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Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation.
This commit is contained in:
Dave Bouvier
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#!/bin/sh
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cd `dirname $0`/../..
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python ./scripts/migrate_tools/migrate_tools.py 0010_tools.xml $@
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<?xml version="1.0"?>
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<toolshed name="toolshed.g2.bx.psu.edu">
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<repository owner="devteam" name="analyze_covariates" changeset_revision="be6bede22459" description="Analyze Covariates">
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<tool id="gatk_analyze_covariates" version="0.0.5" file="gatk/analyze_covariates.xml" />
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</repository>
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<repository owner="devteam" name="basecoverage" changeset_revision="1e6a9e97fa41" description="Base Coverage of all intervals">
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<tool id="gops_basecoverage_1" version="0.0.1" file="new_operations/basecoverage.xml" />
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</repository>
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<repository owner="devteam" name="best_regression_subsets" changeset_revision="54c7a01a2cc7" description="Perform Best-subsets Regression">
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<tool id="BestSubsetsRegression1" version="0.0.1" file="regVariation/best_regression_subsets.xml" />
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</repository>
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<repository owner="devteam" name="cluster" changeset_revision="d5677eecbad4" description="Cluster">
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<tool id="gops_cluster_1" version="0.0.1" file="new_operations/cluster.xml" />
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</repository>
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<repository owner="devteam" name="complement" changeset_revision="d958d5a0d1e8" description="Complement intervals of a dataset">
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<tool id="gops_complement_1" version="0.0.1" file="new_operations/complement.xml" />
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</repository>
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<repository owner="devteam" name="compute_q_values" changeset_revision="63abfc350814" description="Compute q-values based on multiple simultaneous tests p-values">
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<tool id="compute_q_values" version="1.0.1" file="regVariation/compute_q_values.xml" />
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</repository>
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<repository owner="devteam" name="concat" changeset_revision="8aa939ace6ba" description="Concatenate two datasets into one dataset">
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<tool id="gops_concat_1" version="1.0.1" file="new_operations/concat.xml" />
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</repository>
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<repository owner="devteam" name="count_covariates" changeset_revision="14e304b70425" description="Count Covariates on BAM files">
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<tool id="gatk_count_covariates" version="0.0.5" file="gatk/count_covariates.xml" />
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</repository>
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<repository owner="devteam" name="coverage" changeset_revision="1e864693a1c0" description="Coverage of a set of intervals on second set of intervals">
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<tool id="gops_coverage_1" version="0.0.1" file="new_operations/coverage.xml" />
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</repository>
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<repository owner="devteam" name="depth_of_coverage" changeset_revision="c3f08370fc82" description="Depth of Coverage on BAM files">
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<tool id="gatk_depth_of_coverage" version="0.0.2" file="gatk/depth_of_coverage.xml" />
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</repository>
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<repository owner="devteam" name="featurecounter" changeset_revision="ac6218e2b686" description="Feature coverage">
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<tool id="featureCoverage1" version="2.0.0" file="regVariation/featureCounter.xml" />
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</repository>
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<repository owner="devteam" name="flanking_features" changeset_revision="90100b587723" description="Fetch closest non-overlapping feature for every interval">
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<tool id="flanking_features_1" version="4.0.1" file="new_operations/flanking_features.xml" />
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</repository>
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<repository owner="devteam" name="get_flanks" changeset_revision="a72f0decd7b3" description="Get flanks - returns flanking region/s for every gene">
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<tool id="get_flanks1" version="0.0.1" file="new_operations/get_flanks.xml" />
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</repository>
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<repository owner="devteam" name="getindelrates_3way" changeset_revision="d427e5acb9ee" description="Estimate Indel Rates for 3-way alignments">
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<tool id="indelRates_3way" version="1.0.0" file="regVariation/getIndelRates_3way.xml" />
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</repository>
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<repository owner="devteam" name="getindels_2way" changeset_revision="91655316fcf0" description="Fetch Indels from pairwise alignments">
