc/html/RMassBank.html id: rmassbank @@ -15546,9 +17371,12 @@ bunya: '' description: '' galaxy: - - title: Analyse canonical genes against 'peak' data 1.1.0.0 + - description: 'Analyse canonical genes against ''peak'' data: using RnaChipIntegrator' + title: Analyse canonical genes against 'peak' data 1.1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fpjbriggs%2Frnachipintegrator%2Frnachipintegrator_canonical_genes%2F1.1.0.0 - - title: RnaChipIntegrator 1.1.0.0 + - description: 'RnaChipIntegrator: Integrated analysis of ''gene'' and ''peak'' + data' + title: RnaChipIntegrator 1.1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fpjbriggs%2Frnachipintegrator%2Frnachipintegrator_wrapper%2F1.1.0.0 homepage: '' id: rnachipintegrator @@ -15567,7 +17395,9 @@ assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. galaxy: - - title: Roary 3.13.0+galaxy2 + - 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 homepage: https://sanger-pathogens.github.io/Roary/ id: roary @@ -15589,7 +17419,9 @@ bunya: '' description: '' galaxy: - - title: Row Means 0.1 + - description: 'Row Means: Calculates the mean of a row of numbers for an entire + table' + title: Row Means 0.1 url: https://usegalaxy.org.au/root?tool_id=testtoolshed.g2.bx.psu.edu%2Frepos%2Fsimon-gladman%2Frow_means%2Frow_means%2F0.1 homepage: '' id: row_means @@ -15634,49 +17466,84 @@ RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. galaxy: - - title: Gene Body Coverage (Bigwig) 5.0.1+galaxy2 + - description: 'Gene Body Coverage (Bigwig): read coverage over gene body' + title: Gene Body Coverage (Bigwig) 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_geneBody_coverage2%2F5.0.1%2Bgalaxy2 - - title: Read GC 5.0.1+galaxy2 + - description: 'Read GC: determines GC% and read count' + title: Read GC 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_read_GC%2F5.0.1%2Bgalaxy2 - - title: Read Quality 5.0.1+galaxy2 + - description: 'Read Quality: determines Phred quality score' + title: Read Quality 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_read_quality%2F5.0.1%2Bgalaxy2 - - title: Transcript Integrity Number 5.0.1+galaxy2 + - description: 'Transcript Integrity Number: evaluates RNA integrity at a transcript + level' + title: Transcript Integrity Number 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_tin%2F5.0.1%2Bgalaxy2 - - title: Deletion Profile 5.0.1+galaxy2 + - description: 'Deletion Profile: calculates the distributions of deleted nucleotides + across reads' + title: Deletion Profile 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_deletion_profile%2F5.0.1%2Bgalaxy2 - - title: Read Distribution 5.0.1+galaxy2 + - description: 'Read Distribution: calculates how mapped reads were distributed + over genome feature' + title: Read Distribution 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_read_distribution%2F5.0.1%2Bgalaxy2 - - title: FPKM Count 5.0.1+galaxy2 + - description: 'FPKM Count: calculates raw read count, FPM, and FPKM for each gene' + title: FPKM Count 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_FPKM_count%2F5.0.1%2Bgalaxy2 - - title: Junction Annotation 5.0.1+galaxy2 + - description: 'Junction Annotation: compares detected splice junctions to reference + gene model' + title: Junction Annotation 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_junction_annotation%2F5.0.1%2Bgalaxy2 - - title: RNA fragment size 5.0.1+galaxy2 + - description: 'RNA fragment size: calculates the fragment size for each gene/transcript' + title: RNA fragment size 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_RNA_fragment_size%2F5.0.1%2Bgalaxy2 - - title: Insertion Profile 5.0.1+galaxy2 + - description: 'Insertion Profile: calculates the distribution of inserted nucleotides + across reads' + title: Insertion Profile 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_insertion_profile%2F5.0.1%2Bgalaxy2 - - title: RPKM Saturation 5.0.1+galaxy2 + - description: 'RPKM Saturation: calculates raw count and RPKM values for transcript + at exon, intron, and mRNA level' + title: RPKM Saturation 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_RPKM_saturation%2F5.0.1%2Bgalaxy2 - - title: Read Duplication 5.0.1+galaxy2 + - description: 'Read Duplication: determines reads duplication rate with sequence-based + and mapping-based strategies' + title: Read Duplication 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_read_duplication%2F5.0.1%2Bgalaxy2 - - title: Gene Body Coverage (BAM) 5.0.1+galaxy2 + - description: 'Gene Body Coverage (BAM): read coverage over gene body' + title: Gene Body Coverage (BAM) 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_geneBody_coverage%2F5.0.1%2Bgalaxy2 - - title: BAM/SAM Mapping Stats 5.0.1+galaxy2 + - description: 'BAM/SAM Mapping Stats: reads mapping statistics for a provided BAM + or SAM file.' + title: BAM/SAM Mapping Stats 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_bam_stat%2F5.0.1%2Bgalaxy2 - - title: BAM to Wiggle 5.0.1+galaxy2 + - description: 'BAM to Wiggle: converts all types of RNA-seq data from .bam to .wig' + title: BAM to Wiggle 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_bam2wig%2F5.0.1%2Bgalaxy2 - - title: Junction Saturation 5.0.1+galaxy2 + - description: 'Junction Saturation: detects splice junctions from each subset and + compares them to reference gene model' + title: Junction Saturation 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_junction_saturation%2F5.0.1%2Bgalaxy2 - - title: Infer Experiment 5.0.1+galaxy2 + - description: 'Infer Experiment: speculates how RNA-seq were configured' + title: Infer Experiment 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_infer_experiment%2F5.0.1%2Bgalaxy2 - - title: Mismatch Profile 5.0.1+galaxy2 + - description: 'Mismatch Profile: calculates the distribution of mismatches across + reads' + title: Mismatch Profile 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_mismatch_profile%2F5.0.1%2Bgalaxy2 - - title: Hexamer frequency 5.0.1+galaxy2 + - description: 'Hexamer frequency: calculates hexamer (6mer) frequency for reads, + genomes, and mRNA sequences' + title: Hexamer frequency 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_read_hexamer%2F5.0.1%2Bgalaxy2 - - title: Clipping Profile 5.0.1+galaxy2 + - description: 'Clipping Profile: estimates clipping profile of RNA-seq reads from + BAM or SAM file' + title: Clipping Profile 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_clipping_profile%2F5.0.1%2Bgalaxy2 - - title: Read NVC 5.0.1+galaxy2 + - description: 'Read NVC: to check the nucleotide composition bias' + title: Read NVC 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_read_NVC%2F5.0.1%2Bgalaxy2 - - title: Inner Distance 5.0.1+galaxy2 + - description: 'Inner Distance: calculate the inner distance (or insert size) between + two paired RNA reads' + title: Inner Distance 5.0.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnilesh%2Frseqc%2Frseqc_inner_distance%2F5.0.1%2Bgalaxy2 homepage: http://rseqc.sourceforge.net id: rseqc @@ -15698,7 +17565,8 @@ bunya: '' description: Integrated development environment (IDE) for the R programming language. galaxy: - - title: RStudio 0.2 + - description: 'RStudio: ' + title: RStudio 0.2 url: https://usegalaxy.org.au/root?tool_id=interactive_tool_rstudio homepage: https://www.rstudio.com/ id: rstudio @@ -15738,9 +17606,12 @@ bunya: '' description: '' galaxy: - - title: rxDock cavity definition 2013.1.1_148c5bd1+galaxy0 + - description: 'rxDock cavity definition: - generate the active site definition + needed for rxDock docking' + title: rxDock cavity definition 2013.1.1_148c5bd1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Frxdock_rbcavity%2Frxdock_rbcavity%2F2013.1.1_148c5bd1%2Bgalaxy0 - - title: rxDock docking 2013.1.1_148c5bd1+galaxy0 + - description: 'rxDock docking: - perform protein-ligand docking with rxDock' + title: rxDock docking 2013.1.1_148c5bd1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Frxdock_rbdock%2Frxdock_rbdock%2F2013.1.1_148c5bd1%2Bgalaxy0 homepage: '' id: rxdock @@ -15787,7 +17658,8 @@ for the estimation of isoform abundances directly from a set of reference sequences and RNA-seq reads. galaxy: - - title: Sailfish 0.10.1.1 + - description: 'Sailfish: transcript quantification from RNA-seq data' + title: Sailfish 0.10.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsailfish%2Fsailfish%2F0.10.1.1 homepage: http://www.cs.cmu.edu/~ckingsf/software/sailfish/ id: sailfish @@ -15813,7 +17685,9 @@ - 1.9.0-gcc-11.3.0 (D) description: A tool for transcript expression quantification from RNA-seq data galaxy: - - title: Salmon quant 1.10.1+galaxy0 + - description: 'Salmon quant: Perform dual-phase, reads or mapping-based estimation + of transcript abundance from RNA-seq reads' + title: Salmon quant 1.10.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsalmon%2Fsalmon%2F1.10.1%2Bgalaxy0 homepage: https://combine-lab.github.io/salmon id: salmon @@ -15836,7 +17710,9 @@ bunya: '' description: '' galaxy: - - title: salmonKallistoMtxTo10x 0.0.1+galaxy6 + - description: 'salmonKallistoMtxTo10x: Transforms .mtx matrix and associated labels + into a format compatible with tools expecting old-style 10X data' + title: salmonKallistoMtxTo10x 0.0.1+galaxy6 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fsalmon_kallisto_mtx_to_10x%2F_salmon_kallisto_mtx_to_10x%2F0.0.1%2Bgalaxy6 homepage: '' id: salmon_kallisto_mtx_to_10x @@ -15860,7 +17736,8 @@ version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch' galaxy: - - title: SALSA 2.3+galaxy3 + - 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 homepage: https://github.com/machinegun/SALSA id: salsa @@ -15882,7 +17759,8 @@ bunya: '' description: '' galaxy: - - title: Filter SAM 1.0.0 + - description: 'Filter SAM: on bitwise flag values' + title: Filter SAM 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsam_bitwise_flag_filter%2Fsam_bw_filter%2F1.0.0 homepage: '' id: sam_bitwise_flag_filter @@ -15899,7 +17777,8 @@ bunya: '' description: '' galaxy: - - title: Generate pileup 1.1.3 + - description: 'Generate pileup: from BAM dataset' + title: Generate pileup 1.1.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsam_pileup%2Fsam_pileup%2F1.1.3 homepage: '' id: sam_pileup @@ -15916,7 +17795,8 @@ bunya: '' description: '' galaxy: - - title: Convert SAM 1.0.2 + - description: 'Convert SAM: to interval' + title: Convert SAM 1.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsam2interval%2Fsam2interval%2F1.0.2 homepage: '' id: sam2interval @@ -15934,7 +17814,8 @@ description: This tool is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM, BAM and CRAM formats. galaxy: - - title: Sample, Slice or Filter BAM 0.7.1+galaxy1 + - description: 'Sample, Slice or Filter BAM: on flags, fields, and tags using Sambamba' + title: Sample, Slice or Filter BAM 0.7.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fartbio%2Fsambamba%2Fsambamba_sample_or_filter%2F0.7.1%2Bgalaxy1 homepage: http://www.open-bio.org/wiki/Sambamba id: sambamba @@ -15980,7 +17861,8 @@ bunya: '' description: '' galaxy: - - title: Sub-sample sequences files 0.2.5 + - 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 homepage: '' id: sample_seqs @@ -16003,45 +17885,66 @@ and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. galaxy: - - title: Samtools split 1.15.1+galaxy2 + - 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 - - title: Samtools fastx 1.15.1+galaxy2 + - description: 'Samtools fastx: extract FASTA or FASTQ from alignment files' + title: Samtools fastx 1.15.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsamtools_fastx%2Fsamtools_fastx%2F1.15.1%2Bgalaxy2 - - title: Samtools calmd 2.0.4 + - description: 'Samtools calmd: recalculate MD/NM tags' + title: Samtools calmd 2.0.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsamtools_calmd%2Fsamtools_calmd%2F2.0.4 - - title: Samtools stats 2.0.5 + - description: 'Samtools stats: generate statistics for BAM dataset' + title: Samtools stats 2.0.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsamtools_stats%2Fsamtools_stats%2F2.0.5 - - title: Slice 2.0.3 + - description: 'Slice: BAM by genomic regions' + title: Slice 2.0.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsamtools_slice_bam%2Fsamtools_slice_bam%2F2.0.3 - - title: Samtools reheader 2.0.3 + - description: 'Samtools reheader: copy SAM/BAM header between datasets' + title: Samtools reheader 2.0.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsamtools_reheader%2Fsamtools_reheader%2F2.0.3 - - title: Samtools mpileup 2.1.7 + - description: 'Samtools mpileup: multi-way pileup of variants' + title: Samtools mpileup 2.1.7 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsamtools_mpileup%2Fsamtools_mpileup%2F2.1.7 - - title: Samtools idxstats 2.0.5 + - description: 'Samtools idxstats: reports stats of the BAM index file' + title: Samtools idxstats 2.0.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsamtools_idxstats%2Fsamtools_idxstats%2F2.0.5 - - title: Samtools bedcov 2.0.4 + - description: 'Samtools bedcov: calculate read depth for a set of genomic intervals' + title: Samtools bedcov 2.0.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsamtools_bedcov%2Fsamtools_bedcov%2F2.0.4 - - title: BAM-to-SAM 2.0.4 + - description: 'BAM-to-SAM: convert BAM to SAM' + title: BAM-to-SAM 2.0.