From ccf9e7eeb2fca8e8968c7e675b2ac2f49b7c5352 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Wed, 19 Jun 2024 01:55:16 +0000 Subject: [PATCH] Updated the data.yml sourced from australianbiocommons.github.io --- _data/data.yaml | 1146 ++++++++++++++++++++++------------------------- 1 file changed, 544 insertions(+), 602 deletions(-) diff --git a/_data/data.yaml b/_data/data.yaml index 5b51cee..70a8ee4 100644 --- a/_data/data.yaml +++ b/_data/data.yaml @@ -187,10 +187,13 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: anndata + biotools: anndata bunya: '' - description: '' + description: 'From https://anndata.readthedocs.io/en/latest/ + + "Python package for handling annotated data matrices in memory and on disk, positioned + between pandas and xarray."' edam-operations: '' edam-topics: '' galaxy: @@ -206,14 +209,16 @@ - 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: '' + homepage: https://github.com/scverse/anndata id: anndata - license: '' + license: BSD-3-Clause name: anndata nci-gadi: '' nci-if89: '' pawsey: '' - publications: '' + publications: + - title: 10.1101/2021.12.16.473007 + url: https://doi.org/10.1101/2021.12.16.473007 resources: - title: .nan url: .nan @@ -1070,27 +1075,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'BED-to-GFF: converter' - title: BED-to-GFF 2.0.0 - url: https://usegalaxy.org.au/root?tool_id=bed2gff1 - homepage: '' - id: bed2gff1 - license: '' - name: bed2gff1 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: bedtools biotools: bedtools bunya: @@ -2007,27 +1991,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - 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 - license: '' - name: bp_genbank2gff3 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: braker1 biotools: braker1 bunya: @@ -2249,8 +2212,8 @@ edam-topics: '' galaxy: - 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 + title: bwameth 0.2.7+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbwameth%2Fbwameth%2F0.2.7%2Bgalaxy0 homepage: '' id: BWA-meth license: '' @@ -3419,28 +3382,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - 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 - license: '' - name: combine_metaphlan2_humann2 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: '' biotools: '' bunya: '' @@ -4132,27 +4073,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - 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 - license: '' - name: describe_samples_replicates - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: deseq2 biotools: deseq2 bunya: '' @@ -4431,27 +4351,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - 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 - license: '' - name: draw_stacked_barplots - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: '' biotools: '' bunya: '' @@ -4597,27 +4496,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - 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 - license: '' - name: ebi_sra_main - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: edger biotools: edger bunya: '' @@ -5320,14 +5198,25 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: ete + biotools: ete bunya: '' - description: '' - edam-operations: '' - edam-topics: '' + description: The Environment for Tree Exploration (ETE) is a computational framework + that simplifies the reconstruction, analysis, and visualization of phylogenetic + trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous + improvements in the underlying library of methods, and providing a novel set of + standalone tools to perform common tasks in comparative genomics and phylogenetics. + The new features include (i) building gene-based and supermatrix-based phylogenies + using a single command, (ii) testing and visualizing evolutionary models, (iii) + calculating distances between trees of different size or including duplications, + and (iv) providing seamless integration with the NCBI taxonomy database. ETE is + freely available at http://etetoolkit.org + edam-operations: + - Phylogenetic analysis + edam-topics: + - Phylogenetics galaxy: '' - homepage: '' + homepage: http://etetoolkit.org/about/ id: ete3 license: '' name: ete3 @@ -5564,23 +5453,39 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: f5c + biotools: f5c bunya: - 1.1--h0326b38_1 - description: '' - edam-operations: '' - edam-topics: '' + description: GPU Accelerated Adaptive Banded Event Alignment for Rapid Comparative + Nanopore Signal Analysis | Re-engineered and optimised Nanopolish call-methylation + module (supports CUDA acceleration) | An optimised re-implementation of the call-methylation + module in Nanopolish. Given a set of basecalled Nanopore reads and the raw signals, + f5c detects the methylated cytosine bases. f5c can optionally utilise NVIDIA graphics + cards for acceleration + edam-operations: + - Local alignment + - Genotyping + - Base-calling + edam-topics: + - Computer science + - Epigenetics + - Whole genome sequencing galaxy: '' - homepage: '' + homepage: https://hasindu2008.github.io/f5c/ id: f5c - license: '' + license: MIT name: f5c nci-gadi: '' nci-if89: - '1.3' pawsey: '' - publications: '' + publications: + - title: 10.1101/756122 + url: https://doi.org/10.1101/756122 + - title: GPU accelerated adaptive banded event alignment for rapid comparative nanopore + signal analysis + url: https://doi.org/10.1186/s12859-020-03697-x resources: - title: .nan url: .nan @@ -5637,112 +5542,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - 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 - license: '' - name: fasta_concatenate_by_species - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - 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 - license: '' - name: fasta_filter_by_length - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - 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 - license: '' - name: fasta_merge_files_and_filter_unique_sequences - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - 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 - license: '' - name: fasta_stats - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - 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 - license: '' - name: fasta_to_tabular - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: '' biotools: '' bunya: @@ -5880,17 +5679,21 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: fastqe + biotools: fastqe bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: "FASTQE: visualize fastq files with emoji's \U0001F9EC\U0001F60E" - title: FASTQE 0.2.6+galaxy2 + description: Compute quality stats for FASTQ files and print those stats as emoji... + for some reason. + edam-operations: + - Sequencing quality control + edam-topics: + - Sequence analysis + - Sequencing + galaxy: + - description: "FASTQE: visualize fastq files with emoji's \U0001F9EC\U0001F60E" + title: FASTQE 0.2.6+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffastqe%2Ffastqe%2F0.2.6%2Bgalaxy2 - homepage: '' + homepage: https://fastqe.com/ id: fastqe license: '' name: fastqe @@ -6234,24 +6037,36 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: flymine + biotools: flymine bunya: '' - description: '' - edam-operations: '' - edam-topics: '' + description: An integrated database for Drosophila and Anopheles genomics. + edam-operations: + - Data retrieval + - Visualisation + - Gene-set enrichment analysis + - Query and retrieval + edam-topics: + - Data management + - Genomics + - Proteomics galaxy: - description: 'Flymine: server' title: Flymine 1.0.0 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=flymine - homepage: '' + homepage: https://flymine.org/flymine id: flymine - license: '' + license: LGPL-2.1 name: flymine nci-gadi: '' nci-if89: '' pawsey: '' - publications: '' + publications: + - title: 'FlyMine: An integrated database for Drosophila and Anopheles genomics' + url: https://doi.org/10.1186/gb-2007-8-7-r129 + - title: 'InterMine: A flexible data warehouse system for the integration and analysis + of heterogeneous biological data' + url: https://doi.org/10.1093/bioinformatics/bts577 resources: - title: .nan url: .nan @@ -6542,6 +6357,15 @@ edam-operations: '' edam-topics: '' galaxy: + - 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 + - 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 + - description: 'BED-to-GFF: converter' + title: BED-to-GFF 2.0.0 + url: https://usegalaxy.org.au/root?tool_id=bed2gff1 - description: 'AXT to concatenated FASTA: Converts an AXT formatted file to a concatenated FASTA alignment' title: AXT to concatenated FASTA 1.0.0 @@ -6552,190 +6376,190 @@ - 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 - - description: 'Convert FASTA to Tabular: ' - title: Convert FASTA to Tabular 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular - - description: 'Convert GFF to Interval Index: ' - title: Convert GFF to Interval Index 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_interval_index_0 - - description: 'Convert Biom datasets: ' - title: Convert Biom datasets 2.1.5 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_biom - - description: 'Convert FASTQ files to seek locations: ' - title: Convert FASTQ files to seek locations 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fastq_to_fqtoc0 + - description: 'Convert FASTA to Bowtie color space Index: ' + title: Convert FASTA to Bowtie color space Index 1.2.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_color_index - description: 'OpenBabel converter for molecular formats: ' title: OpenBabel converter for molecular formats 2.4.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_molecules - - description: 'Convert uncompressed file to compressed: ' - title: Convert uncompressed file to compressed 1.16+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_uncompressed_to_gz - - description: 'Convert Interval to tabix: ' - title: Convert Interval to tabix 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_tabix_0 - - description: 'Convert PDB to GRO: ' - title: Convert PDB to GRO 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Pdb_to_Gro_0 - - description: 'Convert Interval to BGZIP: ' - title: Convert Interval to BGZIP 1.0.