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<tool id="getIndels_2way" version="0.0.1" file="regVariation/getIndels_2way.xml" />
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</repository>
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<repository owner="devteam" name="indel_realigner" changeset_revision="bb0beda6cf83" description="Indel Realigner - perform local realignment">
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<tool id="gatk_indel_realigner" version="0.0.6" file="gatk/indel_realigner.xml" />
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</repository>
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<repository owner="devteam" name="intersect" changeset_revision="5b3c6135a982" description="Intersect the intervals of two datasets">
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<tool id="gops_intersect_1" version="0.0.1" file="new_operations/intersect.xml" />
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</repository>
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<repository owner="devteam" name="join" changeset_revision="e56b47dce68a" description="Join the intervals of two datasets side-by-side">
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<tool id="gops_join_1" version="0.0.1" file="new_operations/join.xml" />
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</repository>
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<repository owner="devteam" name="linear_regression" changeset_revision="cf431604ec3e" description="Perform Linear Regression">
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<tool id="LinearRegression1" version="1.0.1" file="regVariation/linear_regression.xml" />
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</repository>
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<repository owner="devteam" name="logistic_regression_vif" changeset_revision="bd196d7c1ca9" description="Perform Logistic Regression with vif">
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<tool id="LogisticRegression" version="1.0.1" file="regVariation/logistic_regression_vif.xml" />
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</repository>
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<repository owner="devteam" name="maf_cpg_filter" changeset_revision="7f2a12cb047d" description="Mask CpG/non-CpG sites from MAF file">
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<tool id="cpgFilter" version="1.0.0" file="regVariation/maf_cpg_filter.xml" />
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</repository>
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<repository owner="devteam" name="merge" changeset_revision="b488a1fa07f6" description="Merge the overlapping intervals of a dataset">
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<tool id="gops_merge_1" version="0.0.1" file="new_operations/merge.xml" />
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</repository>
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<repository owner="devteam" name="microsats_alignment_level" changeset_revision="d4368a5a3fc7" description="Extract Orthologous Microsatellites from pair-wise alignments">
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<tool id="microsats_align1" version="0.0.1" file="regVariation/microsats_alignment_level.xml" />
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</repository>
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<repository owner="devteam" name="microsats_mutability" changeset_revision="4aa1ee5d8510" description="Estimate microsatellite mutability by specified attributes">
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<tool id="microsats_mutability1" version="1.1.0" file="regVariation/microsats_mutability.xml" />
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</repository>
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<repository owner="devteam" name="partialr_square" changeset_revision="88ef41de020d" description="Compute partial R square">
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<tool id="partialRsq" version="1.0.0" file="regVariation/partialR_square.xml" />
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</repository>
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<repository owner="devteam" name="print_reads" changeset_revision="e768f4851646" description="Print Reads from BAM files">
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<tool id="gatk_print_reads" version="0.0.1" file="gatk/print_reads.xml" />
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</repository>
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<repository owner="devteam" name="quality_filter" changeset_revision="8d65bbc52dfe" description="Filter nucleotides based on quality scores">
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<tool id="qualityFilter" version="1.0.1" file="regVariation/quality_filter.xml" />
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</repository>
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<repository owner="devteam" name="rcve" changeset_revision="7740956d197b" description="Compute RCVE">
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<tool id="rcve1" version="1.0.0" file="regVariation/rcve.xml" />
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</repository>
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<repository owner="devteam" name="realigner_target_creator" changeset_revision="b83a853a3156" description="Realigner Target Creator for use in local realignment">
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<tool id="gatk_realigner_target_creator" version="0.0.4" file="gatk/realigner_target_creator.xml" />
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</repository>
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<repository owner="devteam" name="substitution_rates" changeset_revision="d1b35bcdaacc" description="Estimate substitution rates for non-coding regions">
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<tool id="subRate1" version="1.0.0" file="regVariation/substitution_rates.xml" />
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</repository>
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<repository owner="devteam" name="substitutions" changeset_revision="c54f5d0bbb58" description="Fetch substitutions from pairwise alignments">