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fbam_to_sam%2Fbam_to_sam%2F2.0.4 - - title: SAM-to-BAM 2.1.2 + - description: 'SAM-to-BAM: convert SAM to BAM' + title: SAM-to-BAM 2.1.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsam_to_bam%2Fsam_to_bam%2F2.1.2 - - title: Filter SAM or BAM, output SAM or BAM 1.8+galaxy1 + - description: 'Filter SAM or BAM, output SAM or BAM: files on FLAG MAPQ RG LN or + by region' + title: Filter SAM or BAM, output SAM or BAM 1.8+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsamtool_filter2%2Fsamtool_filter2%2F1.8%2Bgalaxy1 - - title: Samtools flagstat 2.0.5 + - description: 'Samtools flagstat: tabulate descriptive stats for BAM datset' + title: Samtools flagstat 2.0.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsamtools_flagstat%2Fsamtools_flagstat%2F2.0.5 - - title: Samtools merge 1.15.1+galaxy2 + - description: 'Samtools merge: merge multiple sorted alignment files' + title: Samtools merge 1.15.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsamtools_merge%2Fsamtools_merge%2F1.15.1%2Bgalaxy2 - - title: Samtools phase 2.0.2 + - description: 'Samtools phase: call and phase heterozygous SNPs' + title: Samtools phase 2.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsamtools_phase%2Fsamtools_phase%2F2.0.2 - - title: RmDup 2.0.1 + - description: 'RmDup: remove PCR duplicates' + title: RmDup 2.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsamtools_rmdup%2Fsamtools_rmdup%2F2.0.1 - - title: Samtools sort 2.0.5 + - description: 'Samtools sort: order of storing aligned sequences' + title: Samtools sort 2.0.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsamtools_sort%2Fsamtools_sort%2F2.0.5 - - title: Samtools view 1.15.1+galaxy2 + - description: 'Samtools view: - reformat, filter, or subsample SAM, BAM or CRAM' + title: Samtools view 1.15.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsamtools_view%2Fsamtools_view%2F1.15.1%2Bgalaxy2 - - title: Samtools depth 1.15.1+galaxy2 + - 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 - - title: samtools BAM to CRAM 1.15.1+galaxy2 + - 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 homepage: http://www.htslib.org/ id: samtools @@ -16097,71 +18000,110 @@ and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. galaxy: - - title: Normalize 1.9.6+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_normalize%2Fscanpy_normalize%2F1.9.6%2Bgalaxy1 - - title: Cluster, infer trajectories and embed 1.9.6+galaxy1 - 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%2Bgalaxy1 - - title: Plot 1.9.6+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_plot%2Fscanpy_plot%2F1.9.6%2Bgalaxy1 - - title: Inspect and manipulate 1.9.6+galaxy1 + - 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: 'Remove confounders: with scanpy' + title: Remove confounders 1.9.6+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_remove_confounders%2Fscanpy_remove_confounders%2F1.9.6%2Bgalaxy2 + - description: 'Plot: with scanpy' + title: Plot 1.9.6+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_plot%2Fscanpy_plot%2F1.9.6%2Bgalaxy2 + - description: 'Normalize: and impute with scanpy' + title: Normalize 1.9.6+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_normalize%2Fscanpy_normalize%2F1.9.6%2Bgalaxy2 + - description: 'Cluster, infer trajectories and embed: with scanpy' + title: Cluster, infer trajectories and embed 1.9.6+galaxy2 + 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%2Bgalaxy2 + - description: 'Inspect and manipulate: with scanpy' + title: Inspect and manipulate 1.9.6+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_inspect%2Fscanpy_inspect%2F1.9.6%2Bgalaxy1 - - title: Filter 1.9.6+galaxy1 + - description: 'Filter: with scanpy' + title: Filter 1.9.6+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_filter%2Fscanpy_filter%2F1.9.6%2Bgalaxy1 - - title: Remove confounders 1.9.6+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_remove_confounders%2Fscanpy_remove_confounders%2F1.9.6%2Bgalaxy1 - - title: AnnData Operations 1.8.1+1+galaxy1 + - description: 'AnnData Operations: modifies metadata and flags genes' + title: AnnData Operations 1.8.1+1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fanndata_ops%2Fanndata_ops%2F1.8.1%2B1%2Bgalaxy1 - - title: Scanpy ComputeGraph 1.8.1+1+galaxy1 + - description: 'Scanpy ComputeGraph: to derive kNN graph' + title: Scanpy ComputeGraph 1.8.1+1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_compute_graph%2Fscanpy_compute_graph%2F1.8.1%2B1%2Bgalaxy1 - - title: Scanpy FilterCells 1.8.1+1+galaxy0 + - description: 'Scanpy FilterCells: based on counts and numbers of genes expressed' + title: Scanpy FilterCells 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_filter_cells%2Fscanpy_filter_cells%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy FilterGenes 1.8.1+1+galaxy0 + - description: 'Scanpy FilterGenes: based on counts and numbers of cells expressed' + title: Scanpy FilterGenes 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_filter_genes%2Fscanpy_filter_genes%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy FindCluster 1.8.1+1+galaxy0 + - description: 'Scanpy FindCluster: based on community detection on KNN graph' + title: Scanpy FindCluster 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_find_cluster%2Fscanpy_find_cluster%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy FindMarkers 1.8.1+1+galaxy0 + - description: 'Scanpy FindMarkers: to find differentially expressed genes between + groups' + title: Scanpy FindMarkers 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_find_markers%2Fscanpy_find_markers%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy FindVariableGenes 1.8.1+1+galaxy1 + - description: 'Scanpy FindVariableGenes: based on normalised dispersion of expression' + title: Scanpy FindVariableGenes 1.8.1+1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_find_variable_genes%2Fscanpy_find_variable_genes%2F1.8.1%2B1%2Bgalaxy1 - - title: Scanpy BBKNN 1.8.1+1+galaxy0 + - description: 'Scanpy BBKNN: batch-balanced K-nearest neighbours' + title: Scanpy BBKNN 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_integrate_bbknn%2Fscanpy_integrate_bbknn%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy ComBat 1.8.1+1+galaxy0 + - description: 'Scanpy ComBat: adjust expression for variables that might introduce + batch effect' + title: Scanpy ComBat 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_integrate_combat%2Fscanpy_integrate_combat%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy Harmony 1.8.1+1+galaxy0 + - description: 'Scanpy Harmony: adjust principal components for variables that might + introduce batch effect' + title: Scanpy Harmony 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_integrate_harmony%2Fscanpy_integrate_harmony%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy MNN 1.8.1+3+galaxy0 + - description: 'Scanpy MNN: correct batch effects by matching mutual nearest neighbors' + title: Scanpy MNN 1.8.1+3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_integrate_mnn%2Fscanpy_integrate_mnn%2F1.8.1%2B3%2Bgalaxy0 - - title: Scanpy Scrublet 1.8.1+1+galaxy0 + - description: 'Scanpy Scrublet: remove multiplets from annData objects with Scrublet' + title: Scanpy Scrublet 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_multiplet_scrublet%2Fscanpy_multiplet_scrublet%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy NormaliseData 1.8.1+1+galaxy0 + - description: 'Scanpy NormaliseData: to make all cells having the same total expression' + title: Scanpy NormaliseData 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_normalise_data%2Fscanpy_normalise_data%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy ParameterIterator 0.0.1+galaxy0 + - description: 'Scanpy ParameterIterator: produce an iteration over a defined parameter' + title: Scanpy ParameterIterator 0.0.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_parameter_iterator%2Fscanpy_parameter_iterator%2F0.0.1%2Bgalaxy0 - - title: Scanpy PlotEmbed 1.8.1+1+galaxy0 + - description: 'Scanpy PlotEmbed: visualise cell embeddings' + title: Scanpy PlotEmbed 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_plot_embed%2Fscanpy_plot_embed%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy Plot Scrublet 1.8.1+1+galaxy0 + - description: 'Scanpy Plot Scrublet: visualise multiplet scoring distribution' + title: Scanpy Plot Scrublet 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_plot_scrublet%2Fscanpy_plot_scrublet%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy PlotTrajectory 1.8.1+1+galaxy0 + - description: 'Scanpy PlotTrajectory: visualise cell trajectories' + title: Scanpy PlotTrajectory 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_plot_trajectory%2Fscanpy_plot_trajectory%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy Read10x 1.8.1+1+galaxy0 + - description: 'Scanpy Read10x: into hdf5 object handled by scanpy' + title: Scanpy Read10x 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_read_10x%2Fscanpy_read_10x%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy RegressOut 1.8.1+1+galaxy0 + - description: 'Scanpy RegressOut: variables that might introduce batch effect' + title: Scanpy RegressOut 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_regress_variable%2Fscanpy_regress_variable%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy DiffusionMap 1.8.1+1+galaxy0 + - description: 'Scanpy DiffusionMap: calculate diffusion components' + title: Scanpy DiffusionMap 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_diffmap%2Fscanpy_run_diffmap%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy DPT 1.8.1+1+galaxy0 + - description: 'Scanpy DPT: diffusion pseudotime inference' + title: Scanpy DPT 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_dpt%2Fscanpy_run_dpt%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy RunFDG 1.8.1+1+galaxy0 + - description: 'Scanpy RunFDG: visualise cell clusters using force-directed graph' + title: Scanpy RunFDG 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_fdg%2Fscanpy_run_fdg%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy PAGA 1.8.1+1+galaxy0 + - description: 'Scanpy PAGA: trajectory inference' + title: Scanpy PAGA 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_paga%2Fscanpy_run_paga%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy RunPCA 1.8.1+1+galaxy0 + - description: 'Scanpy RunPCA: for dimensionality reduction' + title: Scanpy RunPCA 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_pca%2Fscanpy_run_pca%2F1.8.1%2B1%2Bgalaxy0 - - title: Scanpy RunTSNE 1.8.1+1+galaxy1 + - description: 'Scanpy RunTSNE: visualise cell clusters using tSNE' + title: Scanpy RunTSNE 1.8.1+1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_tsne%2Fscanpy_run_tsne%2F1.8.1%2B1%2Bgalaxy1 - - title: Scanpy RunUMAP 1.8.1+3+galaxy0 + - description: 'Scanpy RunUMAP: visualise cell clusters using UMAP' + title: Scanpy RunUMAP 1.8.1+3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_umap%2Fscanpy_run_umap%2F1.8.1%2B3%2Bgalaxy0 - - title: Scanpy ScaleData 1.8.1+1+galaxy0 + - description: 'Scanpy ScaleData: to make expression variance the same for all genes' + title: Scanpy ScaleData 1.8.1+1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_scale_data%2Fscanpy_scale_data%2F1.8.1%2B1%2Bgalaxy0 homepage: https://github.com/theislab/Scanpy id: scanpy @@ -16207,17 +18149,25 @@ description: Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. galaxy: - - title: 'Scater: t-SNE plot 1.22.0' + - description: 'Scater: t-SNE plot: of two components' + title: 'Scater: t-SNE plot 1.22.0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscater_plot_tsne%2Fscater_plot_tsne%2F1.22.0 - - title: 'Scater: plot expression frequency 1.12.2' + - description: 'Scater: plot expression frequency: Plot the frequency of expression + against the mean expression level for SCE' + title: 'Scater: plot expression frequency 1.12.2' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscater_plot_exprs_freq%2Fscater_plot_exprs_freq%2F1.12.2 - - title: 'Scater: calculate QC metrics 1.22.0' + - description: 'Scater: calculate QC metrics: from single-cell expression matrix' + title: 'Scater: calculate QC metrics 1.22.0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscater_create_qcmetric_ready_sce%2Fscater_create_qcmetric_ready_sce%2F1.22.0 - - title: 'Scater: filter SCE 1.22.0' + - description: 'Scater: filter SCE: with user-defined parameters or PCA' + title: 'Scater: filter SCE 1.22.0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscater_filter%2Fscater_filter%2F1.22.0 - - title: 'Scater: plot library QC 1.22.0' + - description: 'Scater: plot library QC: to visualise library size, feature counts + and mito gene expression' + title: 'Scater: plot library QC 1.22.0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscater_plot_dist_scatter%2Fscater_plot_dist_scatter%2F1.22.0 - - title: 'Scater: PCA plot 1.22.0' + - description: 'Scater: PCA plot: cell-level reduced dimension of a normalised SCE' + title: 'Scater: PCA plot 1.22.0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscater_plot_pca%2Fscater_plot_pca%2F1.22.0 homepage: http://bioconductor.org/packages/release/bioc/html/scater.html id: scater @@ -16257,19 +18207,26 @@ description: Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. galaxy: - - title: Count objects in label map 0.0.5-2 + - 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 - - title: Threshold image 0.0.5-2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2F2d_auto_threshold%2Fip_threshold%2F0.0.5-2 - - title: Extract 2D features 0.1.1-2 + - 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: 'Extract 2D features: with scikit-image' + title: Extract 2D features 0.1.1-2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2F2d_feature_extraction%2Fip_2d_feature_extraction%2F0.1.1-2 - - title: Filter label map by rules 0.0.1-2 + - 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 - - title: Perform histogram equalization 0.0.1-2 + - 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 - - title: Filter 2D image 0.0.3-3 + - 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: Convert binary image to label map 0.5+galaxy0 + - 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 homepage: http://scikit-image.org id: scikit-image @@ -16291,33 +18248,54 @@ bunya: '' description: '' galaxy: - - title: Estimator attributes 1.0.11.0 + - description: 'Estimator attributes: get important attributes from an estimator + or scikit object' + title: Estimator attributes 1.0.11.