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bgzip_0 - - description: 'Convert Bam to Bai: ' - title: Convert Bam to Bai 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Bam_Bai_0 - - description: 'Convert lped to fped: ' - title: Convert lped to fped 0.02 - url: https://usegalaxy.org.au/root?tool_id=lped2fpedconvert - - description: 'Convert CRAM to BAM: ' - title: Convert CRAM to BAM 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cram_to_bam_0 - - description: 'Convert tar to directory: ' - title: Convert tar to directory 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_tar_to_directory - - description: 'Convert GFF to Feature Location Index: ' - title: Convert GFF to Feature Location Index 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_fli_0 - description: 'Convert FASTA to fai file: ' title: Convert FASTA to fai file 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_fai - - description: 'Convert tabular to dbnsfp: ' - title: Convert tabular to dbnsfp 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=tabular_to_dbnsfp - - description: 'Convert Len file to Linecount: ' - title: Convert Len file to Linecount 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_len_to_linecount - - description: 'Convert BED, GFF, or VCF to BigWig: ' - title: Convert BED, GFF, or VCF to BigWig 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0 + - description: 'Convert GFF to BED: ' + title: Convert GFF to BED 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_bed_0 + - description: 'Convert neostore.zip files to neostore: ' + title: Convert neostore.zip files to neostore 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_neostorezip_to_neostore + - description: 'Convert uncompressed file to compressed: ' + title: Convert uncompressed file to compressed 1.16+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_uncompressed_to_gz - description: 'Convert XTC, DCD, and TRR: ' title: Convert XTC, DCD, and TRR 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mdconvert - description: 'Convert compressed file to uncompressed.: ' title: Convert compressed file to uncompressed. 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gz_to_uncompressed - - description: 'Convert SAM to BAM without sorting: ' - title: Convert SAM to BAM without sorting 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_unsorted_bam + - description: 'Convert BGZ VCF to tabix: ' + title: Convert BGZ VCF to tabix 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0 + - description: 'Convert Interval to BGZIP: ' + title: Convert Interval to BGZIP 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bgzip_0 + - description: 'Convert Genomic Intervals To Strict BED12: ' + title: Convert Genomic Intervals To Strict BED12 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed12_0 + - description: 'Convert Interval to tabix: ' + title: Convert Interval to tabix 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_tabix_0 + - description: 'Convert CRAM to BAM: ' + title: Convert CRAM to BAM 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cram_to_bam_0 - description: 'Convert compressed file to uncompressed.: ' title: Convert compressed file to uncompressed. 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bz2_to_uncompressed + - description: 'Convert Genomic Intervals To Strict BED: ' + title: Convert Genomic Intervals To Strict BED 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0 + - description: 'Convert BED, GFF, or VCF to BigWig: ' + title: Convert BED, GFF, or VCF to BigWig 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0 + - description: 'Convert Wiggle to Interval: ' + title: Convert Wiggle to Interval 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wiggle_to_interval_0 - description: 'Convert MAF to Fasta: ' title: Convert MAF to Fasta 1.0.2 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_fasta_0 + - description: 'Convert SAM to BigWig: ' + title: Convert SAM to BigWig 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_bigwig_0 + - description: 'Convert BAM to coordinate-sorted BAM: ' + title: Convert BAM to coordinate-sorted BAM 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam + - description: 'Convert FASTA to 2bit: ' + title: Convert FASTA to 2bit 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_2bit + - description: 'Convert BED to Feature Location Index: ' + title: Convert BED to Feature Location Index 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_fli_0 + - description: 'Convert Bam to Bai: ' + title: Convert Bam to Bai 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Bam_Bai_0 + - description: 'Convert FASTQ files to seek locations: ' + title: Convert FASTQ files to seek locations 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fastq_to_fqtoc0 + - description: 'Convert BigWig to Wiggle: Convert bigWig to wig' + title: Convert BigWig to Wiggle 377+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=bigwigtowig + - description: 'Convert Biom datasets: ' + title: Convert Biom datasets 2.1.5 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_biom - description: 'Convert tabular to CSV: ' title: Convert tabular to CSV 1.0.0 url: https://usegalaxy.org.au/root?tool_id=tabular_to_csv - - description: 'Convert lped to plink pbed: ' - title: Convert lped to plink pbed 0.02 - url: https://usegalaxy.org.au/root?tool_id=lped2pbedconvert - - description: 'Convert MOL2 to MOL: ' - title: Convert MOL2 to MOL 