mirror of
https://github.com/galaxyproject/galaxy.git
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147 lines
14 KiB
XML
147 lines
14 KiB
XML
<?xml version="1.0"?>
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<toolshed name="toolshed.g2.bx.psu.edu">
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<repository owner="devteam" changeset_revision="dc20f447c0e2" name="bam_to_sam" description="Galaxy wrappers for the tool BAM-to-SAM: converts BAM format to SAM format">
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<tool id="bam_to_sam" version="1.0.3" file="samtools/bam_to_sam.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="586c1f0e1515" name="categorize_elements_satisfying_criteria" description="Galaxy wrappers for the tool Categorize Elements: satisfying criteria">
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<tool id="categorize_elements_satisfying_criteria" version="1.0.0" file="regVariation/categorize_elements_satisfying_criteria.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="acc3dc5d26e3" name="compute_motif_frequencies_for_all_motifs" description="Galaxy wrappers for the tool Compute Motif Frequencies For All Motifs: motif by motif">
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<tool id="compute_motif_frequencies_for_all_motifs" version="1.0.0" file="regVariation/compute_motif_frequencies_for_all_motifs.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="46325357b948" name="compute_motifs_frequency" description="Galaxy wrappers for the tool Compute Motif Frequencies: in indel flanking regions">
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<tool id="compute_motifs_frequency" version="1.0.0" file="regVariation/compute_motifs_frequency.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="4a32700dcaa2" name="ctd_batch" description="Galaxy wrappers for the tool CTD: analysis of chemicals, diseases, or genes">
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<tool id="ctdBatch_1" version="1.0.0" file="phenotype_association/ctd.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="9a3f7a890da6" name="cuffcompare" description="Galaxy wrappers for the Cuffcompare tool.">
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<tool id="cuffcompare" version="0.0.5" file="ngs_rna/cuffcompare_wrapper.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="0dabb2ed6eb1" name="cuffdiff" description="Galaxy wrappers for the Cuffdiff tool.">
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<tool id="cuffdiff" version="0.0.6" file="ngs_rna/cuffdiff_wrapper.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="b01956f26c36" name="cufflinks" description="Galaxy wrappers for the Cufflinks tool.">
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<tool id="cufflinks" version="0.0.6" file="ngs_rna/cufflinks_wrapper.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="fdc55fd74f78" name="cuffmerge" description="Galaxy wrappers for the Cuffmerge tool.">
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<tool id="cuffmerge" version="0.0.5" file="ngs_rna/cuffmerge_wrapper.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="f16000dc644b" name="delete_overlapping_indels" description="Galaxy wrappers for the tool Delete Overlapping Indels: from a chromosome indels file">
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<tool id="delete_overlapping_indels" version="1.0.0" file="regVariation/delete_overlapping_indels.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="de839553d2a2" name="divide_pg_snp" description="Galaxy wrappers for the tool Separate pgSnp alleles: into columns">
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<tool id="dividePgSnp" version="1.0.0" file="phenotype_association/dividePgSnpAlleles.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="063ecbe59faf" name="draw_stacked_barplots" description="Galaxy wrappers for the tool Draw Stacked Bar Plots: for different categories and different criteria">
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<tool id="draw_stacked_barplots" version="1.0.0" file="regVariation/draw_stacked_barplots.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="f2ab5b44870d" name="fasta_clipping_histogram" description="Galaxy wrappers for the tool Length Distribution chart">
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<tool id="cshl_fasta_clipping_histogram" version="1.0.0" file="fastx_toolkit/fasta_clipping_histogram.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="8f0ae92440b8" name="fasta_formatter" description="Galaxy wrappers for the tool FASTA Width: formatter">
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<tool id="cshl_fasta_formatter" version="1.0.0" file="fastx_toolkit/fasta_formatter.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="4b41e3076a50" name="fasta_nucleotide_changer" description="Galaxy wrappers for the tool RNA/DNA: converter">
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<tool id="cshl_fasta_nucleotides_changer" version="1.0.0" file="fastx_toolkit/fasta_nucleotide_changer.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="e359ce20fbd9" name="fastq_quality_boxplot" description="Galaxy wrappers for the tool Draw quality score boxplot">