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsklearn_estimator_attributes%2Fsklearn_estimator_attributes%2F1.0.11.0 - - title: Pipeline Builder 1.0.11.0 + - description: 'Pipeline Builder: an all-in-one platform to build pipeline, single + estimator, preprocessor and custom wrappers' + title: Pipeline Builder 1.0.11.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsklearn_build_pipeline%2Fsklearn_build_pipeline%2F1.0.11.0 - - title: Numeric Clustering 1.0.11.0 + - description: 'Numeric Clustering: ' + title: Numeric Clustering 1.0.11.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsklearn_numeric_clustering%2Fsklearn_numeric_clustering%2F1.0.11.0 - - title: Nearest Neighbors Classification 1.0.11.0 + - description: 'Nearest Neighbors Classification: ' + title: Nearest Neighbors Classification 1.0.11.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsklearn_nn_classifier%2Fsklearn_nn_classifier%2F1.0.11.0 - - title: Machine Learning Visualization Extension 1.0.11.0 + - description: 'Machine Learning Visualization Extension: includes several types + of plotting for machine learning' + title: Machine Learning Visualization Extension 1.0.11.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fml_visualization_ex%2Fml_visualization_ex%2F1.0.11.0 - - title: Create a deep learning model architecture 1.0.11.0 + - description: 'Create a deep learning model architecture: using Keras' + title: Create a deep learning model architecture 1.0.11.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fkeras_model_config%2Fkeras_model_config%2F1.0.11.0 - - title: Ensemble methods 1.0.11.0 + - description: 'Ensemble methods: for classification and regression' + title: Ensemble methods 1.0.11.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsklearn_ensemble%2Fsklearn_ensemble%2F1.0.11.0 - - title: To categorical 1.0.11.0 + - description: 'To categorical: Converts a class vector (integers) to binary class + matrix' + title: To categorical 1.0.11.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsklearn_to_categorical%2Fsklearn_to_categorical%2F1.0.11.0 - - title: Support vector machines (SVMs) 1.0.11.0 + - description: 'Support vector machines (SVMs): for classification' + title: Support vector machines (SVMs) 1.0.11.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsklearn_svm_classifier%2Fsklearn_svm_classifier%2F1.0.11.0 - - title: Hyperparameter Search 1.0.11.0 + - description: 'Hyperparameter Search: performs hyperparameter optimization using + various SearchCVs' + title: Hyperparameter Search 1.0.11.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsklearn_searchcv%2Fsklearn_searchcv%2F1.0.11.0 - - title: Create deep learning model 1.0.11.0 + - description: 'Create deep learning model: with an optimizer, loss function and + fit parameters' + title: Create deep learning model 1.0.11.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fkeras_model_builder%2Fkeras_model_builder%2F1.0.11.0 - - title: Deep learning training and evaluation 1.0.11.0 + - description: 'Deep learning training and evaluation: conduct deep training and + evaluation either implicitly or explicitly' + title: Deep learning training and evaluation 1.0.11.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fkeras_train_and_eval%2Fkeras_train_and_eval%2F1.0.11.0 - - title: Model Prediction 1.0.11.0 + - description: 'Model Prediction: predicts on new data using a preffited model' + title: Model Prediction 1.0.11.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fmodel_prediction%2Fmodel_prediction%2F1.0.11.0 - - title: Generalized linear models 1.0.11.0 + - description: 'Generalized linear models: for classification and regression' + title: Generalized linear models 1.0.11.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsklearn_generalized_linear%2Fsklearn_generalized_linear%2F1.0.11.0 homepage: http://scikit-learn.org id: scikit @@ -16366,7 +18344,8 @@ bunya: '' description: '' galaxy: - - title: Extract values from an SD-file 2020.03.4+galaxy0 + - description: 'Extract values from an SD-file: into a tabular file using RDKit' + title: Extract values from an SD-file 2020.03.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsdf_to_tab%2Fsdf_to_tab%2F2020.03.4%2Bgalaxy0 homepage: '' id: sdf_to_tab @@ -16398,7 +18377,8 @@ bunya: '' description: '' galaxy: - - title: Send to cloud 0.1.0 + - description: 'Send to cloud: ' + title: Send to cloud 0.1.0 url: https://usegalaxy.org.au/root?tool_id=send_to_cloud homepage: '' id: send_to_cloud @@ -16437,7 +18417,8 @@ bunya: '' description: '' galaxy: - - title: Filter sequences by ID 0.2.9 + - 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 homepage: '' id: seq_filter_by_id @@ -16454,7 +18435,8 @@ bunya: '' description: '' galaxy: - - title: Select sequences by ID 0.0.14 + - description: 'Select sequences by ID: from a tabular file' + title: Select sequences by ID 0.0.14 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fpeterjc%2Fseq_select_by_id%2Fseq_select_by_id%2F0.0.14 homepage: '' id: seq_select_by_id @@ -16548,35 +18530,51 @@ description: A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. galaxy: - - title: seqtk_telo 1.4+galaxy0 + - description: 'seqtk_telo: find telomeres' + title: seqtk_telo 1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqtk%2Fseqtk_telo%2F1.4%2Bgalaxy0 - - title: seqtk_mutfa 1.4+galaxy0 + - description: 'seqtk_mutfa: point mutate FASTA at specified positions' + title: seqtk_mutfa 1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqtk%2Fseqtk_mutfa%2F1.4%2Bgalaxy0 - - title: seqtk_subseq 1.4+galaxy0 + - description: 'seqtk_subseq: extract subsequences from FASTA/Q files' + title: seqtk_subseq 1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqtk%2Fseqtk_subseq%2F1.4%2Bgalaxy0 - - title: seqtk_cutN 1.4+galaxy0 + - description: 'seqtk_cutN: cut sequence at long N' + title: seqtk_cutN 1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqtk%2Fseqtk_cutN%2F1.4%2Bgalaxy0 - - title: seqtk_listhet 1.4+galaxy0 + - description: 'seqtk_listhet: extract the position of each het' + title: seqtk_listhet 1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqtk%2Fseqtk_listhet%2F1.4%2Bgalaxy0 - - title: seqtk_mergepe 1.4+galaxy0 + - description: 'seqtk_mergepe: interleave two unpaired FASTA/Q files for a paired-end + file' + title: seqtk_mergepe 1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqtk%2Fseqtk_mergepe%2F1.4%2Bgalaxy0 - - title: seqtk_seq 1.4+galaxy0 + - description: 'seqtk_seq: common transformation of FASTA/Q' + title: seqtk_seq 1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqtk%2Fseqtk_seq%2F1.4%2Bgalaxy0 - - title: seqtk_mergefa 1.4+galaxy0 + - description: 'seqtk_mergefa: merge two FASTA/Q files' + title: seqtk_mergefa 1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqtk%2Fseqtk_mergefa%2F1.4%2Bgalaxy0 - - title: seqtk_sample 1.4+galaxy0 + - description: 'seqtk_sample: random subsample of fasta or fastq sequences' + title: seqtk_sample 1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqtk%2Fseqtk_sample%2F1.4%2Bgalaxy0 - - title: seqtk_dropse 1.4+galaxy0 + - description: 'seqtk_dropse: drop unpaired from interleaved Paired End FASTA/Q' + title: seqtk_dropse 1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqtk%2Fseqtk_dropse%2F1.4%2Bgalaxy0 - - title: seqtk_fqchk 1.4+galaxy0 + - description: 'seqtk_fqchk: fastq QC (base/quality summary)' + title: seqtk_fqchk 1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqtk%2Fseqtk_fqchk%2F1.4%2Bgalaxy0 - - title: seqtk_trimfq 1.4+galaxy0 + - description: 'seqtk_trimfq: trim FASTQ using the Phred algorithm' + title: seqtk_trimfq 1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqtk%2Fseqtk_trimfq%2F1.4%2Bgalaxy0 - - title: seqtk_randbase 1.4+galaxy0 + - description: 'seqtk_randbase: choose a random base from hets' + title: seqtk_randbase 1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqtk%2Fseqtk_randbase%2F1.4%2Bgalaxy0 - - title: seqtk_hety 1.4+galaxy0 + - description: 'seqtk_hety: regional heterozygosity' + title: seqtk_hety 1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqtk%2Fseqtk_hety%2F1.4%2Bgalaxy0 - - title: seqtk_comp 1.4+galaxy0 + - description: 'seqtk_comp: get the nucleotide composition of FASTA/Q' + title: seqtk_comp 1.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqtk%2Fseqtk_comp%2F1.4%2Bgalaxy0 homepage: https://github.com/lh3/seqtk id: seqtk @@ -16617,7 +18615,8 @@ sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. galaxy: - - title: Seurat 4.3.0.1+galaxy1 + - 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 homepage: https://satijalab.org/seurat/ id: seurat @@ -16638,7 +18637,8 @@ bunya: '' description: '' galaxy: - - title: SFF converter 1.0.1 + - description: 'SFF converter: ' + title: SFF converter 1.0.1 url: https://usegalaxy.org.au/root?tool_id=Sff_extractor homepage: '' id: Sff_extractor @@ -16675,7 +18675,8 @@ bunya: '' description: De novo assembly from Oxford Nanopore reads. galaxy: - - title: Shasta 0.6.0+galaxy0 + - description: 'Shasta: De novo assembly of long read sequencing data' + title: Shasta 0.6.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fshasta%2Fshasta%2F0.6.0%2Bgalaxy0 homepage: https://github.com/chanzuckerberg/shasta id: shasta @@ -16703,7 +18704,8 @@ can take advantage of the pre- and post-processing the Shovill provides with those too. galaxy: - - title: Shovill 1.1.0+galaxy2 + - description: 'Shovill: Faster SPAdes assembly of Illumina reads' + title: Shovill 1.1.0+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fshovill%2Fshovill%2F1.1.0%2Bgalaxy2 homepage: https://github.com/tseemann/shovill id: shovill @@ -16754,7 +18756,9 @@ description: A clustering approach for identification of enriched domains from histone modification ChIP-seq data. galaxy: - - title: SICER 1.1 + - description: 'SICER: Statistical approach for the Identification of ChIP-Enriched + Regions' + title: SICER 1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsicer%2Fpeakcalling_sicer%2F1.1 homepage: http://home.gwu.edu/%7Ewpeng/Software.htm id: sicer @@ -16806,9 +18810,12 @@ For all PMIDs in each row of a table the according abstracts are saved in additional columns.' galaxy: - - title: PMIDs to PubTator 0.0.2 + - description: 'PMIDs to PubTator: binary matrix' + title: PMIDs to PubTator 0.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpmids_to_pubtator_matrix%2Fpmids_to_pubtator_matrix%2F0.0.2 - - title: PubMed query 0.0.2 + - description: 'PubMed query: download a defined number of abstracts or PMIDs from + PubMed' + title: PubMed query 0.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpubmed_by_queries%2Fpubmed_by_queries%2F0.0.2 homepage: https://github.com/mgramm1/simtext id: simtext @@ -16849,11 +18856,13 @@ and freely available web application for rapid in silico typing and serovar prediction from Salmonella genome assemblies using cgMLST and O and H antigen gene searching. galaxy: - - title: sistr_cmd 1.1.1+galaxy1 + - description: 'sistr_cmd: Salmonella In Silico Typing Resource commandline tool + for serovar prediction' + title: sistr_cmd 1.1.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fsistr_cmd%2Fsistr_cmd%2F1.1.1%2Bgalaxy1 - homepage: https://lfz.corefacility.ca/sistr-app/ + homepage: https://github.com/phac-nml/sistr_cmd id: sistr - license: '' + license: Apache-2.0 name: sistr nci-gadi: '' nci-if89: '' @@ -16994,7 +19003,9 @@ Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568' galaxy: - - title: Smudgeplot 0.2.5+galaxy3 + - description: 'Smudgeplot: inference of ploidy and heterozygosity structure using + whole genome sequencing' + title: Smudgeplot 0.2.5+galaxy3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxy-australia%2Fsmudgeplot%2Fsmudgeplot%2F0.2.5%2Bgalaxy3 homepage: https://github.com/KamilSJaron/smudgeplot id: Smudgeplots @@ -17043,7 +19054,8 @@ - '2013_11_29' description: The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. galaxy: - - title: Train SNAP 2013_11_29+galaxy1 + - description: 'Train SNAP: ab-initio gene predictor' + title: Train SNAP 2013_11_29+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnap_training%2Fsnap_training%2F2013_11_29%2Bgalaxy1 homepage: https://korflab.ucdavis.edu/software.html id: snap @@ -17100,7 +19112,8 @@ description: An algorithm for structural variation detection from third generation sequencing alignment. galaxy: - - title: sniffles 1.0.12+galaxy0 + - description: 'sniffles: Structural variation caller using third generation sequencing' + title: sniffles 1.0.12+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsniffles%2Fsniffles%2F1.0.12%2Bgalaxy0 homepage: https://github.com/fritzsedlazeck/Sniffles id: sniffles @@ -17123,11 +19136,16 @@ bunya: '' description: Rapid haploid variant calling and core SNP phylogeny generation. galaxy: - - title: snippy-clean_full_aln 4.6.0+galaxy0 + - description: 'snippy-clean_full_aln: Replace any non-standard sequence characters + in snippy ''core.full.aln'' file.' + title: snippy-clean_full_aln 4.6.