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mol2_to_mol - - description: 'Convert Picard Interval List to BED6: converter' - title: Convert Picard Interval List to BED6 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_picard_interval_list_to_bed6 + - description: 'Convert GFF to Feature Location Index: ' + title: Convert GFF to Feature Location Index 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_fli_0 + - description: 'Convert PDB to GRO: ' + title: Convert PDB to GRO 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Pdb_to_Gro_0 - description: 'Convert BAM to BigWig: ' title: Convert BAM to BigWig 1.0.2 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_bigwig_0 + - description: 'SMILES to SMILES: ' + title: SMILES to SMILES 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_smiles_to_smiles - description: 'Convert BED to GFF: ' title: Convert BED to GFF 2.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_gff_0 - - description: 'Convert CSV to tabular: ' - title: Convert CSV to tabular 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=csv_to_tabular - - description: 'Convert Parquet to csv: ' - title: Convert Parquet to csv 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_parquet_to_csv + - description: 'Convert BedGraph to BigWig: ' + title: Convert BedGraph to BigWig 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bedgraph_to_bigwig + - description: 'Convert Genomic Intervals To Coverage: ' + title: Convert Genomic Intervals To Coverage 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bigwig_0 + - description: 'Convert plink pbed to linkage lped: ' + title: Convert plink pbed to linkage lped 0.02 + url: https://usegalaxy.org.au/root?tool_id=pbed2lpedconvert + - description: 'Convert GFF to Interval Index: ' + title: Convert GFF to Interval Index 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_interval_index_0 + - description: 'Convert Wiggle to BigWig: ' + title: Convert Wiggle to BigWig 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wig_to_bigwig + - description: 'Convert lped to fped: ' + title: Convert lped to fped 0.02 + url: https://usegalaxy.org.au/root?tool_id=lped2fpedconvert + - description: 'Convert SAM to BAM without sorting: ' + title: Convert SAM to BAM without sorting 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_unsorted_bam + - description: 'Convert MOL2 to MOL: ' + title: Convert MOL2 to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mol2_to_mol + - description: 'Convert MAF to Genomic Intervals: ' + title: Convert MAF to Genomic Intervals 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_interval_0 + - description: 'Convert Len file to Linecount: ' + title: Convert Len file to Linecount 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_len_to_linecount + - description: 'Convert FASTA to Tabular: ' + title: Convert FASTA to Tabular 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular + - description: 'Convert Picard Interval List to BED6: converter' + title: Convert Picard Interval List to BED6 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_picard_interval_list_to_bed6 - description: 'Convert GRO to PDB: ' title: Convert GRO to PDB 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Gro_to_Pdb_0 - - description: 'Convert compressed and uncompressed BCF files: ' - title: Convert compressed and uncompressed BCF files 0.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf - - description: 'Convert BAM to queryname-sorted BAM: ' - title: Convert BAM to queryname-sorted BAM 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_qname_sorted_bam - - description: 'Convert BAM to coordinate-sorted BAM: ' - title: Convert BAM to coordinate-sorted BAM 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam - - description: 'Convert Genomic Intervals To BED: ' - title: Convert Genomic Intervals To BED 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed_0 - - description: 'SMILES to SMILES: ' - title: SMILES to SMILES 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_smiles_to_smiles + - description: 'Convert CSV to tabular: ' + title: Convert CSV to tabular 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=csv_to_tabular + - description: 'Convert FASTA to len file: ' + title: Convert FASTA to len file 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_len - description: 'Convert CML to SMILES: ' title: Convert CML to SMILES 2.4.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cml_to_smiles - - description: 'Convert plink pbed to linkage lped: ' - title: Convert plink pbed to linkage lped 0.02 - url: https://usegalaxy.org.au/root?tool_id=pbed2lpedconvert - - description: 'Convert plink pbed to ld reduced format: ' - title: Convert plink pbed to ld reduced format 0.02 - url: https://usegalaxy.org.au/root?tool_id=pbed2ldindepconvert - - description: 'Convert Wiggle to Interval: ' - title: Convert Wiggle to Interval 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wiggle_to_interval_0 - - description: 'Convert FASTA to Bowtie color space Index: ' - title: Convert FASTA to Bowtie color space Index 1.2.