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<tool id="cshl_fastq_quality_boxplot" version="1.0.0" file="fastx_toolkit/fastq_quality_boxplot.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="b87c74b61d81" name="fastq_quality_converter" description="Galaxy wrappers for the tool Quality format converter: (ASCII-Numeric)">
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<tool id="cshl_fastq_quality_converter" version="1.0.0" file="fastx_toolkit/fastq_quality_converter.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="b145b9b26648" name="fastq_quality_filter" description="Galaxy wrappers for the Filter by quality tool.">
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<tool id="cshl_fastq_quality_filter" version="1.0.0" file="fastx_toolkit/fastq_quality_filter.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="04614cf6ed39" name="fastq_to_fasta" description="Galaxy wrappers for the tool FASTQ to FASTA: converter">
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<tool id="cshl_fastq_to_fasta" version="1.0.0" file="fastx_toolkit/fastq_to_fasta.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="7f9660a246c0" name="fastx_artifacts_filter" description="Galaxy wrappers for the Remove sequencing artifacts tool.">
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<tool id="cshl_fastx_artifacts_filter" version="1.0.0" file="fastx_toolkit/fastx_artifacts_filter.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="a12850d0559b" name="fastx_barcode_splitter" description="Galaxy wrappers for the Barcode Splitter tool.">
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<tool id="cshl_fastx_barcode_splitter" version="1.0.0" file="fastx_toolkit/fastx_barcode_splitter.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="2fe2d2b9e8e4" name="fastx_clipper" description="Galaxy wrappers for the tool Clip: adapter sequences">
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<tool id="cshl_fastx_clipper" version="1.0.1" file="fastx_toolkit/fastx_clipper.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="e942fd3a76a5" name="fastx_collapser" description="Galaxy wrappers for the tool Collapse: sequences">
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<tool id="cshl_fastx_collapser" version="1.0.0" file="fastx_toolkit/fastx_collapser.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="bcc5424a4a3c" name="fastx_nucleotides_distribution" description="Galaxy wrappers for the Draw nucleotides distribution chart tool.">
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<tool id="cshl_fastx_nucleotides_distribution" version="1.0.0" file="fastx_toolkit/fastx_nucleotides_distribution.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="45f077341b24" name="fastx_quality_statistics" description="Galaxy wrappers for the Compute quality statistics tool.">
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<tool id="cshl_fastx_quality_statistics" version="1.0.0" file="fastx_toolkit/fastx_quality_statistics.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="d7bce63e6e09" name="fastx_renamer" description="Galaxy wrappers for the Rename sequences tool.">
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<tool id="cshl_fastx_renamer" version="0.0.11" file="fastx_toolkit/fastx_renamer.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="c58871138668" name="fastx_reverse_complement" description="Galaxy wrappers for the Reverse-Complement tool.">
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<tool id="cshl_fastx_reverse_complement" version="1.0.0" file="fastx_toolkit/fastx_reverse_complement.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="9cb372481a71" name="fastx_trimmer" description="Galaxy wrappers for the Trim sequences tool.">
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<tool id="cshl_fastx_trimmer" version="1.0.0" file="fastx_toolkit/fastx_trimmer.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="64133669255f" name="hgv_fundo" description="Galaxy wrappers for the tool FunDO: human genes associated with disease terms">
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<tool id="hgv_funDo" version="1.0.0" file="phenotype_association/funDo.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="0e80ffa5b7f7" name="hgv_hilbertvis" description="Galaxy wrappers for the tool HVIS: visualization of genomic data with the Hilbert curve">
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<tool id="hgv_hilbertvis" version="1.0.0" file="phenotype_association/hilbertvis.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="5ad24b81dd10" name="indels_3way" description="Galaxy wrappers for the tool Fetch Indels: from 3-way alignments">
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<tool id="indels_3way" version="1.0.3" file="regVariation/getIndels_3way.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="4e31fad3f08e" name="microsatellite_birthdeath" description="Galaxy wrappers for the tool Identify microsatellite births and deaths: and causal mutational mechanisms from previously identified orthologous microsatellite sets">