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnippy%2Fsnippy_clean_full_aln%2F4.6.0%2Bgalaxy0 - - title: snippy-core 4.6.0+galaxy0 + - description: 'snippy-core: Combine multiple Snippy outputs into a core SNP alignment' + title: snippy-core 4.6.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnippy%2Fsnippy_core%2F4.6.0%2Bgalaxy0 - - title: snippy 4.6.0+galaxy0 + - description: 'snippy: Snippy finds SNPs between a haploid reference genome and + your NGS sequence reads.' + title: snippy 4.6.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnippy%2Fsnippy%2F4.6.0%2Bgalaxy0 homepage: https://github.com/tseemann/snippy id: snippy @@ -17148,7 +19166,8 @@ bunya: '' description: '' galaxy: - - title: Finds SNP sites 2.5.1+galaxy0 + - description: 'Finds SNP sites: from a multi-FASTA alignment file' + title: Finds SNP sites 2.5.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnp_sites%2Fsnp_sites%2F2.5.1%2Bgalaxy0 homepage: '' id: snp_sites @@ -17165,7 +19184,9 @@ bunya: '' description: '' galaxy: - - title: SNP distance matrix 0.8.2+galaxy0 + - description: 'SNP distance matrix: Compute distance in SNPs between all sequences + in a FASTA file' + title: SNP distance matrix 0.8.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnp_dists%2Fsnp_dists%2F0.8.2%2Bgalaxy0 homepage: '' id: snp-dists @@ -17183,17 +19204,23 @@ description: Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). galaxy: - - title: 'SnpEff chromosome-info: 4.3+T.galaxy2' + - description: 'SnpEff chromosome-info:: list chromosome names/lengths' + title: 'SnpEff chromosome-info: 4.3+T.galaxy2' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2FsnpEff_get_chr_names%2F4.3%2BT.galaxy2 - - title: 'SnpEff build: 4.3+T.galaxy6' + - description: 'SnpEff build:: database from Genbank or GFF record' + title: 'SnpEff build: 4.3+T.galaxy6' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2FsnpEff_build_gb%2F4.3%2BT.galaxy6 - - title: 'SnpEff databases: 4.3+T.galaxy2' + - description: 'SnpEff databases:: list available databases' + title: 'SnpEff databases: 4.3+T.galaxy2' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2FsnpEff_databases%2F4.3%2BT.galaxy2 - - title: 'SnpEff download: 4.3+T.galaxy2' + - description: 'SnpEff download:: download a pre-built database' + title: 'SnpEff download: 4.3+T.galaxy2' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2FsnpEff_download%2F4.3%2BT.galaxy2 - - title: 'SnpEff eff: 4.3+T.galaxy2' + - description: 'SnpEff eff:: annotate variants' + title: 'SnpEff eff: 4.3+T.galaxy2' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2FsnpEff%2F4.3%2BT.galaxy2 - - title: 'SnpEff eff: 4.5covid19' + - description: 'SnpEff eff:: annotate variants for SARS-CoV-2' + title: 'SnpEff eff: 4.5covid19' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff_sars_cov_2%2Fsnpeff_sars_cov_2%2F4.5covid19 homepage: http://snpeff.sourceforge.net/ id: snpeff @@ -17215,7 +19242,8 @@ bunya: '' description: '' galaxy: - - title: snpFreq 1.0.1 + - description: 'snpFreq: significant SNPs in case-control data' + title: snpFreq 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsnpfreq%2Fhgv_snpFreq%2F1.0.1 homepage: '' id: snpfreq @@ -17232,7 +19260,9 @@ bunya: '' description: '' galaxy: - - title: Variant Frequency Plot 1.0+galaxy3 + - description: 'Variant Frequency Plot: Generates a heatmap of allele frequencies + grouped by variant type for SnpEff-annotated SARS-CoV-2 data' + title: Variant Frequency Plot 1.0+galaxy3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpfreqplot%2Fsnpfreqplot%2F1.0%2Bgalaxy3 homepage: '' id: snpfreqplot @@ -17249,21 +19279,30 @@ bunya: '' description: Toolbox that allows you to filter and manipulate annotated vcf files. galaxy: - - title: SnpSift CaseControl 4.3+t.galaxy0 + - description: 'SnpSift CaseControl: Count samples are in ''case'' and ''control'' + groups.' + title: SnpSift CaseControl 4.3+t.galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpsift%2FsnpSift_caseControl%2F4.3%2Bt.galaxy0 - - title: SnpSift vcfCheck 4.3+t.galaxy0 + - description: 'SnpSift vcfCheck: basic checks for VCF specification compliance' + title: SnpSift vcfCheck 4.3+t.galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpsift%2FsnpSift_vcfCheck%2F4.3%2Bt.galaxy0 - - title: SnpSift Variant Type 4.3+t.galaxy0 + - description: 'SnpSift Variant Type: Annotate with variant type' + title: SnpSift Variant Type 4.3+t.galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpsift%2Fsnpsift_vartype%2F4.3%2Bt.galaxy0 - - title: SnpSift Extract Fields 4.3+t.galaxy0 + - description: 'SnpSift Extract Fields: from a VCF file into a tabular file' + title: SnpSift Extract Fields 4.3+t.galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpsift%2FsnpSift_extractFields%2F4.3%2Bt.galaxy0 - - title: SnpSift Annotate 4.3+t.galaxy1 + - description: 'SnpSift Annotate: SNPs from dbSnp' + title: SnpSift Annotate 4.3+t.galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpsift%2FsnpSift_annotate%2F4.3%2Bt.galaxy1 - - title: SnpSift Filter 4.3+t.galaxy1 + - description: 'SnpSift Filter: Filter variants using arbitrary expressions' + title: SnpSift Filter 4.3+t.galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpsift%2FsnpSift_filter%2F4.3%2Bt.galaxy1 - - title: SnpSift rmInfo 4.3+t.galaxy0 + - description: 'SnpSift rmInfo: remove INFO field annotations' + title: SnpSift rmInfo 4.3+t.galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpsift%2FsnpSift_rmInfo%2F4.3%2Bt.galaxy0 - - title: SnpSift Intervals 4.3+t.galaxy0 + - description: 'SnpSift Intervals: Filter variants using intervals' + title: SnpSift Intervals 4.3+t.galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpsift%2FsnpSift_int%2F4.3%2Bt.galaxy0 homepage: http://snpeff.sourceforge.net/SnpSift.html id: snpsift @@ -17389,7 +19428,8 @@ - 4.3.6--h9ee0642_0 description: Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. galaxy: - - title: Filter with SortMeRNA 4.3.6+galaxy0 + - description: 'Filter with SortMeRNA: of ribosomal RNAs in metatranscriptomic data' + title: Filter with SortMeRNA 4.3.6+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fsortmerna%2Fbg_sortmerna%2F4.3.6%2Bgalaxy0 homepage: https://bioinfo.cristal.univ-lille.fr/RNA/sortmerna/ id: sortmerna @@ -17433,21 +19473,33 @@ \ Oxford Nanopore and Sanger reads. Additional contigs can be provided and can\ \ be used as long reads." galaxy: - - title: SPAdes 3.15.5+galaxy0 + - description: 'SPAdes: genome assembler for genomes of regular and single-cell + projects' + title: SPAdes 3.15.5+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fspades%2Fspades%2F3.15.5%2Bgalaxy0 - - title: rnaviralSPAdes 3.15.5+galaxy1 + - description: 'rnaviralSPAdes: de novo assembler for transcriptomes, metatranscriptomes + and metaviromes' + title: rnaviralSPAdes 3.15.5+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fspades_rnaviralspades%2Fspades_rnaviralspades%2F3.15.5%2Bgalaxy1 - - title: metaviralSPAdes 3.15.5+galaxy1 + - description: 'metaviralSPAdes: extract and assembly viral genomes from metagenomic + data' + title: metaviralSPAdes 3.15.5+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fspades_metaviralspades%2Fspades_metaviralspades%2F3.15.5%2Bgalaxy1 - - title: metaplasmidSPAdes 3.15.5+galaxy1 + - description: 'metaplasmidSPAdes: extract and assembly plasmids from metagenomic + data' + title: metaplasmidSPAdes 3.15.5+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fspades_metaplasmidspades%2Fspades_metaplasmidspades%2F3.15.5%2Bgalaxy1 - - title: coronaSPAdes 3.15.5+galaxy1 + - description: 'coronaSPAdes: SARS-CoV-2 de novo genome assembler' + title: coronaSPAdes 3.15.5+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fspades_coronaspades%2Fspades_coronaspades%2F3.15.5%2Bgalaxy1 - - title: biosyntheticSPAdes 3.15.5+galaxy1 + - description: 'biosyntheticSPAdes: biosynthetic gene cluster assembly' + title: biosyntheticSPAdes 3.15.5+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fspades_biosyntheticspades%2Fspades_biosyntheticspades%2F3.15.5%2Bgalaxy1 - - title: rnaSPAdes 3.15.5+galaxy1 + - description: 'rnaSPAdes: de novo transcriptome assembler' + title: rnaSPAdes 3.15.5+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Frnaspades%2Frnaspades%2F3.15.5%2Bgalaxy1 - - title: plasmidSPAdes 3.15.4+galaxy2 + - description: 'plasmidSPAdes: extract and assembly plasmids from WGS data' + title: plasmidSPAdes 3.15.4+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fspades_plasmidspades%2Fspades_plasmidspades%2F3.15.4%2Bgalaxy2 homepage: http://cab.spbu.ru/software/spades/ id: spades @@ -17508,7 +19560,8 @@ bunya: '' description: '' galaxy: - - title: Split file 0.5.1 + - description: 'Split file: to dataset collection' + title: Split file 0.5.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsplit_file_to_collection%2Fsplit_file_to_collection%2F0.5.1 homepage: '' id: split_file_to_collection @@ -17541,7 +19594,8 @@ bunya: '' description: '' galaxy: - - title: SQLite to tabular 3.2.0 + - 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 homepage: '' id: sqlite_to_tabular @@ -17583,7 +19637,8 @@ bunya: '' description: '' galaxy: - - title: SRA 1.0.1 + - description: 'SRA: server' + title: SRA 1.0.1 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=sra_source homepage: '' id: sra_source @@ -17603,12 +19658,15 @@ description: The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. galaxy: - - title: Download and Extract Reads in BAM 3.0.8+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Fsam_dump%2F3.0.8%2Bgalaxy1 - - title: Faster Download and Extract Reads in FASTQ 3.0.8+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffasterq_dump%2F3.0.8%2Bgalaxy1 - - title: Download and Extract Reads in FASTQ 3.0.8+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffastq_dump%2F3.0.8%2Bgalaxy1 + - description: 'Download and Extract Reads in BAM: format from NCBI SRA' + title: Download and Extract Reads in BAM 3.0.10+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Fsam_dump%2F3.0.10%2Bgalaxy0 + - description: 'Faster Download and Extract Reads in FASTQ: format from NCBI SRA' + title: Faster Download and Extract Reads in FASTQ 3.0.10+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffasterq_dump%2F3.0.10%2Bgalaxy0 + - description: 'Download and Extract Reads in FASTQ: format from NCBI SRA' + title: Download and Extract Reads in FASTQ 3.0.10+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffastq_dump%2F3.0.10%2Bgalaxy0 homepage: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc id: sra-tools license: '' @@ -17671,55 +19729,89 @@ as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. galaxy: - - title: 'Stacks2: clone filter 2.55+galaxy4' + - description: 'Stacks2: clone filter: Identify PCR clones' + title: 'Stacks2: clone filter 2.55+galaxy4' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_clonefilter%2Fstacks2_clonefilter%2F2.55%2Bgalaxy4 - - title: 'Stacks2: cstacks 2.55+galaxy4' + - description: 'Stacks2: cstacks: Generate catalog of loci' + title: 'Stacks2: cstacks 2.55+galaxy4' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_cstacks%2Fstacks2_cstacks%2F2.55%2Bgalaxy4 - - title: 'Stacks2: de novo map 2.55+galaxy4' + - description: 'Stacks2: de novo map: the Stacks pipeline without a reference genome + (denovo_map.pl)' + title: 'Stacks2: de novo map 2.55+galaxy4' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_denovomap%2Fstacks2_denovomap%2F2.55%2Bgalaxy4 - - title: 'Stacks2: gstacks 2.55+galaxy4' + - description: 'Stacks2: gstacks: Call variants, genotypes and haplotype' + title: 'Stacks2: gstacks 2.55+galaxy4' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_gstacks%2Fstacks2_gstacks%2F2.55%2Bgalaxy4 - - title: 'Stacks2: kmer filter 2.55+galaxy4' + - description: 'Stacks2: kmer filter: Identify PCR clones' + title: 'Stacks2: kmer filter 2.55+galaxy4' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_kmerfilter%2Fstacks2_kmerfilter%2F2.55%2Bgalaxy4 - - title: 'Stacks2: populations 2.55+galaxy4' + - description: 'Stacks2: populations: Calculate population-level summary statistics' + title: 'Stacks2: populations 2.55+galaxy4' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_populations%2Fstacks2_populations%2F2.55%2Bgalaxy4 - - title: 'Stacks2: process radtags 2.55+galaxy4' + - description: 'Stacks2: process radtags: the Stacks demultiplexing script' + title: 'Stacks2: process radtags 