deeptools · y9c · Jan 19, 2023 · May 31, 2023 · Jun 1, 2023 · Jun 1, 2023
diff --git a/deeptools/countReadsPerBin.py b/deeptools/countReadsPerBin.py
@@ -899,7 +899,7 @@ def get_fragment_from_read(self, read):
             fragmentStart = int(fragmentCenter - read.infer_query_length(always=False) / 2)
             fragmentEnd = fragmentStart + read.infer_query_length(always=False)
 
-        assert fragmentStart < fragmentEnd, "fragment start greater than fragment" \
+        assert fragmentStart <= fragmentEnd, "fragment start greater than fragment" \
                                             "end for read {}".format(read.query_name)
         return [(fragmentStart, fragmentEnd)]
 

diff --git a/galaxy/wrapper/alignmentSieve.xml b/galaxy/wrapper/alignmentSieve.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/bamCompare.xml b/galaxy/wrapper/bamCompare.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/bamCoverage.xml b/galaxy/wrapper/bamCoverage.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/bamPEFragmentSize.xml b/galaxy/wrapper/bamPEFragmentSize.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/bigwigAverage.xml b/galaxy/wrapper/bigwigAverage.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/bigwigCompare.xml b/galaxy/wrapper/bigwigCompare.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/computeGCBias.xml b/galaxy/wrapper/computeGCBias.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/computeMatrix.xml b/galaxy/wrapper/computeMatrix.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/computeMatrixOperations.xml b/galaxy/wrapper/computeMatrixOperations.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/correctGCBias.xml b/galaxy/wrapper/correctGCBias.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml
@@ -1,10 +1,11 @@
 <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" />

diff --git a/galaxy/wrapper/estimateReadFiltering.xml b/galaxy/wrapper/estimateReadFiltering.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/multiBamSummary.xml b/galaxy/wrapper/multiBamSummary.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/multiBigwigSummary.xml b/galaxy/wrapper/multiBigwigSummary.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/plotCorrelation.xml b/galaxy/wrapper/plotCorrelation.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/plotCoverage.xml b/galaxy/wrapper/plotCoverage.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/plotEnrichment.xml b/galaxy/wrapper/plotEnrichment.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/plotFingerprint.xml b/galaxy/wrapper/plotFingerprint.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/plotHeatmap.xml b/galaxy/wrapper/plotHeatmap.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/plotPCA.xml b/galaxy/wrapper/plotPCA.xml
@@ -1,4 +1,4 @@
-<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>

diff --git a/galaxy/wrapper/plotProfiler.xml b/galaxy/wrapper/plotProfiler.xml
@@ -1,4 +1,4 @@
-<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>