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fix fully overlap reads #1220

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fix fully overlap reads #1220

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d89bb84
fix numpy
y9c Jan 19, 2023
2d93f8f
update versions of tool wrappers
lldelisle May 31, 2023
dd04af4
macrofy the profile version
lldelisle Jun 1, 2023
810c135
Merge pull request #1218 from lldelisle/galaxy_tools_update
bgruening Jun 1, 2023
780019b
Merge branch 'deeptools:master' into master
y9c Jun 4, 2023
d8ebbb9
Update countReadsPerBin.py
y9c Jun 4, 2023
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2 changes: 1 addition & 1 deletion galaxy/wrapper/alignmentSieve.xml
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<tool id="deeptools_alignmentsieve" name="alignmentsieve" version="@[email protected]">
<tool id="deeptools_alignmentsieve" name="alignmentsieve" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>Filter BAM/CRAM files according to specified parameters</description>
<macros>
<token name="@BINARY@">alignmentSieve</token>
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2 changes: 1 addition & 1 deletion galaxy/wrapper/bamCompare.xml
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<tool id="deeptools_bam_compare" name="bamCompare" version="@[email protected]">
<tool id="deeptools_bam_compare" name="bamCompare" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>normalizes and compares two BAM or CRAM files to obtain the ratio, log2ratio or difference between them</description>
<macros>
<token name="@BINARY@">bamCompare</token>
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2 changes: 1 addition & 1 deletion galaxy/wrapper/bamCoverage.xml
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<tool id="deeptools_bam_coverage" name="bamCoverage" version="@[email protected]">
<tool id="deeptools_bam_coverage" name="bamCoverage" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>generates a coverage bigWig file from a given BAM or CRAM file</description>
<macros>
<token name="@BINARY@">bamCoverage</token>
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2 changes: 1 addition & 1 deletion galaxy/wrapper/bamPEFragmentSize.xml
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<tool id="deeptools_bam_pe_fragmentsize" name="bamPEFragmentSize" version="@[email protected]" profile="18.01">
<tool id="deeptools_bam_pe_fragmentsize" name="bamPEFragmentSize" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files</description>
<macros>
<token name="@BINARY@">bamPEFragmentSize</token>
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2 changes: 1 addition & 1 deletion galaxy/wrapper/bigwigAverage.xml
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<tool id="deeptools_bigwig_average" name="bigwigAverage" version="@WRAPPER_VERSION@+galaxy0">
<tool id="deeptools_bigwig_average" name="bigwigAverage" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>normalizes and average multiple bigWig files</description>
<macros>
<token name="@BINARY@">bigwigAverage</token>
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2 changes: 1 addition & 1 deletion galaxy/wrapper/bigwigCompare.xml
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<tool id="deeptools_bigwig_compare" name="bigwigCompare" version="@[email protected]">
<tool id="deeptools_bigwig_compare" name="bigwigCompare" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them</description>
<macros>
<token name="@BINARY@">bigwigCompare</token>
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2 changes: 1 addition & 1 deletion galaxy/wrapper/computeGCBias.xml
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<tool id="deeptools_compute_gc_bias" name="computeGCBias" version="@[email protected]" profile="18.01">
<tool id="deeptools_compute_gc_bias" name="computeGCBias" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>Determine the GC bias of your sequenced reads</description>
<macros>
<token name="@BINARY@">computeGCBias</token>
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2 changes: 1 addition & 1 deletion galaxy/wrapper/computeMatrix.xml
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<tool id="deeptools_compute_matrix" name="computeMatrix" version="@[email protected]">
<tool id="deeptools_compute_matrix" name="computeMatrix" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>prepares data for plotting a heatmap or a profile of given regions</description>
<macros>
<token name="@BINARY@">computeMatrix</token>
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2 changes: 1 addition & 1 deletion galaxy/wrapper/computeMatrixOperations.xml
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<tool id="deeptools_compute_matrix_operations" name="computeMatrixOperations" version="@[email protected]">
<tool id="deeptools_compute_matrix_operations" name="computeMatrixOperations" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>Modify or combine the output of computeMatrix in a variety of ways.</description>
<macros>
<token name="@BINARY@">computeMatrixOperations</token>
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2 changes: 1 addition & 1 deletion galaxy/wrapper/correctGCBias.xml
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<tool id="deeptools_correct_gc_bias" name="correctGCBias" version="@[email protected]">
<tool id="deeptools_correct_gc_bias" name="correctGCBias" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>uses the output from computeGCBias to generate GC-corrected BAM/CRAM files</description>
<macros>
<token name="@BINARY@">correctGCBias</token>
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5 changes: 3 additions & 2 deletions galaxy/wrapper/deepTools_macros.xml
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<macros>