2.55+galaxy4' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_procrad%2Fstacks2_procrad%2F2.55%2Bgalaxy4 - - title: 'Stacks2: reference map 2.55+galaxy4' + - description: 'Stacks2: reference map: the Stacks pipeline with a reference genome + (ref_map.pl)' + title: 'Stacks2: reference map 2.55+galaxy4' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_refmap%2Fstacks2_refmap%2F2.55%2Bgalaxy4 - - title: 'Stacks2: process shortreads 2.55+galaxy4' + - description: 'Stacks2: process shortreads: fast cleaning of randomly sheared genomic + or transcriptomic data' + title: 'Stacks2: process shortreads 2.55+galaxy4' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_shortreads%2Fstacks2_shortreads%2F2.55%2Bgalaxy4 - - title: 'Stacks2: sstacks 2.55+galaxy4' + - description: 'Stacks2: sstacks: Match samples to the catalog' + title: 'Stacks2: sstacks 2.55+galaxy4' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_sstacks%2Fstacks2_sstacks%2F2.55%2Bgalaxy4 - - title: 'Stacks2: tsv2bam 2.55+galaxy4' + - description: 'Stacks2: tsv2bam: Sort reads by RAD locus' + title: 'Stacks2: tsv2bam 2.55+galaxy4' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_tsv2bam%2Fstacks2_tsv2bam%2F2.55%2Bgalaxy4 - - title: 'Stacks2: ustacks 2.55+galaxy4' + - description: 'Stacks2: ustacks: Identify unique stacks' + title: 'Stacks2: ustacks 2.55+galaxy4' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_ustacks%2Fstacks2_ustacks%2F2.55%2Bgalaxy4 - - title: 'Stacks: assemble read pairs by locus 1.46.1' + - description: 'Stacks: assemble read pairs by locus: run the STACKS sort_read_pairs.pl + and exec_velvet.pl wrappers' + title: 'Stacks: assemble read pairs by locus 1.46.1' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_assembleperead%2Fstacks_assembleperead%2F1.46.1 - - title: 'Stacks: clone filter 1.46.0' + - description: 'Stacks: clone filter: Identify PCR clones' + title: 'Stacks: clone filter 1.46.0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_clonefilter%2Fstacks_clonefilter%2F1.46.0 - - title: 'Stacks: cstacks 1.46.0' + - description: 'Stacks: cstacks: build a catalogue of loci' + title: 'Stacks: cstacks 1.46.0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_cstacks%2Fstacks_cstacks%2F1.46.0 - - title: 'Stacks: de novo map 1.46.0' + - description: 'Stacks: de novo map: the Stacks pipeline without a reference genome + (denovo_map.pl)' + title: 'Stacks: de novo map 1.46.0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_denovomap%2Fstacks_denovomap%2F1.46.0 - - title: 'Stacks: genotypes 1.46.0' + - description: 'Stacks: genotypes: analyse haplotypes or genotypes in a genetic + cross (''genotypes'' program)' + title: 'Stacks: genotypes 1.46.0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_genotypes%2Fstacks_genotypes%2F1.46.0 - - title: 'Stacks: populations 1.46.3' + - description: 'Stacks: populations: analyze a population of individual samples + (''populations'' program)' + title: 'Stacks: populations 1.46.3' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_populations%2Fstacks_populations%2F1.46.3 - - title: 'Stacks: process radtags 1.46.0' + - description: 'Stacks: process radtags: the Stacks demultiplexing script' + title: 'Stacks: process radtags 1.46.0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_procrad%2Fstacks_procrad%2F1.46.0 - - title: 'Stacks: pstacks 1.46.0' + - description: 'Stacks: pstacks: find stacks from short reads mapped to a reference + genome' + title: 'Stacks: pstacks 1.46.0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_pstacks%2Fstacks_pstacks%2F1.46.0 - - title: 'Stacks: reference map 1.46.0' + - description: 'Stacks: reference map: the Stacks pipeline with a reference genome + (ref_map.pl)' + title: 'Stacks: reference map 1.46.0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_refmap%2Fstacks_refmap%2F1.46.0 - - title: 'Stacks: rxstacks 1.46.0' + - description: 'Stacks: rxstacks: make corrections to genotype and haplotype calls' + title: 'Stacks: rxstacks 1.46.0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_rxstacks%2Fstacks_rxstacks%2F1.46.0 - - title: 'Stacks: sstacks 1.46.1' + - description: 'Stacks: sstacks: match stacks to a catalog' + title: 'Stacks: sstacks 1.46.1' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_sstacks%2Fstacks_sstacks%2F1.46.1 - - title: 'Stacks: statistics 1.46.0' + - description: 'Stacks: statistics: on stacks found for multiple samples' + title: 'Stacks: statistics 1.46.0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_stats%2Fstacks_stats%2F1.46.0 - - title: 'Stacks: ustacks 1.46.0' + - description: 'Stacks: ustacks: align short reads into stacks' + title: 'Stacks: ustacks 1.46.0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_ustacks%2Fstacks_ustacks%2F1.46.0 homepage: http://catchenlab.life.illinois.edu/stacks/ id: stacks @@ -17743,7 +19835,8 @@ - 2.7.10a--h9ee0642_0 description: Ultrafast universal RNA-seq data aligner galaxy: - - title: RNA STAR 2.7.11a+galaxy0 + - description: 'RNA STAR: Gapped-read mapper for RNA-seq data' + title: RNA STAR 2.7.11a+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Frgrnastar%2Frna_star%2F2.7.11a%2Bgalaxy0 homepage: http://code.google.com/p/rna-star/ id: star @@ -17770,7 +19863,9 @@ bunya: '' description: '' galaxy: - - title: staramr 0.10.0+galaxy1 + - description: 'staramr: Scans genome assemblies against the ResFinder, PlasmidFinder, + and PointFinder databases searching for AMR genes.' + title: staramr 0.10.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fstaramr%2Fstaramr_search%2F0.10.0%2Bgalaxy1 homepage: '' id: staramr @@ -17788,7 +19883,8 @@ description: STAR-Fusion, a method that is both fast and accurate in identifying fusion transcripts from RNA-Seq data galaxy: - - title: STAR-Fusion 0.5.4-3+galaxy1 + - description: 'STAR-Fusion: detect fusion genes in RNA-Seq data' + title: STAR-Fusion 0.5.4-3+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstar_fusion%2Fstar_fusion%2F0.5.4-3%2Bgalaxy1 homepage: https://github.com/STAR-Fusion/STAR-Fusion id: star_fusion @@ -17811,9 +19907,11 @@ novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. galaxy: - - title: StringTie merge 2.2.1+galaxy1 + - description: 'StringTie merge: transcripts' + title: StringTie merge 2.2.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstringtie%2Fstringtie_merge%2F2.2.1%2Bgalaxy1 - - title: StringTie 2.2.1+galaxy1 + - description: 'StringTie: transcript assembly and quantification' + title: StringTie 2.2.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstringtie%2Fstringtie%2F2.2.1%2Bgalaxy1 homepage: https://ccb.jhu.edu/software/stringtie/ id: stringtie @@ -17895,7 +19993,8 @@ bunya: '' description: '' galaxy: - - title: Summary Statistics 1.1.2 + - description: 'Summary Statistics: for any numerical column' + title: Summary Statistics 1.1.2 url: https://usegalaxy.org.au/root?tool_id=Summary_Statistics1 homepage: '' id: Summary_Statistics1 @@ -18109,7 +20208,8 @@ bunya: '' description: '' galaxy: - - title: T Test for Two Samples 1.0.1 + - description: 'T Test for Two Samples: ' + title: T Test for Two Samples 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ft_test_two_samples%2Ft_test_two_samples%2F1.0.1 homepage: '' id: t_test_two_samples @@ -18126,7 +20226,8 @@ bunya: '' description: '' galaxy: - - title: Table Compute 1.2.4+galaxy0 + - 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 homepage: '' id: table_compute @@ -18143,7 +20244,8 @@ bunya: '' description: '' galaxy: - - title: Tabular-to-FASTA 1.1.1 + - description: 'Tabular-to-FASTA: converts tabular file to FASTA format' + title: Tabular-to-FASTA 1.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftabular_to_fasta%2Ftab2fasta%2F1.1.1 homepage: '' id: tabular_to_fasta @@ -18183,7 +20285,8 @@ description: Targetfinder.org provides a web based resource that allows users to find genes that have a similar expression to a query gene signature. galaxy: - - title: TargetFinder 1.7.0+galaxy1 + - description: 'TargetFinder: plant small RNA target prediction tool' + title: TargetFinder 1.7.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Ftargetfinder%2Ftargetfinder%2F1.7.0%2Bgalaxy1 homepage: https://github.com/carringtonlab/TargetFinder id: targetfinder @@ -18253,7 +20356,8 @@ bunya: '' description: '' galaxy: - - title: TB Variant Filter 0.4.0+galaxy0 + - description: 'TB Variant Filter: M. tuberculosis H37Rv VCF filter' + title: TB Variant Filter 0.4.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftb_variant_filter%2Ftb_variant_filter%2F0.4.0%2Bgalaxy0 homepage: '' id: tb_variant_filter @@ -18287,7 +20391,9 @@ bunya: '' description: '' galaxy: - - title: TB-Profiler Profile 4.4.1+galaxy0 + - description: 'TB-Profiler Profile: Infer strain types and drug resistance markers + from sequences' + title: TB-Profiler Profile 4.4.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftbprofiler%2Ftb_profiler_profile%2F4.4.1%2Bgalaxy0 homepage: '' id: tbprofiler @@ -18304,7 +20410,9 @@ bunya: '' description: '' galaxy: - - title: TB Variant Report 0.1.10+galaxy0 + - description: 'TB Variant Report: - generate HTML report from SnpEff annotated + M.tb VCF(s)' + title: TB Variant Report 0.1.10+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftbvcfreport%2Ftbvcfreport%2F0.1.10%2Bgalaxy0 homepage: '' id: tbvcfreport @@ -18390,7 +20498,8 @@ bunya: '' description: '' galaxy: - - title: TEtranscripts 2.2.3+galaxy0 + - description: 'TEtranscripts: annotates reads to genes and transposable elements' + title: TEtranscripts 2.2.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftetoolkit_tetranscripts%2Ftetoolkit_tetranscripts%2F2.2.3%2Bgalaxy0 homepage: '' id: TEtranscripts @@ -18407,43 +20516,62 @@ bunya: '' description: '' galaxy: - - title: Join 9.3+galaxy0 + - description: 'Join: two files' + title: Join 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_easyjoin_tool%2F9.3%2Bgalaxy0 - - title: Sort a row 9.3+galaxy0 + - description: 'Sort a row: according to their columns' + title: Sort a row 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_sort_rows%2F9.3%2Bgalaxy0 - - title: Text transformation 9.3+galaxy0 + - description: 'Text transformation: with sed' + title: Text transformation 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_sed_tool%2F9.3%2Bgalaxy0 - - title: Select first 9.3+galaxy0 + - description: 'Select first: lines from a dataset (head)' + title: Select first 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_head_tool%2F9.3%2Bgalaxy0 - - title: Create text file 9.3+galaxy0 + - description: 'Create text file: with recurring lines' + title: Create text file 9.3+galaxy0 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%2Bgalaxy0 - - title: Concatenate datasets 9.3+galaxy0 + - description: 'Concatenate datasets: tail-to-head (cat)' + title: Concatenate datasets 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_cat%2F9.3%2Bgalaxy0 - - title: tac 9.3+galaxy0 + - description: 'tac: reverse a file (reverse cat)' + title: tac 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_tac%2F9.3%2Bgalaxy0 - - title: Unfold 9.3+galaxy0 + - description: 'Unfold: columns from a table' + title: Unfold 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_unfold_column_tool%2F9.3%2Bgalaxy0 - - title: Search in textfiles 9.3+galaxy0 + - description: 'Search in textfiles: (grep)' + title: Search in textfiles 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_grep_tool%2F9.3%2Bgalaxy0 - - title: Advanced Cut 9.3+galaxy0 + - description: 'Advanced Cut: columns from a table (cut)' + title: Advanced Cut 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_cut_tool%2F9.3%2Bgalaxy0 - - title: Sort 9.3+galaxy0 + - description: 'Sort: data in ascending or descending order' + title: Sort 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_sort_header_tool%2F9.3%2Bgalaxy0 - - title: Replace Text 9.3+galaxy0 + - description: 'Replace Text: in entire line' + title: Replace Text 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_replace_in_line%2F9.3%2Bgalaxy0 - - title: Replace Text 9.3+galaxy0 + - description: 'Replace Text: in a specific column' + title: Replace Text 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_replace_in_column%2F9.3%2Bgalaxy0 - - title: Replace 9.3+galaxy0 + - description: 'Replace: parts of text' + title: Replace 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_find_and_replace%2F9.3%2Bgalaxy0 - - title: Multi-Join 9.3+galaxy0 + - description: 'Multi-Join: (combine multiple files)' + title: Multi-Join 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_multijoin_tool%2F9.3%2Bgalaxy0 - - title: Select last 9.3+galaxy0 + - description: 'Select last: lines from a dataset (tail)' + title: Select last 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_tail_tool%2F9.3%2Bgalaxy0 - - title: Unique 9.3+galaxy0 + - description: 'Unique: occurrences of each record' + title: Unique 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_sorted_uniq%2F9.3%2Bgalaxy0 - - title: Unique lines 9.3+galaxy0 + - description: 'Unique lines: assuming sorted input file' + title: Unique lines 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_uniq_tool%2F9.3%2Bgalaxy0 - - title: Text reformatting 9.3+galaxy0 + - description: 'Text reformatting: with awk' + title: Text reformatting 9.