mirror of
https://github.com/galaxyproject/galaxy.git
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132 lines
11 KiB
XML
132 lines
11 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="96d2e31a3938" name="bowtie2" description="Bowtie2">
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<tool id="bowtie2" version="0.2" file="sr_mapping/bowtie2_wrapper.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="a0c8dc671a23" name="ccat" description="Control-based ChIP-seq Analysis Tool">
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<tool id="peakcalling_ccat" version="0.0.1" file="peak_calling/ccat_wrapper.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="7cc64024fe92" name="clustalw" description="ClustalW multiple sequence alignment program for DNA or proteins">
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<tool id="clustalw" version="0.1" file="rgenetics/rgClustalw.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="6708501767b6" name="dwt_cor_ava_perclass" description="Compute P-values and Correlation Coefficients for Feature Occurrences">
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<tool id="compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom" version="1.0.0" file="discreteWavelet/execute_dwt_cor_aVa_perClass.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="0f2eda4ea8dc" name="dwt_cor_avb_all" description="Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features">
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<tool id="compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom" version="1.0.0" file="discreteWavelet/execute_dwt_cor_aVb_all.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="0b89b03ad760" name="dwt_ivc_all" description="Compute P-values and Second Moments for Feature Occurrences">
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<tool id="compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom" version="1.0.0" file="discreteWavelet/execute_dwt_IvC_all.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="cb422b6f49d2" name="dwt_var_perclass" description="Compute P-values and Max Variances for Feature Occurrences">
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<tool id="compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom" version="1.0.0" file="discreteWavelet/execute_dwt_var_perClass.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="d56c5d2e1a29" name="dwt_var_perfeature" description="Wavelet variance using Discrete Wavelet Transfoms">
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<tool id="dwt_var1" version="1.0.0" file="discreteWavelet/execute_dwt_var_perFeature.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="7b0708761d05" name="express" description="Quantify the abundances of a set of target sequences from sampled subsequences">
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<tool id="express" version="1.1.1" file="ngs_rna/express_wrapper.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="e28c965eeed4" name="fastqc" description="Read QC reports using FastQC">
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<tool id="fastqc" version="1.0.0" file="rgenetics/rgFastQC.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="94306bdd58f7" name="fastq_combiner" description="Combine FASTA and QUAL into FASTQ.">
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<tool id="fastq_combiner" version="1.0.1" file="fastq/fastq_combiner.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="30d9ece6c752" name="fastq_filter" description="Filter FASTQ reads by quality score and length">
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<tool id="fastq_filter" version="1.0.0" file="fastq/fastq_filter.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="1298445c852b" name="fastq_groomer" description="Convert between various FASTQ quality formats.">
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<tool id="fastq_groomer" version="1.0.4" file="fastq/fastq_groomer.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="5d1e9e13e8db" name="fastq_manipulation" description="Manipulate FASTQ reads on various attributes.">
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<tool id="fastq_manipulation" version="1.0.1" file="fastq/fastq_manipulation.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="5a7b5751617b" name="fastq_masker_by_quality" description="FASTQ Masker by quality score">
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<tool id="fastq_masker_by_quality" version="1.0.0" file="fastq/fastq_masker_by_quality.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="f0949bc49926" name="fastq_paired_end_deinterlacer" description="FASTQ de-interlacer on paired end reads.">
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<tool id="fastq_paired_end_deinterlacer" version="1.1" file="fastq/fastq_paired_end_deinterlacer.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="b89bdf6acb6c" name="fastq_paired_end_interlacer" description="FASTQ interlacer on paired end reads">
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<tool id="fastq_paired_end_interlacer" version="1.1" file="fastq/fastq_paired_end_interlacer.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="2793d1d765b9" name="fastq_paired_end_joiner" description="FASTQ joiner on paired end reads">
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<tool id="fastq_paired_end_joiner" version="1.0.0" file="fastq/fastq_paired_end_joiner.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="c549e99026db" name="fastq_paired_end_splitter" description="FASTQ splitter on joined paired end reads">
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<tool id="fastq_paired_end_splitter" version="1.0.0" file="fastq/fastq_paired_end_splitter.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="9b7b4e0ca9db" name="fastq_stats" description="FASTQ Summary Statistics by column">
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<tool id="fastq_stats" version="1.0.0" file="fastq/fastq_stats.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="3571553aeb20" name="fastqtofasta" description="FASTQ to FASTA converter">