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_color_index + - description: 'Convert lped to plink pbed: ' + title: Convert lped to plink pbed 0.02 + url: https://usegalaxy.org.au/root?tool_id=lped2pbedconvert + - description: 'Convert Genomic Intervals To Strict BED6: ' + title: Convert Genomic Intervals To Strict BED6 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed6_0 + - description: 'Convert BAM to queryname-sorted BAM: ' + title: Convert BAM to queryname-sorted BAM 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_qname_sorted_bam + - description: 'Convert SMILES to MOL: ' + title: Convert SMILES to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_SMILES_to_MOL + - description: 'Convert FASTA to Bowtie base space Index: ' + title: Convert FASTA to Bowtie base space Index 1.3.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_base_index + - description: 'Convert compressed and uncompressed BCF files: ' + title: Convert compressed and uncompressed BCF files 0.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf - description: 'Convert InChI to MOL: ' title: Convert InChI to MOL 2.4.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_inchi_to_mol + - description: 'Convert tar to directory: ' + title: Convert tar to directory 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_tar_to_directory + - description: 'Convert tabular to dbnsfp: ' + title: Convert tabular to dbnsfp 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=tabular_to_dbnsfp - description: 'Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format' title: Convert Ref taxonomy to Seq Taxonomy 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_ref_to_seq_taxomony - - description: 'Convert MAF to Genomic Intervals: ' - title: Convert MAF to Genomic Intervals 1.0.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_interval_0 - - description: 'Convert FASTA to Bowtie base space Index: ' - title: Convert FASTA to Bowtie base space Index 1.3.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_base_index - - description: 'Convert Genomic Intervals To Strict BED: ' - title: Convert Genomic Intervals To Strict BED 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0 - - description: 'Convert Genomic Intervals To Strict BED6: ' - title: Convert Genomic Intervals To Strict BED6 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed6_0 - - description: 'Convert FASTA to 2bit: ' - title: Convert FASTA to 2bit 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_2bit - - description: 'Convert GFF to BED: ' - title: Convert GFF to BED 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_bed_0 - - description: 'Convert BGZ VCF to tabix: ' - title: Convert BGZ VCF to tabix 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0 - - description: 'Convert neostore.zip files to neostore: ' - title: Convert neostore.zip files to neostore 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_neostorezip_to_neostore - - description: 'Convert SMILES to MOL: ' - title: Convert SMILES to MOL 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_SMILES_to_MOL - - description: 'Convert SAM to BigWig: ' - title: Convert SAM to BigWig 1.0.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_bigwig_0 - - description: 'Convert Wiggle to BigWig: ' - title: Convert Wiggle to BigWig 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wig_to_bigwig - - description: 'Convert Genomic Intervals To Strict BED12: ' - title: Convert Genomic Intervals To Strict BED12 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed12_0 - - description: 'Convert Genomic Intervals To Coverage: ' - title: Convert Genomic Intervals To Coverage 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bigwig_0 - - description: 'Convert FASTA to len file: ' - title: Convert FASTA to len file 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_len - - description: 'Convert BedGraph to BigWig: ' - title: Convert BedGraph to BigWig 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bedgraph_to_bigwig - - description: 'Convert BED to Feature Location Index: ' - title: Convert BED to Feature Location Index 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_fli_0 - - description: 'Convert BigWig to Wiggle: Convert bigWig to wig' - title: Convert BigWig to Wiggle 377+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=bigwigtowig + - description: 'Convert Genomic Intervals To BED: ' + title: Convert Genomic Intervals To BED 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed_0 + - description: 'Convert Parquet to csv: ' + title: Convert Parquet to csv 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_parquet_to_csv + - description: 'Convert plink pbed to ld reduced format: ' + title: Convert plink pbed to ld reduced format 0.02 + url: https://usegalaxy.org.au/root?tool_id=pbed2ldindepconvert homepage: '' id: Galaxy CONVERTER license: '' @@ -6747,6 +6571,33 @@ resources: - title: .nan url: .nan +- biocontainers: '' + biotools: '' + bunya: '' + description: '' + edam-operations: '' + edam-topics: '' + galaxy: + - 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 + - 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 + - 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: galaxy_data_sources + license: '' + name: 'Galaxy: Data sources' + nci-gadi: '' + nci-if89: '' + pawsey: '' + publications: '' + resources: + - title: .nan + url: .nan - biocontainers: '' biotools: '' bunya: '' @@ -6796,6 +6647,12 @@ edam-operations: '' edam-topics: '' galaxy: + - 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 + - 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 - description: 'Bar chart: for multiple columns' title: Bar chart 1.0.0 url: https://usegalaxy.org.au/root?tool_id=barchart_gnuplot @@ -6810,6 +6667,30 @@ resources: - title: .nan url: .nan +- biocontainers: '' + biotools: '' + bunya: '' + description: '' + edam-operations: '' + edam-topics: '' + galaxy: + - 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 + - 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: galaxy_fetch_alignments_sequences + license: '' + name: 'Galaxy: Fetch Alignments/Sequences' + nci-gadi: '' + nci-if89: '' + pawsey: '' + publications: '' + resources: + - title: .nan + url: .nan - biocontainers: '' biotools: '' bunya: '' @@ -6908,6 +6789,12 @@ - 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 + - description: 'Replace column: by values which are defined in a convert file' + title: Replace column 0.2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Freplace_column_by_key_value_file%2Freplace_column_with_key_value_file%2F0.2 + - description: 'Replace column: by values which are defined in a convert file' + title: Replace column 0.2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Freplace_column_by_key_value_file%2Freplace_column_with_key_value_file%2F0.2 - description: 'Add column: to an existing dataset' title: Add column 1.0.0 url: https://usegalaxy.org.au/root?tool_id=addValue @@ -6974,6 +6861,19 @@ edam-operations: '' edam-topics: '' galaxy: + - 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 + - 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 + - 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 + - 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 - 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 @@ -7314,62 +7214,59 @@ - Genomics - Homology modeling galaxy: '' - homepage: http://www.jstacs.de/index.php/GeMoMa - id: gemoma - license: GPL-3.0 - name: gemoma - nci-gadi: '' - nci-if89: - - '1.8' - - '1.9' - pawsey: '' - publications: - - title: Combining RNA-seq data and homology-based gene prediction for plants, animals - and fungi - url: https://doi.org/10.1186/s12859-018-2203-5 - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - 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 - license: '' - name: GeneBed_Maf_Fasta2 + homepage: http://www.jstacs.de/index.php/GeMoMa + id: gemoma + license: GPL-3.0 + name: gemoma nci-gadi: '' - nci-if89: '' + nci-if89: + - '1.8' + - '1.9' pawsey: '' - publications: '' + publications: + - title: Combining RNA-seq data and homology-based gene prediction for plants, animals + and fungi + url: https://doi.org/10.1186/s12859-018-2203-5 resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: gene.iobio + biotools: gene.iobio bunya: '' - description: '' - edam-operations: '' - edam-topics: '' + description: 'An interactive web tool for versatile, clinically-driven variant interrogation + and prioritization. + + + IOBIO is a suite of web apps for visually driven real-time analysis of genomic + data. + + + Visually driven real-time analysis of genomic data.' + edam-operations: + - Variant prioritisation + - Variant calling + - Variant classification + edam-topics: + - Exome sequencing + - Genomics + - Medicine + - Genetic variation + - Genotype and phenotype galaxy: - 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: '' + homepage: http://iobio.io/ id: geneiobio license: '' name: geneiobio nci-gadi: '' nci-if89: '' pawsey: '' - publications: '' + publications: + - title: 10.1101/2020.11.05.20224865 + url: https://doi.org/10.1101/2020.11.05.20224865 resources: - title: .nan url: .nan @@ -8904,6 +8801,10 @@ - Metabolic pathway prediction edam-topics: '' galaxy: + - 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 - description: 'HUMAnN2: to profile presence/absence and abundance of microbial pathways and gene families' title: HUMAnN2 0.11.1.3 @@ -8936,24 +8837,50 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: HybPiper + biotools: HybPiper bunya: '' - description: '' - edam-operations: '' - edam-topics: '' + description: 'Paralogs and off-target sequences improve phylogenetic resolution + in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae). + + + Recovering genes from targeted sequence capture data. + + + Current version: 1.3.1 (August 2018). + + + -- Read our article in Applications in Plant Sciences (Open Access). + + + HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries + are enriched for gene regions of interest, especially for phylogenetics. HybPiper + is a suite of Python scripts that wrap and connect bioinformatics tools in order + to extract target sequences from high-throughput DNA sequencing reads.' + edam-operations: + - Sequence trimming + - Sequence assembly + - Read mapping + edam-topics: + - Phylogenetics + - Plant biology + - Gene transcripts + - Sequence assembly + - Phylogenomics galaxy: - 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: '' + homepage: https://github.com/mossmatters/HybPiper id: hybpiper - license: '' - name: hybpiper + license: GPL-3.0 + name: HybPiper nci-gadi: '' nci-if89: '' pawsey: '' - publications: '' + publications: + - title: 10.1101/854232 + url: https://doi.org/10.1101/854232 resources: - title: .nan url: .nan @@ -9192,24 +9119,36 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: intermine + biotools: intermine bunya: '' - description: '' - edam-operations: '' - edam-topics: '' + description: Open source data warehouse built specifically for the integration and + analysis of complex biological data. It enables the creation of biological databases + accessed by sophisticated web query tools. Parsers are provided for integrating + data from many common biological data sources and formats, and there is a framework + for adding your own data. + edam-operations: + - Database search + edam-topics: + - Data integration and warehousing + - Rare diseases galaxy: - description: 'InterMine: server' title: InterMine 1.0.0 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=intermine - homepage: '' + homepage: http://www.intermine.org id: intermine - license: '' + license: LGPL-2.1 name: intermine nci-gadi: '' nci-if89: '' pawsey: '' - publications: '' + publications: + - title: 'InterMine: A flexible data warehouse system for the integration and analysis + of heterogeneous biological data' + url: https://doi.org/10.1093/bioinformatics/bts577 + - title: 'InterMine: Extensive web services for modern biology' + url: http://www.ncbi.nlm.nih.gov/pubmed/24753429 resources: - title: .nan url: .nan @@ -9264,27 +9203,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - 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 - license: '' - name: Interval_Maf_Merged_Fasta2 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: '' biotools: '' bunya: '' @@ -10341,6 +10259,51 @@ resources: - title: .nan url: .nan +- biocontainers: LFQ-Analyst + biotools: LFQ-Analyst + bunya: '' + description: "An Easy-To-Use Interactive Web Platform To Analyze and Visualize Label-Free\ + \ Proteomics Data Preprocessed with MaxQuant.\n\nA tool for analysing label-free\ + \ quantitative proteomics dataset https://bioinformatics.erc.monash.edu/apps/LFQ-Analyst/.\n\ + \nLFQ-Analyst: An easy-to-use interactive web-platform to analyze and visualize\ + \ proteomics data preprocessed with MaxQuant.\n\nLFQ-Analyst is an easy-to-use,\ + \ interactive web application developed to perform differential expression analysis\ + \ with \u201Cone click\u201D and to visualize label-free quantitative proteomic\ + \ datasets preprocessed with MaxQuant. LFQ-Analyst provides a wealth of user-analytic\ + \ features and offers numerous publication-quality result output graphics and\ + \ tables to facilitate statistical and exploratory analysis of label-free quantitative\ + \ datasets" + edam-operations: + - Essential dynamics + - Principal component visualisation + - Label-free quantification + - Imputation + - Standardisation and normalisation + edam-topics: + - Proteomics + - Sequence analysis + - Small molecules + - Metabolomics + - Proteomics experiment + galaxy: + - description: 'LFQ Analyst: Analyze and Visualize Label-Free Proteomics output + from MaxQuant' + title: LFQ Analyst 1.2.6+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=interactive_tool_lfqanalyst_2 + homepage: https://bioinformatics.erc.monash.edu/apps/LFQ-Analyst + id: LFQ-Analyst + license: GPL-3.0 + name: LFQ-Analyst + nci-gadi: '' + nci-if89: '' + pawsey: '' + publications: + - title: 'Lfq-Analyst: An easy-To-use interactive web platform to analyze and visualize + label-free proteomics data preprocessed with maxquant' + url: https://doi.org/10.1021/ACS.JPROTEOME.9B00496 + resources: + - title: .nan + url: .nan - biocontainers: '' biotools: '' bunya: '' @@ -17522,27 +17485,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - 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 - license: '' - name: replace_column_with_key_value_file - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: rjags biotools: rjags bunya: @@ -18766,12 +18708,12 @@ - Database management - Sequence analysis galaxy: + - description: 'SeqKit sort: FASTA or FASTQ files' + title: SeqKit sort 2.8.1+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqkit_sort%2Fseqkit_sort%2F2.8.1%2Bgalaxy0 - description: 'SeqKit statistics: of FASTA/Q files' title: SeqKit statistics 2.8.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqkit_stats%2Fseqkit_stats%2F2.8.1%2Bgalaxy0 - - description: 'SeqKit sort: FASTA or FASTQ files' - title: SeqKit sort 2.3.