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Ftp_awk_tool%2F9.3%2Bgalaxy0 homepage: '' id: text_processing @@ -18461,7 +20589,8 @@ description: Open-source, crossplatform tool that converts Thermo RAW files into open file formats such as MGF and to the HUPO-PSI standard file format mzML galaxy: - - title: Thermo 1.3.4+galaxy0 + - description: 'Thermo: RAW file converter' + title: Thermo 1.3.4+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fthermo_raw_file_converter%2Fthermo_raw_file_converter%2F1.3.4%2Bgalaxy0 homepage: https://github.com/compomics/ThermoRawFileParser id: ThermoRawFileParser @@ -18485,9 +20614,11 @@ exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie. A stable SAMtools version is now packaged with the program. galaxy: - - title: TopHat 2.1.1 + - description: 'TopHat: Gapped-read mapper for RNA-seq data' + title: TopHat 2.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftophat2%2Ftophat2%2F2.1.1 - - title: Tophat Fusion Post 0.1 + - description: 'Tophat Fusion Post: post-processing to identify fusion genes' + title: Tophat Fusion Post 0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftophat_fusion_post%2Ftophat_fusion_post%2F0.1 homepage: http://ccb.jhu.edu/software/tophat/index.shtml id: tophat @@ -18549,7 +20680,8 @@ Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. galaxy: - - title: TransDecoder 5.5.0+galaxy2 + - description: 'TransDecoder: finds coding regions within transcripts' + title: TransDecoder 5.5.0+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftransdecoder%2Ftransdecoder%2F5.5.0%2Bgalaxy2 homepage: https://github.com/TransDecoder/TransDecoder/wiki id: transdecoder @@ -18574,15 +20706,20 @@ graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. galaxy: - - title: TRANSIT Tn5Gaps 3.0.2+galaxy1 + - description: 'TRANSIT Tn5Gaps: - determine essential genes' + title: TRANSIT Tn5Gaps 3.0.2+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftransit_tn5gaps%2Ftransit_tn5gaps%2F3.0.2%2Bgalaxy1 - - title: Convert GFF3 3.0.2+galaxy0 + - description: 'Convert GFF3: to prot_table for TRANSIT' + title: Convert GFF3 3.0.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgff_to_prot%2Fgff_to_prot%2F3.0.2%2Bgalaxy0 - - title: TRANSIT Resampling 3.0.2+galaxy1 + - description: 'TRANSIT Resampling: - determine per-gene p-values' + title: TRANSIT Resampling 3.0.2+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftransit_resampling%2Ftransit_resampling%2F3.0.2%2Bgalaxy1 - - title: TRANSIT HMM 3.0.2+galaxy1 + - description: 'TRANSIT HMM: - determine essentiality of a genome' + title: TRANSIT HMM 3.0.2+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftransit_hmm%2Ftransit_hmm%2F3.0.2%2Bgalaxy1 - - title: TRANSIT Gumbel 3.0.2+galaxy1 + - description: 'TRANSIT Gumbel: - determine essential genes' + title: TRANSIT Gumbel 3.0.2+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftransit_gumbel%2Ftransit_gumbel%2F3.0.2%2Bgalaxy1 homepage: http://saclab.tamu.edu/essentiality/transit/ id: transit @@ -18619,15 +20756,24 @@ bunya: '' description: Institute for Systems Biology "Trans-Proteomic Pipeline" galaxy: - - title: Protein Prophet 1.1.1 + - description: 'Protein Prophet: Calculate Protein Prophet statistics on search + results' + title: Protein Prophet 1.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Firacooke%2Ftpp_prophets%2Fproteomics_search_protein_prophet_1%2F1.1.1 - - title: PepXML to Table 1.1.1 + - description: 'PepXML to Table: Converts a pepXML file to a tab delimited text + file' + title: PepXML to Table 1.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Firacooke%2Ftpp_prophets%2Fpepxml_to_table_1%2F1.1.1 - - title: InterProphet 1.1.1 + - description: 'InterProphet: Combine Peptide Prophet results from multiple search + engines' + title: InterProphet 1.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Firacooke%2Ftpp_prophets%2Fproteomics_search_interprophet_1%2F1.1.1 - - title: Peptide Prophet 1.1.1 + - description: 'Peptide Prophet: Calculate Peptide Prophet statistics on search + results' + title: Peptide Prophet 1.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Firacooke%2Ftpp_prophets%2Fproteomics_search_peptide_prophet_1%2F1.1.1 - - title: ProtXML to Table 1.1.1 + - description: 'ProtXML to Table: Converts a ProtXML file to a table' + title: ProtXML to Table 1.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Firacooke%2Ftpp_prophets%2Fprotxml_to_table_1%2F1.1.1 homepage: http://tools.proteomecenter.org/software.php id: tpp @@ -18739,7 +20885,8 @@ and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. galaxy: - - title: Trim Galore! 0.6.7+galaxy0 + - description: 'Trim Galore!: Quality and adapter trimmer of reads' + title: Trim Galore! 0.6.7+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftrim_galore%2Ftrim_galore%2F0.6.7%2Bgalaxy0 homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ id: trim_galore @@ -18773,7 +20920,8 @@ - 0.39-java-11 description: A flexible read trimming tool for Illumina NGS data galaxy: - - title: Trimmomatic 0.36.6 + - description: 'Trimmomatic: flexible read trimming tool for Illumina NGS data' + title: Trimmomatic 0.36.6 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fpjbriggs%2Ftrimmomatic%2Ftrimmomatic%2F0.36.6 homepage: http://www.usadellab.org/cms/index.php?page=trimmomatic id: trimmomatic @@ -18802,29 +20950,46 @@ tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. galaxy: - - title: Generate SuperTranscripts 2.15.1+galaxy0 + - description: 'Generate SuperTranscripts: from a Trinity assembly' + title: Generate SuperTranscripts 2.15.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftrinity_super_transcripts%2Ftrinity_super_transcripts%2F2.15.1%2Bgalaxy0 - - title: Trinity Stats 2.15.1+galaxy0 + - description: 'Trinity Stats: ' + title: Trinity Stats 2.15.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftrinity_stats%2Ftrinity_stats%2F2.15.1%2Bgalaxy0 - - title: Trinity 2.15.1+galaxy1 + - description: 'Trinity: de novo assembly of RNA-Seq data' + title: Trinity 2.15.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftrinity%2Ftrinity%2F2.15.1%2Bgalaxy1 - - title: Build expression matrix 2.15.1+galaxy0 + - description: 'Build expression matrix: for a de novo assembly of RNA-Seq data + by Trinity' + title: Build expression matrix 2.15.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftrinity_abundance_estimates_to_matrix%2Ftrinity_abundance_estimates_to_matrix%2F2.15.1%2Bgalaxy0 - - title: Align reads and estimate abundance 2.15.1+galaxy0 + - description: 'Align reads and estimate abundance: on a de novo assembly of RNA-Seq + data' + title: Align reads and estimate abundance 2.15.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftrinity_align_and_estimate_abundance%2Ftrinity_align_and_estimate_abundance%2F2.15.1%2Bgalaxy0 - - title: Extract and cluster differentially expressed transcripts 2.15.1+galaxy0 + - description: 'Extract and cluster differentially expressed transcripts: from a + Trinity assembly' + title: Extract and cluster differentially expressed transcripts 2.15.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftrinity_analyze_diff_expr%2Ftrinity_analyze_diff_expr%2F2.15.1%2Bgalaxy0 - - title: Compute contig Ex90N50 statistic and Ex90 transcript count 2.15.1+galaxy0 + - description: 'Compute contig Ex90N50 statistic and Ex90 transcript count: from + a Trinity assembly' + title: Compute contig Ex90N50 statistic and Ex90 transcript count 2.15.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftrinity_contig_exn50_statistic%2Ftrinity_contig_exn50_statistic%2F2.15.1%2Bgalaxy0 - - title: Partition genes into expression clusters 2.15.1+galaxy0 + - description: 'Partition genes into expression clusters: after differential expression + analysis using a Trinity assembly' + title: Partition genes into expression clusters 2.15.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftrinity_define_clusters_by_cutting_tree%2Ftrinity_define_clusters_by_cutting_tree%2F2.15.1%2Bgalaxy0 - - title: Filter low expression transcripts 2.15.1+galaxy0 + - description: 'Filter low expression transcripts: from a Trinity assembly' + title: Filter low expression transcripts 2.15.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftrinity_filter_low_expr_transcripts%2Ftrinity_filter_low_expr_transcripts%2F2.15.1%2Bgalaxy0 - - title: Generate gene to transcript map 2.15.1+galaxy0 + - description: 'Generate gene to transcript map: for Trinity assembly' + title: Generate gene to transcript map 2.15.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftrinity_gene_to_trans_map%2Ftrinity_gene_to_trans_map%2F2.15.1%2Bgalaxy0 - - title: Differential expression analysis 2.15.1+galaxy0 + - description: 'Differential expression analysis: using a Trinity assembly' + title: Differential expression analysis 2.15.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftrinity_run_de_analysis%2Ftrinity_run_de_analysis%2F2.15.1%2Bgalaxy0 - - title: RNASeq samples quality check 2.15.1+galaxy0 + - description: 'RNASeq samples quality check: for transcript quantification' + title: RNASeq samples quality check 2.15.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftrinity_samples_qccheck%2Ftrinity_samples_qccheck%2F2.15.1%2Bgalaxy0 homepage: https://github.com/trinityrnaseq/trinityrnaseq/wiki id: trinity @@ -18856,7 +21021,8 @@ of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. galaxy: - - title: Trinotate 3.2.2+galaxy0 + - description: 'Trinotate: functional transcript annotation' + title: Trinotate 3.2.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftrinotate%2Ftrinotate%2F3.2.2%2Bgalaxy0 homepage: https://github.com/Trinotate/Trinotate.github.io id: trinotate @@ -18878,7 +21044,8 @@ bunya: '' description: A program for improved detection of transfer RNA genes in genomic sequence. galaxy: - - title: tRNA prediction 0.4 + - description: 'tRNA prediction: (tRNAscan)' + title: tRNA prediction 0.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftrna_prediction%2Ftrnascan%2F0.4 homepage: http://trna.ucsc.edu/tRNAscan-SE/ id: trnascan-se @@ -18903,15 +21070,24 @@ bunya: '' description: 'Trycycler: consensus long-read assemblies for bacterial genomes' galaxy: - - title: Trycycler cluster 0.5.4 + - description: 'Trycycler cluster: cluster the contigs of your input assemblies + into per-replicon groups' + title: Trycycler cluster 0.5.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftrycycler_cluster%2Ftrycycler_cluster%2F0.5.4 - - title: Trycycler consensus 0.5.4 + - description: 'Trycycler consensus: generate a consensus contig sequence for each + cluster' + title: Trycycler consensus 0.5.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftrycycler_consensus%2Ftrycycler_consensus%2F0.5.4 - - title: Trycycler partition 0.5.4 + - description: 'Trycycler partition: assign the reads to the clusters' + title: Trycycler partition 0.5.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftrycycler_partition%2Ftrycycler_partition%2F0.5.4 - - title: Trycycler reconcile/msa 0.5.4 + - description: 'Trycycler reconcile/msa: reconcile the contigs within each cluster + and perform a multiple sequence alignment' + title: Trycycler reconcile/msa 0.5.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftrycycler_reconcile_msa%2Ftrycycler_reconcile_msa%2F0.5.4 - - title: Trycycler subsample 0.5.4 + - description: 'Trycycler subsample: make a maximally-independent read subsets of + an appropiate depth for your genome' + title: Trycycler subsample 0.5.