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<tool id="fastq_to_fasta_python" version="1.0.0" file="fastq/fastq_to_fasta.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="bc9269529e88" name="fastq_to_tabular" description="FASTQ to Tabular converter">
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<tool id="fastq_to_tabular" version="1.1.0" file="fastq/fastq_to_tabular.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="0b9feb0ed628" name="fastq_trimmer" description="FASTQ Trimmer by quality">
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<tool id="fastq_trimmer" version="1.0.0" file="fastq/fastq_trimmer.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="1cdcaf5fc1da" name="fastq_trimmer_by_quality" description="FASTQ Quality Trimmer by sliding window">
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<tool id="fastq_quality_trimmer" version="1.0.0" file="fastq/fastq_trimmer_by_quality.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="31154ff9f5e1" name="filter_transcripts_via_tracking" description="Filter Combined Transcripts">
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<tool id="filter_combined_via_tracking" version="0.1" file="ngs_rna/filter_transcripts_via_tracking.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="acf51ff24c7d" name="find_diag_hits" description="Identify sequence reads corresponding to a particular taxonomic group">
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<tool id="find_diag_hits" version="1.0.0" file="taxonomy/find_diag_hits.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="33a0e6aca936" name="freebayes_wrapper" description="Call SNPS with Freebayes">
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<tool id="freebayes_wrapper" version="0.5.0" file="phenotype_association/freebayes.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="7b1b03c4465d" name="gi2taxonomy" description="Fetch taxonomic representation">
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<tool id="Fetch Taxonomic Ranks" version="1.1.0" file="taxonomy/gi2taxonomy.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="2cd5ee197ec7" name="gmaj" description="GMAJ Multiple Alignment Viewer">
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<tool id="gmaj_1" version="2.0.1" file="visualization/GMAJ.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="33e8ed5a4601" name="lca_wrapper" description="Find lowest diagnostic rank">
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<tool id="lca1" version="1.0.1" file="taxonomy/lca.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="ae2ec275332a" name="macs" description="Model-based Analysis of ChIP-Seq">
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<tool id="peakcalling_macs" version="1.0.1" file="peak_calling/macs_wrapper.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="8cd5945559b8" name="poisson2test" description="Poisson two-sample test">
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<tool id="poisson2test" version="1.0.0" file="taxonomy/poisson2test.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="82a8234e03f2" name="sicer" description="Statistical approach for the Identification of ChIP-Enriched Regions">
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<tool id="peakcalling_sicer" version="0.0.1" file="peak_calling/sicer_wrapper.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="9e2b9ca7f33a" name="t2ps" description="Draw phylogeny">
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<tool id="Draw_phylogram" version="1.0.0" file="taxonomy/t2ps_wrapper.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="592acb9505fc" name="t2t_report" description="Summarize taxonomy">
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<tool id="t2t_report" version="1.0.0" file="taxonomy/t2t_report.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="b334cd1095ea" name="tabular_to_fastq" description="Tabular to FASTQ converter">
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<tool id="tabular_to_fastq" version="1.0.0" file="fastq/tabular_to_fastq.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="1030acbecce6" name="tophat" description="Find splice junctions using RNA-seq data">
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<tool id="tophat" version="1.5.0" file="ngs_rna/tophat_wrapper.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="ffa30bedbee3" name="tophat2" description="Gapped-read mapper for RNA-seq data">
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<tool id="tophat2" version="0.6" file="ngs_rna/tophat2_wrapper.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="b001b50f2009" name="vcf_annotate" description="Annotate a VCF file (dbSNP, hapmap)">
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<tool id="vcf_annotate" version="1.0.0" file="vcf_tools/annotate.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="76ad0b7865b9" name="vcf_extract" description="Extract reads from a specified region">
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<tool id="vcf_extract" version="1.0.0" file="vcf_tools/extract.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="da1a6f33b504" name="vcf_filter" description="Filter a VCF file">
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<tool id="vcf_filter" version="1.0.0" file="vcf_tools/filter.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="9d162bde4113" name="vcf_intersect" description="Generate the intersection of two VCF files">
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<tool id="vcf_intersect" version="1.0.0" file="vcf_tools/intersect.xml" />
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</repository>
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<repository owner="devteam" changeset_revision="66253fc0a69b" name="weblogo3" description="Sequence Logo generator for fasta (eg Clustal alignments)">
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<tool id="rgweblogo3" version="0.4" file="rgenetics/rgWebLogo3.xml" />
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</repository>
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</toolshed> |