<token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
<token name="@WRAPPER_VERSION@">3.5.1.0</token>
<token name="@TOOL_VERSION@">3.5.2</token>
<token name="@GALAXY_VERSION@">20.01</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="3.5.1">deeptools</requirement>
<requirement type="package" version="@TOOL_VERSION@">deeptools</requirement>
<requirement type="package" version="1.9">samtools</requirement>
</requirements>
<expand macro="stdio" />
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2 changes: 1 addition & 1 deletion galaxy/wrapper/estimateReadFiltering.xml
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<tool id="deeptools_estimatereadfiltering" name="estimateReadFiltering" version="@[email protected]">
<tool id="deeptools_estimatereadfiltering" name="estimateReadFiltering" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>estimates the number of reads that would be filtered given certain criteria</description>
<macros>
<token name="@BINARY@">estimateReadFiltering</token>
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2 changes: 1 addition & 1 deletion galaxy/wrapper/multiBamSummary.xml
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<tool id="deeptools_multi_bam_summary" name="multiBamSummary" version="@[email protected]">
<tool id="deeptools_multi_bam_summary" name="multiBamSummary" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>calculates average read coverages for a list of two or more BAM/CRAM files</description>
<macros>
<token name="@BINARY@">multiBamSummary</token>
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2 changes: 1 addition & 1 deletion galaxy/wrapper/multiBigwigSummary.xml
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<tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@[email protected]">
<tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>calculates average scores for a list of two or more bigwig files</description>
<macros>
<token name="@BINARY@">multiBigwigSummary</token>
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2 changes: 1 addition & 1 deletion galaxy/wrapper/plotCorrelation.xml
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<tool id="deeptools_plot_correlation" name="plotCorrelation" version="@[email protected]" profile="18.01">
<tool id="deeptools_plot_correlation" name="plotCorrelation" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>Create a heatmap or scatterplot of correlation scores between different samples </description>
<macros>
<token name="@BINARY@">plotCorrelation</token>
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2 changes: 1 addition & 1 deletion galaxy/wrapper/plotCoverage.xml
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<tool id="deeptools_plot_coverage" name="plotCoverage" version="@[email protected]" profile="18.01">
<tool id="deeptools_plot_coverage" name="plotCoverage" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>assesses the sequencing depth of BAM/CRAM files </description>
<macros>
<token name="@BINARY@">plotCoverage</token>
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2 changes: 1 addition & 1 deletion galaxy/wrapper/plotEnrichment.xml
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<tool id="deeptools_plot_enrichment" name="plotEnrichment" version="@[email protected]" profile="18.01">
<tool id="deeptools_plot_enrichment" name="plotEnrichment" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>plots read/fragment coverage over sets of regions</description>
<macros>
<token name="@BINARY@">plotEnrichment</token>
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2 changes: 1 addition & 1 deletion galaxy/wrapper/plotFingerprint.xml
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<tool id="deeptools_plot_fingerprint" name="plotFingerprint" version="@[email protected]" profile="18.01">
<tool id="deeptools_plot_fingerprint" name="plotFingerprint" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>plots profiles of BAM files; useful for assessing ChIP signal strength</description>
<macros>
<token name="@BINARY@">plotFingerprint</token>
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2 changes: 1 addition & 1 deletion galaxy/wrapper/plotHeatmap.xml
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<tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@[email protected]" profile="18.01">
<tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>creates a heatmap for score distributions across genomic regions</description>
<macros>
<token name="@BINARY@">plotHeatmap</token>
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2 changes: 1 addition & 1 deletion galaxy/wrapper/plotPCA.xml
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<tool id="deeptools_plot_pca" name="plotPCA" version="@[email protected]" profile="18.01">
<tool id="deeptools_plot_pca" name="plotPCA" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output</description>
<macros>
<token name="@BINARY@">plotPCA</token>
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2 changes: 1 addition & 1 deletion galaxy/wrapper/plotProfiler.xml
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<tool id="deeptools_plot_profile" name="plotProfile" version="@[email protected]" profile="18.01">
<tool id="deeptools_plot_profile" name="plotProfile" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
<description>
creates a profile plot for score distributions across genomic regions
</description>
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