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftrycycler_subsample%2Ftrycycler_subsample%2F0.5.4 homepage: http://github.com/rrwick/Trycycler-paper id: trycycler @@ -18936,15 +21112,21 @@ description: Utilities for handling sequences and assemblies from the UCSC Genome Browser project. galaxy: - - title: wigtobigwig 447+galaxy0 + - description: 'wigtobigwig: bedGraph or Wig to bigWig converter' + title: wigtobigwig 447+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fucsc_wigtobigwig%2Fucsc_wigtobigwig%2F447%2Bgalaxy0 - - title: faToVcf 448+galaxy0 + - description: 'faToVcf: Convert a FASTA alignment file to Variant Call Format (VCF) + single-nucleotide diffs' + title: faToVcf 448+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fucsc_fatovcf%2Ffatovcf%2F448%2Bgalaxy0 - - title: twoBitToFa 377 + - description: 'twoBitToFa: Convert all or part of .2bit file to FASTA' + title: twoBitToFa 377 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fucsc_twobittofa%2Fucsc-twobittofa%2F377 - - title: Convert GTF to BED12 357 + - description: 'Convert GTF to BED12: ' + title: Convert GTF to BED12 357 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgtftobed12%2Fgtftobed12%2F357 - - title: BED-to-bigBed 1.0.1 + - description: 'BED-to-bigBed: converter' + title: BED-to-bigBed 1.0.1 url: https://usegalaxy.org.au/root?tool_id=bed_to_bigBed homepage: http://hgdownload.cse.ucsc.edu/downloads.html id: ucsc @@ -18962,7 +21144,8 @@ bunya: '' description: '' galaxy: - - title: UCSC Archaea 1.0.0 + - description: 'UCSC Archaea: table browser' + title: UCSC Archaea 1.0.0 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=ucsc_table_direct_archaea1 homepage: '' id: ucsc_table_direct_archaea1 @@ -18979,7 +21162,8 @@ bunya: '' description: '' galaxy: - - title: UCSC Main 1.0.0 + - 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 homepage: '' id: ucsc_table_direct1 @@ -18996,15 +21180,20 @@ bunya: '' description: Tools for handling Unique Molecular Identifiers in NGS data sets. galaxy: - - title: UMI-tools whitelist 1.1.2+galaxy2 + - description: 'UMI-tools whitelist: Extract cell barcodes from FASTQ files' + title: UMI-tools whitelist 1.1.2+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fumi_tools_whitelist%2Fumi_tools_whitelist%2F1.1.2%2Bgalaxy2 - - title: UMI-tools group 1.1.2+galaxy2 + - description: 'UMI-tools group: Extract UMI from fastq files' + title: UMI-tools group 1.1.2+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fumi_tools_group%2Fumi_tools_group%2F1.1.2%2Bgalaxy2 - - title: UMI-tools count 1.1.2+galaxy2 + - description: 'UMI-tools count: performs quantification of UMIs from BAM files' + title: UMI-tools count 1.1.2+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fumi_tools_count%2Fumi_tools_count%2F1.1.2%2Bgalaxy2 - - title: UMI-tools extract 1.1.2+galaxy2 + - description: 'UMI-tools extract: Extract UMI from fastq files' + title: UMI-tools extract 1.1.2+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fumi_tools_extract%2Fumi_tools_extract%2F1.1.2%2Bgalaxy2 - - title: UMI-tools deduplicate 1.1.2+galaxy2 + - description: 'UMI-tools deduplicate: Extract UMI from fastq files' + title: UMI-tools deduplicate 1.1.2+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fumi_tools_dedup%2Fumi_tools_dedup%2F1.1.2%2Bgalaxy2 homepage: https://github.com/CGATOxford/UMI-tools id: umi_tools @@ -19028,7 +21217,8 @@ description: A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. galaxy: - - title: Create assemblies with Unicycler 0.5.0+galaxy1 + - 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 homepage: https://github.com/rrwick/Unicycler id: unicycler @@ -19052,7 +21242,8 @@ bunya: '' description: Metaproteomics data analysis with a focus on interactive data visualizations. galaxy: - - title: Unipept 4.5.1 + - description: 'Unipept: retrieve taxonomy for peptides' + title: Unipept 4.5.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Funipept%2Funipept%2F4.5.1 homepage: http://unipept.ugent.be/ id: unipept @@ -19078,7 +21269,8 @@ bunya: '' description: '' galaxy: - - title: UniProt 2.4.0 + - description: 'UniProt: download proteome as XML or fasta' + title: UniProt 2.4.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Funiprotxml_downloader%2Funiprotxml_downloader%2F2.4.0 homepage: '' id: UniProt_Downloader @@ -19095,7 +21287,8 @@ bunya: '' description: '' galaxy: - - title: UniProt 0.4 + - 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 homepage: '' id: uniprot_rest_interface @@ -19115,7 +21308,8 @@ - 6.0-gcccore-12.3.0 (D) description: '' galaxy: - - title: Unzip 6.0+galaxy0 + - description: 'Unzip: Unzip a file' + title: Unzip 6.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2Funzip%2Funzip%2F6.0%2Bgalaxy0 homepage: '' id: unzip @@ -19156,13 +21350,19 @@ description: VarScan, an open source tool for variant detection that is compatible with several short read align-ers. galaxy: - - title: VarScan copynumber 2.4.3.2 + - description: 'VarScan copynumber: Determine relative tumor copy number from tumor-normal + pileups' + title: VarScan copynumber 2.4.3.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvarscan_copynumber%2Fvarscan_copynumber%2F2.4.3.2 - - title: VarScan mpileup 2.4.3.1 + - description: 'VarScan mpileup: for variant detection' + title: VarScan mpileup 2.4.3.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvarscan_mpileup%2Fvarscan_mpileup%2F2.4.3.1 - - title: VarScan somatic 2.4.3.6 + - description: 'VarScan somatic: Call germline/somatic and LOH variants from tumor-normal + sample pairs' + title: VarScan somatic 2.4.3.6 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvarscan_somatic%2Fvarscan_somatic%2F2.4.3.6 - - title: VarScan 2.4.2 + - description: 'VarScan: for variant detection' + title: VarScan 2.4.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvarscan_version_2%2Fvarscan%2F2.4.2 homepage: http://dkoboldt.github.io/varscan/ id: varscan @@ -19203,7 +21403,8 @@ bunya: '' description: '' galaxy: - - title: VCF to MAF Custom Track 1.0.1 + - description: 'VCF to MAF Custom Track: for display at UCSC' + title: VCF to MAF Custom Track 1.0.1 url: https://usegalaxy.org.au/root?tool_id=vcf_to_maf_customtrack1 homepage: '' id: vcf_to_maf_customtrack1 @@ -19220,7 +21421,8 @@ bunya: '' description: '' galaxy: - - title: Convert VCF to MAF 1.6.21+galaxy1 + - description: 'Convert VCF to MAF: with vcf2maf' + title: Convert VCF to MAF 1.6.21+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvcf2maf%2Fvcf2maf%2F1.6.21%2Bgalaxy1 homepage: '' id: vcf2maf @@ -19238,51 +21440,85 @@ - 1.0.3-foss-2021a-r-4.1.0 description: API and command line utilities for the manipulation of VCF files. galaxy: - - title: 'VCFtoTab-delimited: 1.0.0_rc3+galaxy0' + - description: 'VCFtoTab-delimited:: Convert VCF data into TAB-delimited format' + title: 'VCFtoTab-delimited: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcf2tsv%2Fvcf2tsv%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCFaddinfo: 1.0.0_rc3+galaxy0' + - description: 'VCFaddinfo:: Adds info fields from the second dataset which are + not present in the first dataset' + title: 'VCFaddinfo: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfaddinfo%2Fvcfaddinfo%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VcfAllelicPrimitives: 1.0.0_rc3+galaxy0' + - description: 'VcfAllelicPrimitives:: Split alleleic primitives (gaps or mismatches) + into multiple VCF lines' + title: 'VcfAllelicPrimitives: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfallelicprimitives%2Fvcfallelicprimitives%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCFannotate: 1.0.0_rc3+galaxy0' + - description: 'VCFannotate:: Intersect VCF records with BED annotations' + title: 'VCFannotate: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfannotate%2Fvcfannotate%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCFannotateGenotypes: 1.0.0_rc3+galaxy0' + - description: 'VCFannotateGenotypes:: Annotate genotypes in a VCF dataset using + genotypes from another VCF dataset' + title: 'VCFannotateGenotypes: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfannotategenotypes%2Fvcfannotategenotypes%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCF-BEDintersect: 1.0.0_rc3+galaxy0' + - description: 'VCF-BEDintersect:: Intersect VCF and BED datasets' + title: 'VCF-BEDintersect: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfbedintersect%2Fvcfbedintersect%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCFbreakCreateMulti: 1.0.0_rc3+galaxy0' + - description: 'VCFbreakCreateMulti:: Break multiple alleles into multiple records, + or combine overallpoing alleles into a single record' + title: 'VCFbreakCreateMulti: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfbreakcreatemulti%2Fvcfbreakcreatemulti%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCFcheck: 1.0.0_rc3+galaxy0' + - description: 'VCFcheck:: Verify that the reference allele matches the reference + genome' + title: 'VCFcheck: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfcheck%2Fvcfcheck%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCFcombine: 1.0.0_rc3+galaxy0' + - description: 'VCFcombine:: Combine multiple VCF datasets' + title: 'VCFcombine: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfcombine%2Fvcfcombine%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCFcommonSamples: 1.0.0_rc3+galaxy0' + - description: 'VCFcommonSamples:: Output records belonging to samples common between + two datasets' + title: 'VCFcommonSamples: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfcommonsamples%2Fvcfcommonsamples%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCFdistance: 1.0.0_rc3+galaxy0' + - description: 'VCFdistance:: Calculate distance to the nearest variant' + title: 'VCFdistance: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfdistance%2Fvcfdistance%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCFfilter: 1.0.0_rc3+galaxy3' + - description: 'VCFfilter:: filter VCF data in a variety of attributes' + title: 'VCFfilter: 1.0.0_rc3+galaxy3' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcffilter%2Fvcffilter2%2F1.0.0_rc3%2Bgalaxy3 - - title: 'VCFfixup: 1.0.0_rc3+galaxy0' + - description: 'VCFfixup:: Count the allele frequencies across alleles present in + each record in the VCF file' + title: 'VCFfixup: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcffixup%2Fvcffixup%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCFflatten: 1.0.0_rc3+galaxy0' + - description: 'VCFflatten:: Removes multi-allelic sites by picking the most common + alternate' + title: 'VCFflatten: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfflatten%2Fvcfflatten2%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCFgenotype-to-haplotype: 1.0.0_rc3+galaxy0' + - description: 'VCFgenotype-to-haplotype:: Convert genotype-based phased alleles + into haplotype alleles' + title: 'VCFgenotype-to-haplotype: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfgeno2haplo%2Fvcfgeno2haplo%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCFgenotypes: 1.0.0_rc3+galaxy0' + - description: 'VCFgenotypes:: Convert numerical representation of genotypes to + allelic' + title: 'VCFgenotypes: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfgenotypes%2Fvcfgenotypes%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCFhetHomAlleles: 1.0.0_rc3+galaxy0' + - description: 'VCFhetHomAlleles:: Count the number of heterozygotes and alleles, + compute het/hom ratio' + title: 'VCFhetHomAlleles: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfhethom%2Fvcfhethom%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCFleftAlign: 1.0.0_rc3+galaxy0' + - description: 'VCFleftAlign:: Left-align indels and complex variants in VCF dataset' + title: 'VCFleftAlign: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfleftalign%2Fvcfleftalign%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCFprimers: 1.0.0_rc3+galaxy0' + - description: 'VCFprimers:: Extract flanking sequences for each VCF record' + title: 'VCFprimers: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfprimers%2Fvcfprimers%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCFrandomSample: 1.0.0_rc3+galaxy0' + - description: 'VCFrandomSample:: Randomly sample sites from VCF dataset' + title: 'VCFrandomSample: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfrandomsample%2Fvcfrandomsample%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCFselectsamples: 1.0.0_rc3+galaxy0' + - description: 'VCFselectsamples:: Select samples from a VCF dataset' + title: 'VCFselectsamples: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfselectsamples%2Fvcfselectsamples%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCFsort: 1.0.0_rc3+galaxy0' + - description: 'VCFsort:: Sort VCF dataset by coordinate' + title: 'VCFsort: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfsort%2Fvcfsort%2F1.0.0_rc3%2Bgalaxy0 - - title: 'VCF-VCFintersect: 1.0.0_rc3+galaxy0' + - description: 'VCF-VCFintersect:: Intersect two VCF datasets' + title: 'VCF-VCFintersect: 1.0.0_rc3+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcfvcfintersect%2Fvcfvcfintersect%2F1.0.0_rc3%2Bgalaxy0 homepage: https://github.com/vcflib/vcflib id: vcflib @@ -19306,9 +21542,11 @@ description: Provide easily accessible methods for working with complex genetic variation data in the form of VCF files. galaxy: - - title: Intersect 0.1.1 + - description: 'Intersect: multiple VCF datasets' + title: Intersect 0.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcftools_isec%2Fvcftools_isec%2F0.1.1 - - title: Merge 0.1.1 + - description: 'Merge: multiple VCF datasets' + title: Merge 0.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvcftools_merge%2Fvcftools_merge%2F0.1.1 homepage: https://vcftools.github.io/index.html id: vcftools @@ -19331,11 +21569,14 @@ description: A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. galaxy: - - title: velvetg 1.2.10.2 + - description: 'velvetg: Velvet sequence assembler for very short reads' + title: velvetg 1.2.10.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvelvet%2Fvelvetg%2F1.2.10.2 - - title: velveth 1.2.10.3 + - description: 'velveth: Prepare a dataset for the Velvet velvetg Assembler' + title: velveth 1.2.10.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fvelvet%2Fvelveth%2F1.2.10.3 - - title: VelvetOptimiser 2.2.6+galaxy2 + - description: 'VelvetOptimiser: Automatically optimize Velvet assemblies' + title: VelvetOptimiser 2.2.6+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fsimon-gladman%2Fvelvetoptimiser%2Fvelvetoptimiser%2F2.2.6%2Bgalaxy2 homepage: https://github.com/dzerbino/velvet id: velvet @@ -19410,7 +21651,8 @@ bunya: '' description: '' galaxy: - - title: Volcano Plot 0.0.5 + - description: 'Volcano Plot: create a volcano plot' + title: Volcano Plot 0.0.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvolcanoplot%2Fvolcanoplot%2F0.0.5 homepage: '' id: volcanoplot @@ -19431,21 +21673,29 @@ exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. galaxy: - - title: VSearch clustering 2.8.3.0 + - description: 'VSearch clustering: ' + title: VSearch clustering 2.8.3.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvsearch%2Fvsearch_clustering%2F2.8.3.0 - - title: VSearch masking 2.8.3.0 + - description: 'VSearch masking: ' + title: VSearch masking 2.8.3.