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Merge galaxy/galaxy-central default branch.
This commit is contained in:
Nicola Soranzo
@@ -3,17 +3,17 @@
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<repository owner="devteam" name="analyze_covariates" changeset_revision="738bc749f9a3" 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 owner="devteam" name="basecoverage" changeset_revision="642849141ae9" description="Base Coverage of all intervals">
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<tool id="gops_basecoverage_1" version="1.0.0" file="new_operations/basecoverage.xml" />
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</repository>
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<repository owner="devteam" name="best_regression_subsets" changeset_revision="e769cde223a5" 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 owner="devteam" name="best_regression_subsets" changeset_revision="4f33ec73e445" description="Perform Best-subsets Regression">
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<tool id="BestSubsetsRegression1" version="1.0.0" 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 owner="devteam" name="cluster" changeset_revision="9fcc3a1c3d26" description="Cluster">
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<tool id="gops_cluster_1" version="1.0.0" 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 owner="devteam" name="complement" changeset_revision="67c4ed724bfd" description="Complement intervals of a dataset">
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<tool id="gops_complement_1" version="1.0.0" 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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@@ -24,8 +24,8 @@
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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 owner="devteam" name="coverage" changeset_revision="16b62a897aac" description="Coverage of a set of intervals on second set of intervals">
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<tool id="gops_coverage_1" version="1.0.0" 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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@@ -36,23 +36,23 @@
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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 owner="devteam" name="get_flanks" changeset_revision="c3b1781c6fd1" description="Get flanks - returns flanking region/s for every gene">
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<tool id="get_flanks1" version="1.0.0" 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 owner="devteam" name="getindels_2way" changeset_revision="f1dc6f5fce6e" description="Fetch Indels from pairwise alignments">
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<tool id="getIndels_2way" version="1.0.0" 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 owner="devteam" name="intersect" changeset_revision="81ad85f731b9" description="Intersect the intervals of two datasets">
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<tool id="gops_intersect_1" version="1.0.0" 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 owner="devteam" name="join" changeset_revision="11a49f94d086" description="Join the intervals of two datasets side-by-side">
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<tool id="gops_join_1" version="1.0.0" 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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@@ -63,11 +63,11 @@
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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 owner="devteam" name="merge" changeset_revision="55e88307811d" description="Merge the overlapping intervals of a dataset">
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<tool id="gops_merge_1" version="1.0.0" 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 owner="devteam" name="microsats_alignment_level" changeset_revision="7852385470f3" description="Extract Orthologous Microsatellites from pair-wise alignments">
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<tool id="microsats_align1" version="1.0.0" 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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@@ -93,8 +93,8 @@
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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 owner="devteam" name="subtract" changeset_revision="7bf44b9d7a8b" description="Subtract the intervals of two datasets">
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<tool id="gops_subtract_1" version="1.0.0" 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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@@ -135,7 +135,7 @@
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<repository owner="devteam" name="weightedaverage" changeset_revision="90611e86a998" 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 owner="devteam" name="windowsplitter" changeset_revision="75abda2290cc" description="Make windows">
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<tool id="winSplitter" version="1.0.0" file="regVariation/windowSplitter.xml" />
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</repository>
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</toolshed>
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