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<tool id="microsatellite_birthdeath" version="1.0.0" file="regVariation/microsatellite_birthdeath.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="275433d3a395" name="multispecies_orthologous_microsats" description="Galaxy wrappers for the tool Extract orthologous microsatellites: for multiple (>2) species alignments">
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<tool id="multispecies_orthologous_microsats" version="1.0.0" file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="8f0af7251167" name="mutate_snp_codon" description="Galaxy wrappers for the tool Mutate Codons: with SNPs">
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<tool id="mutate_snp_codon_1" version="1.0.0" file="evolution/mutate_snp_codon.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="a110f9d6ae24" name="pileup_interval" description="Galaxy wrappers for the tool Pileup-to-Interval: condenses pileup format into ranges of bases">
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<tool id="pileup_interval" version="1.0.0" file="samtools/pileup_interval.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="ff1ba9b75337" name="pileup_parser" description="Galaxy wrappers for the tool Filter pileup: on coverage and SNPs">
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<tool id="pileup_parser" version="1.0.2" file="samtools/pileup_parser.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="8c737b8ddc45" name="sam2interval" description="Galaxy wrappers for the tool Convert SAM: to interval">
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<tool id="sam2interval" version="1.0.1" file="samtools/sam2interval.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="0b2424a404d9" name="sam_bitwise_flag_filter" description="Galaxy wrappers for the tool Filter SAM: on bitwise flag values">
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<tool id="sam_bw_filter" version="1.0.0" file="samtools/sam_bitwise_flag_filter.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="a7a49d31c5cf" name="sam_merge" description="Galaxy wrappers for the tool Merge BAM Files: merges BAM files together">
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<tool id="sam_merge2" version="1.1.2" file="samtools/sam_merge.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="95612c159681" name="sam_pileup" description="Galaxy wrappers for the tool Generate pileup: from BAM dataset">
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<tool id="sam_pileup" version="1.1.1" file="samtools/sam_pileup.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="30fdbaccb96b" name="sam_to_bam" description="Galaxy wrappers for the tool SAM-to-BAM: converts SAM format to BAM format">
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<tool id="sam_to_bam" version="1.1.2" file="samtools/sam_to_bam.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="13c4ad597626" name="samtools_flagstat" description="Galaxy wrappers for the tool flagstat: provides simple stats on BAM files">
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<tool id="samtools_flagstat" version="1.0.0" file="samtools/samtools_flagstat.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="44a18a94d7a9" name="samtools_mpileup" description="Galaxy wrappers for the tool MPileup: SNP and indel caller">
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<tool id="samtools_mpileup" version="0.0.1" file="samtools/samtools_mpileup.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="7e92b2a53aab" name="samtools_rmdup" description="Galaxy wrappers for the tool rmdup: remove PCR duplicates">
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<tool id="samtools_rmdup" version="1.0.0" file="samtools/samtools_rmdup.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="68ba55e96489" name="samtools_slice_bam" description="Galaxy wrappers for the tool Slice BAM: by provided regions">
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<tool id="samtools_slice_bam" version="0.0.1" file="samtools/samtools_slice_bam.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="36163bff76cc" name="split_paired_reads" description="Galaxy wrappers for the Split paired end reads tool.">
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<tool id="split_paired_reads" version="1.0.0" file="metag_tools/split_paired_reads.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="e6a85a9297b3" name="t_test_two_samples" description="Galaxy wrappers for the T Test for Two Samples tool.">
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<tool id="t_test_two_samples" version="1.0.0" file="regVariation/t_test_two_samples.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="acf952549b53" name="xy_plot" description="Galaxy wrappers for the tool Plotting tool: for multiple series and graph types">
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<tool id="XY_Plot_1" version="1.0.1" file="plotting/xy_plot.xml" />
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</repository>
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</toolshed> |