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvsearch%2Fvsearch_masking%2F2.8.3.0 - - title: VSearch dereplication 2.8.3.0 + - description: 'VSearch dereplication: ' + title: VSearch dereplication 2.8.3.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvsearch%2Fvsearch_dereplication%2F2.8.3.0 - - title: VSearch chimera detection 2.8.3.0 + - description: 'VSearch chimera detection: ' + title: VSearch chimera detection 2.8.3.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvsearch%2Fvsearch_chimera_detection%2F2.8.3.0 - - title: VSearch search 2.8.3.1 + - description: 'VSearch search: ' + title: VSearch search 2.8.3.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvsearch%2Fvsearch_search%2F2.8.3.1 - - title: VSearch sorting 2.8.3.0 + - description: 'VSearch sorting: ' + title: VSearch sorting 2.8.3.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvsearch%2Fvsearch_sorting%2F2.8.3.0 - - title: VSearch alignment 2.8.3.0 + - description: 'VSearch alignment: ' + title: VSearch alignment 2.8.3.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvsearch%2Fvsearch_alignment%2F2.8.3.0 - - title: VSearch shuffling 2.8.3.0 + - description: 'VSearch shuffling: ' + title: VSearch shuffling 2.8.3.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvsearch%2Fvsearch_shuffling%2F2.8.3.0 homepage: https://github.com/torognes/vsearch id: vsearch @@ -19481,7 +21731,8 @@ bunya: '' description: '' galaxy: - - title: Sequence Logo 3.5.0 + - description: 'Sequence Logo: generator for fasta (eg Clustal alignments)' + title: Sequence Logo 3.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fweblogo3%2Frgweblogo3%2F3.5.0 homepage: '' id: weblogo3 @@ -19523,7 +21774,8 @@ bunya: '' description: '' galaxy: - - title: Wig/BedGraph-to-bigWig 1.1.1 + - description: 'Wig/BedGraph-to-bigWig: converter' + title: Wig/BedGraph-to-bigWig 1.1.1 url: https://usegalaxy.org.au/root?tool_id=wig_to_bigWig homepage: '' id: wig_to_bigWig @@ -19541,9 +21793,12 @@ description: windowmasker identifies and masks highly repetitive DNA sequences in a genome, using only the sequence of the genome itself. galaxy: - - title: WindowMasker ustat 1.0 + - description: 'WindowMasker ustat: Mask sequences using a WindowMasker unit counts + table' + title: WindowMasker ustat 1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fwindowmasker%2Fwindowmasker_ustat%2F1.0 - - title: WindowMasker mkcounts 1.0 + - description: 'WindowMasker mkcounts: Construct WindowMasker unit counts table' + title: WindowMasker mkcounts 1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fwindowmasker%2Fwindowmasker_mkcounts%2F1.0 homepage: http://nebc.nox.ac.uk/bioinformatics/docs/windowmasker.html id: windowmasker @@ -19609,43 +21864,70 @@ metabolomics. It includes preprocessing, normalization, quality control, statistical analysis of LC/MS, FIA-MS, GC/MS and NMR data. galaxy: - - title: Determine_batch_correction 2.1.2 + - description: 'Determine_batch_correction: to choose between linear, lowess and + loess methods' + title: Determine_batch_correction 2.1.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fmelpetera%2Fbatchcorrection%2FDetermine_BC%2F2.1.2 - - title: Batch_correction 2.1.2 + - description: 'Batch_correction: Corrects intensities for signal drift and batch-effects' + title: Batch_correction 2.1.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fmelpetera%2Fbatchcorrection%2FBatch_correction%2F2.1.2 - - title: Check Format 3.0.0 + - description: 'Check Format: Checking/formatting the sample and variable names + of the dataMatrix, sampleMetadata, and variableMetadata files' + title: Check Format 3.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fethevenot%2Fcheckformat%2FcheckFormat%2F3.0.0 - - title: Generic_Filter 2017.06 + - description: 'Generic_Filter: Removes elements according to numerical or qualitative + values' + title: Generic_Filter 2017.06 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fmelpetera%2Fgeneric_filter%2Fgeneric_filter%2F2017.06 - - title: HMDB MS search 1.6.1 + - description: 'HMDB MS search: search by masses on HMDB online LCMS bank' + title: HMDB MS search 1.6.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Ffgiacomoni%2Fhmdb_ms_search%2Fwsdl_hmdb%2F1.6.1 - - title: LCMS matching 4.0.2 + - description: 'LCMS matching: Annotation of LCMS peaks using matching on a in-house + spectra database or on PeakForest spectra database.' + title: LCMS matching 4.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fprog%2Flcmsmatching%2Flcmsmatching%2F4.0.2 - - title: MSnbase readMSData 2.8.2.1 + - description: 'MSnbase readMSData: Imports mass-spectrometry data files' + title: MSnbase readMSData 2.8.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Flecorguille%2Fmsnbase_readmsdata%2Fmsnbase_readmsdata%2F2.8.2.1 - - title: NMR spectra alignment 2.0.4 + - description: 'NMR spectra alignment: based on the Cluster-based Peak Alignment + (CluPA) algorithm' + title: NMR spectra alignment 2.0.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fmarie-tremblay-metatoul%2Fnmr_alignment%2FNmrAlignment%2F2.0.4 - - title: NMR_Bucketing 2.0.3 + - description: 'NMR_Bucketing: Bucketing and integration of NMR Bruker raw data' + title: NMR_Bucketing 2.0.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fmarie-tremblay-metatoul%2Fnmr_bucketing%2FNmrBucketing%2F2.0.3 - - title: NMR_Read 3.3.0 + - description: 'NMR_Read: Read Bruker NMR raw files' + title: NMR_Read 3.3.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fmarie-tremblay-metatoul%2Fnmr_preprocessing%2FNMR_Read%2F3.3.0 - - title: NMR_Preprocessing 3.3.0 + - description: 'NMR_Preprocessing: Preprocessing of 1D NMR spectra' + title: NMR_Preprocessing 3.3.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fmarie-tremblay-metatoul%2Fnmr_preprocessing%2FNMR_Preprocessing%2F3.3.0 - - title: Normalization 2.0.1 + - description: 'Normalization: Normalization of (preprocessed) spectra' + title: Normalization 2.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fmarie-tremblay-metatoul%2Fnormalization%2Fnormalization%2F2.0.1 - - title: Quality Metrics 2.2.8 + - description: 'Quality Metrics: Metrics and graphics to check the quality of the + data' + title: Quality Metrics 2.2.8 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fethevenot%2Fqualitymetrics%2Fquality_metrics%2F2.2.8 - - title: Table Merge 1.0.1 + - description: 'Table Merge: Merging dataMatrix with a metadata table' + title: Table Merge 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fmelpetera%2Ftablemerge%2Ftablemerge%2F1.0.1 - - title: Univariate 2.2.4 + - description: 'Univariate: Univariate statistics' + title: Univariate 2.2.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fethevenot%2Funivariate%2FUnivariate%2F2.2.4 - - title: W4m Data Subset 0.98.11 + - description: 'W4m Data Subset: Filter W4m data by values or metadata' + title: W4m Data Subset 0.98.11 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Feschen42%2Fw4mclassfilter%2Fw4mclassfilter%2F0.98.11 - - title: OPLS-DA_Contrasts 0.98.17 + - description: 'OPLS-DA_Contrasts: OPLS-DA Contrasts of Univariate Results' + title: OPLS-DA_Contrasts 0.98.17 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Feschen42%2Fw4mcorcov%2Fw4mcorcov%2F0.98.17 - - title: Join +/- Ions 0.98.2 + - description: 'Join +/- Ions: Join positive and negative ionization-mode W4M datasets + for the same samples' + title: Join +/- Ions 0.98.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Feschen42%2Fw4mjoinpn%2Fw4mjoinpn%2F0.98.2 - - title: Multilevel 0.5.0 + - description: 'Multilevel: Data transformation: Within matrix decomposition for + repeated measurements (cross-over design) with mixOmics package' + title: Multilevel 0.5.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fyguitton%2Fwithinvariation%2Fmixomics_multilevel%2F0.5.0 homepage: https://workflow4metabolomics.org/ id: workflow4metabolomics @@ -19672,7 +21954,8 @@ bunya: '' description: '' galaxy: - - title: WormBase 1.0.1 + - description: 'WormBase: server' + title: WormBase 1.0.1 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=wormbase homepage: '' id: wormbase @@ -19713,9 +21996,12 @@ bunya: '' description: '' galaxy: - - title: NetCDF xarray Metadata Info 0.15.1 + - description: 'NetCDF xarray Metadata Info: summarize content of a Netcdf file' + title: NetCDF xarray Metadata Info 0.15.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fecology%2Fxarray_metadata_info%2Fxarray_metadata_info%2F0.15.1 - - title: NetCDF xarray Selection 0.15.1 + - description: 'NetCDF xarray Selection: extracts variable values with custom conditions + on dimensions' + title: NetCDF xarray Selection 0.15.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fecology%2Fxarray_select%2Fxarray_select%2F0.15.1 homepage: http://xarray.pydata.org/en/stable/ id: xarray @@ -19735,21 +22021,33 @@ NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling. galaxy: - - title: xcms get a sampleMetadata file 3.4.4.0 + - description: 'xcms get a sampleMetadata file: which need to be filled with extra + information' + title: xcms get a sampleMetadata file 3.4.4.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Flecorguille%2Fxcms_export_samplemetadata%2Fxcms_export_samplemetadata%2F3.4.4.0 - - title: xcms fillChromPeaks (fillPeaks) 3.4.4.0 + - description: 'xcms fillChromPeaks (fillPeaks): Integrate areas of missing peaks' + title: xcms fillChromPeaks (fillPeaks) 3.4.4.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Flecorguille%2Fxcms_fillpeaks%2Fabims_xcms_fillPeaks%2F3.4.4.0 - - title: xcms groupChromPeaks (group) 3.4.4.0 + - description: 'xcms groupChromPeaks (group): Perform the correspondence, the grouping + of chromatographic peaks within and between samples.' + title: xcms groupChromPeaks (group) 3.4.4.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Flecorguille%2Fxcms_group%2Fabims_xcms_group%2F3.4.4.0 - - title: xcms findChromPeaks Merger 3.4.4.0 + - description: 'xcms findChromPeaks Merger: Merge xcms findChromPeaks RData into + a unique file to be used by group' + title: xcms findChromPeaks Merger 3.4.4.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Flecorguille%2Fxcms_merge%2Fxcms_merge%2F3.4.4.0 - - title: xcms plot chromatogram 3.4.4.0 + - description: 'xcms plot chromatogram: Plots base peak intensity chromatogram (BPI) + and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s)' + title: xcms plot chromatogram 3.4.4.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Flecorguille%2Fxcms_plot_chromatogram%2Fxcms_plot_chromatogram%2F3.4.4.0 - - title: xcms adjustRtime (retcor) 3.4.4.1 + - description: 'xcms adjustRtime (retcor): Retention Time Correction' + title: xcms adjustRtime (retcor) 3.4.4.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Flecorguille%2Fxcms_retcor%2Fabims_xcms_retcor%2F3.4.4.1 - - title: xcms process history 3.4.4.0 + - description: 'xcms process history: Create a summary of XCMS analysis' + title: xcms process history 3.4.4.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Flecorguille%2Fxcms_summary%2Fabims_xcms_summary%2F3.4.4.0 - - title: xcms findChromPeaks (xcmsSet) 3.4.4.1 + - description: 'xcms findChromPeaks (xcmsSet): Chromatographic peak detection' + title: xcms findChromPeaks (xcmsSet) 3.4.4.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Flecorguille%2Fxcms_xcmsset%2Fabims_xcms_xcmsSet%2F3.4.4.1 homepage: http://bioconductor.org/packages/release/bioc/html/xcms.html id: xcms @@ -19815,9 +22113,11 @@ bunya: '' description: Matches tandem mass spectra with peptide sequences. galaxy: - - title: X!Tandem MSMS Search 1.1.1 + - description: 'X!Tandem MSMS Search: Run an X!Tandem Search' + title: X!Tandem MSMS Search 1.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Firacooke%2Fxtandem%2Fproteomics_search_tandem_1%2F1.1.1 - - title: Tandem to pepXML 1.1.1 + - description: 'Tandem to pepXML: Converts a tandem result file to pepXML' + title: Tandem to pepXML 1.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Firacooke%2Fxtandem%2Ftandem_to_pepxml_1%2F1.1.1 homepage: http://www.thegpm.org/TANDEM/ id: xtandem @@ -19838,7 +22138,8 @@ bunya: '' description: '' galaxy: - - title: Plotting tool 1.0.2 + - description: 'Plotting tool: for multiple series and graph types' + title: Plotting tool 1.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fxy_plot%2FXY_Plot_1%2F1.0.2 homepage: '' id: xy_plot @@ -19857,7 +22158,8 @@ for contig joining detection which considers the topological distribution of Hi-C signals aiming to distinguish real interaction signals from mapping noises. galaxy: - - title: YAHS 1.2a.2+galaxy1 + - description: 'YAHS: yet another HI-C scaffolding tool' + title: YAHS 1.2a.2+galaxy1 url: 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-
- +
+

Please note:

    -
  • This table was last updated on 2024-03-12.
    • +
  • This table was last updated on 2024-03-21.
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-
- +
+

Note:

    -
  • Table last updated 2024-03-12.
    • +
  • Table last updated 2024-03-21.
  • The Tool identifier column (hidden by default) contains an identifier for the tool / workflow: typically the module name (used for matching to HPC lists).
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