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<tool id="substitutions1" version="1.0.0" file="regVariation/substitutions.xml" />
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</repository>
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<repository owner="devteam" name="subtract" changeset_revision="5bc2dacbe729" description="Subtract the intervals of two datasets">
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<tool id="gops_subtract_1" version="0.0.1" file="new_operations/subtract.xml" />
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</repository>
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<repository owner="devteam" name="subtract_query" changeset_revision="5f6ebef89722" description="Subtract Whole Dataset from another dataset">
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<tool id="subtract_query1" version="0.1" file="new_operations/subtract_query.xml" />
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</repository>
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<repository owner="devteam" name="table_recalibration" changeset_revision="53dd1bfced54" description="Table Recalibration on BAM files">
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<tool id="gatk_table_recalibration" version="0.0.5" file="gatk/table_recalibration.xml" />
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</repository>
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<repository owner="devteam" name="tables_arithmetic_operations" changeset_revision="82fa5062d611" description="Arithmetic Operations on tables">
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<tool id="tables_arithmetic_operations" version="1.0.0" file="new_operations/tables_arithmetic_operations.xml" />
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</repository>
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<repository owner="devteam" name="unified_genotyper" changeset_revision="66dd4d4c1743" description="Unified Genotyper SNP and indel caller">
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<tool id="gatk_unified_genotyper" version="0.0.6" file="gatk/unified_genotyper.xml" />
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</repository>
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<repository owner="devteam" name="variant_annotator" changeset_revision="ae9d0a543e9b" description="Variant Annotator">
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<tool id="gatk_variant_annotator" version="0.0.5" file="gatk/variant_annotator.xml" />
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</repository>
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<repository owner="devteam" name="variant_apply_recalibration" changeset_revision="350a4d0d1678" description="Apply Variant Recalibration">
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<tool id="gatk_variant_apply_recalibration" version="0.0.4" file="gatk/variant_apply_recalibration.xml" />
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</repository>
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<repository owner="devteam" name="variant_combine" changeset_revision="1a6e16391727" description="Combine Variants">
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<tool id="gatk_variant_combine" version="0.0.4" file="gatk/variant_combine.xml" />
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</repository>
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<repository owner="devteam" name="variant_eval" changeset_revision="fbca1c0956d2" description="Eval Variants">
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<tool id="gatk_variant_eval" version="0.0.8" file="gatk/variant_eval.xml" />
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</repository>
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<repository owner="devteam" name="variant_filtration" changeset_revision="da6e2503c62d" description="Variant Filtration on VCF files">
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<tool id="gatk_variant_filtration" version="0.0.5" file="gatk/variant_filtration.xml" />
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</repository>
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<repository owner="devteam" name="variant_recalibrator" changeset_revision="cb7cf57397a7" description="Variant Recalibrator">
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<tool id="gatk_variant_recalibrator" version="0.0.4" file="gatk/variant_recalibrator.xml" />
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</repository>
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<repository owner="devteam" name="variant_select" changeset_revision="135e8721ffc5" description="Select Variants from VCF files">
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<tool id="gatk_variant_select" version="0.0.2" file="gatk/variant_select.xml" />
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</repository>
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<repository owner="devteam" name="variants_validate" changeset_revision="7e1ecaa64370" description="Validate Variants">
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<tool id="gatk_validate_variants" version="0.0.4" file="gatk/variants_validate.xml" />
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</repository>
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<repository owner="devteam" name="weightedaverage" changeset_revision="9b7b4009f2c0" description="Assign weighted-average of the values of features overlapping an interval">
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<tool id="wtavg" version="1.0.0" file="regVariation/WeightedAverage.xml" />
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</repository>
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<repository owner="devteam" name="windowsplitter" changeset_revision="e5490ea33640" description="Make windows">
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<tool id="winSplitter" version="0.0.1" file="regVariation/windowSplitter.xml" />
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</repository>
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</toolshed>
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