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqkit_sort%2Fseqkit_sort%2F2.3.1%2Bgalaxy1 homepage: https://bioinf.shenwei.me/seqkit/ id: seqkit license: '' @@ -19156,10 +19098,25 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: slow5tools + biotools: slow5tools bunya: '' - description: '' + description: 'Slow5tools is a simple toolkit for converting (FAST5 <-> SLOW5), compressing, + viewing, indexing and manipulating data in SLOW5 format. + + + About SLOW5 format: + + SLOW5 is a new file format for storing signal data from Oxford Nanopore Technologies + (ONT) devices. SLOW5 was developed to overcome inherent limitations in the standard + FAST5 signal data format that prevent efficient, scalable analysis and cause many + headaches for developers. SLOW5 can be encoded in human-readable ASCII format, + or a more compact and efficient binary format (BLOW5) - this is analogous to the + seminal SAM/BAM format for storing DNA sequence alignments. The BLOW5 binary format + supports zlib (DEFLATE) compression, or other compression methods, thereby minimising + the data storage footprint while still permitting efficient parallel access. Detailed + benchmarking experiments have shown that SLOW5 format is an order of magnitude + faster and significantly smaller than FAST5.' edam-operations: '' edam-topics: '' galaxy: '' @@ -20491,8 +20448,8 @@ galaxy: - 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 + title: TB-Profiler Profile 6.2.1+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftbprofiler%2Ftb_profiler_profile%2F6.2.1%2Bgalaxy0 homepage: '' id: tbprofiler license: '' @@ -20513,8 +20470,8 @@ galaxy: - description: 'TB Variant Report: - generate HTML report from SnpEff annotated M.tb VCF(s)' - title: TB Variant Report 1.0.0+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftbvcfreport%2Ftbvcfreport%2F1.0.0%2Bgalaxy0 + title: TB Variant Report 1.0.1+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftbvcfreport%2Ftbvcfreport%2F1.0.1%2Bgalaxy0 homepage: '' id: tbvcfreport license: '' @@ -20729,6 +20686,28 @@ resources: - title: .nan url: .nan +- biocontainers: '' + biotools: '' + bunya: '' + description: '' + edam-operations: '' + edam-topics: '' + galaxy: + - description: 'TMT Analyst: Analyze and Visualize Label-Free Proteomics output + from MaxQuant' + title: TMT Analyst 0.11+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=interactive_tool_tmtanalyst + homepage: '' + id: tmt-analyst + license: '' + name: TMT Analyst + nci-gadi: '' + nci-if89: '' + pawsey: '' + publications: '' + resources: + - title: .nan + url: .nan - biocontainers: tophat biotools: tophat bunya: '' @@ -21084,6 +21063,9 @@ - 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 + - 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 - 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 @@ -21287,48 +21269,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - 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 - license: '' - name: ucsc_table_direct_archaea1 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - 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 - license: '' - name: ucsc_table_direct1 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: umi-tools biotools: umi-tools bunya: '' @@ -21568,27 +21508,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - 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 - license: '' - name: vcf_to_maf_customtrack1 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: '' biotools: '' bunya: '' @@ -22103,24 +22022,34 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: wormbase + biotools: wormbase bunya: '' - description: '' - edam-operations: '' - edam-topics: '' + description: Caenorhabditis elegans genome database. International consortium of + biologists and computer scientists dedicated to providing the research community + with accurate, current, accessible information concerning the genetics, genomics + and biology of C. elegans and related nematodes. Founded in 2000, the Consortium + is led by Paul Sternberg of CalTech, Paul Kersey of the EBI, Matt Berriman of + the Wellcome Trust Sanger Institute, and Lincoln Stein of the Ontario Institute + for Cancer Research. + edam-operations: + - Query and retrieval + edam-topics: + - Model organisms galaxy: - description: 'WormBase: server' title: WormBase 1.0.1 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=wormbase - homepage: '' + homepage: http://www.wormbase.org/ id: wormbase license: '' name: wormbase nci-gadi: '' nci-if89: '' pawsey: '' - publications: '' + publications: + - title: 'WormBase 2014: New views of curated biology' + url: https://doi.org/10.1093/nar/gkt1063 resources: - title: .nan url: .nan @@ -22369,24 +22298,37 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: ZebrafishMine + biotools: ZebrafishMine bunya: '' - description: '' - edam-operations: '' - edam-topics: '' + description: "ZebrafishMine is powered by the InterMIne data warehouse system, and\ + \ integrates biological data sets from multiple sources.\r\nIt currently includes\ + \ updates of data from ZFIN, the zebrafish model organism database. There is also\ + \ data from the Panther database." + edam-operations: + - Data retrieval + - Visualisation + - Gene-set enrichment analysis + - Query and retrieval + edam-topics: + - Data management + - Genomics + - Proteomics galaxy: - description: 'ZebrafishMine: server' title: ZebrafishMine 1.0.0 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=zebrafishmine - homepage: '' + homepage: http://zebrafishmine.org id: zebrafishmine - license: '' + license: LGPL-2.1 name: zebrafishmine nci-gadi: '' nci-if89: '' pawsey: '' - publications: '' + publications: + - title: 'InterMine: A flexible data warehouse system for the integration and analysis + of heterogeneous biological data' + url: https://doi.org/10.1093/bioinformatics/bts577 resources: - title: .nan url: .nan