# HG changeset patch
# User bgruening
# Date 1490966925 14400
# Node ID babca70c3586739481fe991c5c6886efe4336f83
# Parent  6b592142ce93de7b8976dfdefcf7218b5e0b9090
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289

diff -r 6b592142ce93 -r babca70c3586 computeMatrix.xml
--- a/computeMatrix.xml	Tue Jan 24 04:59:41 2017 -0500
+++ b/computeMatrix.xml	Fri Mar 31 09:28:45 2017 -0400
@@ -7,17 +7,20 @@
     <expand macro="requirements" />
     <command>
 <![CDATA[
+        #import re
         #import tempfile
         #set bw_files=[]
-        #for $counter, $bigwig in enumerate($scoreFileName):
-            ln -s "${bigwig}" "file_${counter}.bw" &&
-            #silent $bw_files.append('file_%s.bw' % $counter)
+        #for $counter, $bigwig, in enumerate($scoreFileName):
+            #set identifier = re.sub('[^\s\w\-]', '_', str($bigwig.element_identifier))
+            ln -f -s "${bigwig}" "${identifier}_${counter}.bw" &&
+            #silent $bw_files.append('%s_%s.bw' % ($identifier, $counter))
         #end for
 
         #set bed_files=[]
-        #for $counter, $rf in enumerate($regionsFiles):
-            ln -s "${rf.regionsFile}" "group_${counter}.bed" &&
-            #silent $bed_files.append('group_%s.bed' % $counter)
+        #for $counter, $rf, in enumerate($regionsFiles):
+            #set identifier = re.sub('[^\s\w\-]', '_', str($rf.regionsFile.element_identifier))
+            ln -f -s "${rf.regionsFile}" "${identifier}_${counter}.bed" &&
+            #silent $bed_files.append('%s_%s.bed' % ($identifier, $counter))
         #end for
 
         @BINARY@
diff -r 6b592142ce93 -r babca70c3586 deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Jan 24 04:59:41 2017 -0500
+++ b/deepTools_macros.xml	Fri Mar 31 09:28:45 2017 -0400
@@ -1,5 +1,17 @@
 <macros>
 
+    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
+    <token name="@WRAPPER_VERSION@">2.5.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.7.10">python</requirement>
+            <requirement type="package" version="@WRAPPER_VERSION@">deeptools</requirement>
+            <yield />
+        </requirements>
+        <expand macro="stdio" />
+        <version_command>@BINARY@ --version</version_command>
+    </xml>
+
     <xml name="advancedOpt_scaffold">
         <conditional name="advancedOpt">
             <param name="showAdvancedOpt" type="select" label="Show advanced options" >
@@ -97,18 +109,6 @@
         </param>
     </xml>
 
-    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.4.2</token>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="2.7.10">python</requirement>
-            <requirement type="package" version="2.4.2">deeptools</requirement>
-            <yield />
-        </requirements>
-        <expand macro="stdio" />
-        <version_command>@BINARY@ --version</version_command>
-    </xml>
-
     <xml name="smoothLength">
         <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
             label="Smooth values using the following length (in bases)"
@@ -181,10 +181,10 @@
     <xml name="fragLength">
         <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
             label="Minimum fragment length for inclusion."
-            help="A value greater than 0 will filter out ALL single-end reads. This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
+            help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
         <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
             label="Maximum fragment length for inclusion."
-            help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." />
+            help="A value of 0 (the default) is equivalent to no maximum." />
     </xml>
 
     <xml name="read_processing_options">
@@ -324,9 +324,7 @@
 
     <xml name="scaleFactor">
         <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
-            help="When used in combination with --normalizeTo1x or
-                --normalizeUsingRPKM, the computed scaling factor will
-                be multiplied by the given scale factor." />
+            help="The computed scaling factor will be multiplied by this (default 1)." />
     </xml>
 
     <xml name="scaleFactors">
@@ -441,19 +439,22 @@
 <![CDATA[
         #set files=[]
         #set labels=[]
+        #import re
         #if $multibam_conditional.orderMatters == "No":
             #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
+                #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
                 ln -s "${bamfile}" "./${counter}.bam" &&
                 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
                 #silent $files.append('%s.bam' % $counter)
-                #silent $labels.append("'%s'" % ($bamfile.display_name))
+                #silent $labels.append("'%s'" % identifier)
             #end for
         #else:
             #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
+                #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
                 ln -s "${f.bamfiles}" "./${counter}.bam" &&
                 ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
                 #silent $files.append('%s.bam' % $counter)
-                #silent $labels.append("'%s'" % ($f.bamfiles.display_name))
+                #silent $labels.append("'%s'" % $identifier)
             #end for
         #end if
 ]]>
@@ -463,17 +464,20 @@
 <![CDATA[
         #set files=[]
         #set labels=[]
+        #import re
         #if $multibigwig_conditional.orderMatters == "No":
             #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
+            #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
                 ln -s "${bigwig}" "${counter}.bw" &&
                 #silent $files.append('%s.bw' % $counter)
-                #silent $labels.append("'%s'" % ($bigwig.display_name))
+                #silent $labels.append("'%s'" % $identifier)
             #end for
         #else:
             #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
+                #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
                 ln -s "${f.bigwigfiles}" "${counter}.bw" &&
                 #silent $files.append('%s.bw' % $counter)
-                #silent $labels.append("'%s'" % ($f.bigwigfiles.display_name))
+                #silent $labels.append("'%s'" % $identifier)
             #end for
         #end if
 ]]>
diff -r 6b592142ce93 -r babca70c3586 test-data/bamCompare_result2.bw
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diff -r 6b592142ce93 -r babca70c3586 test-data/bamCoverage_result1.bw
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diff -r 6b592142ce93 -r babca70c3586 test-data/bamCoverage_result2.bw
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diff -r 6b592142ce93 -r babca70c3586 test-data/bamCoverage_result6.bw
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diff -r 6b592142ce93 -r babca70c3586 test-data/bamPEFragmentSize_histogram_result1.png
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diff -r 6b592142ce93 -r babca70c3586 test-data/bigwigCompare_result1.bw
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diff -r 6b592142ce93 -r babca70c3586 test-data/computeMatrixOperations.txt
--- a/test-data/computeMatrixOperations.txt	Tue Jan 24 04:59:41 2017 -0500
+++ b/test-data/computeMatrixOperations.txt	Fri Mar 31 09:28:45 2017 -0400
@@ -1,4 +1,4 @@
 Groups:
 	genes
 Samples:
-	file_0
+	bamCoverage_result4_bw_0
diff -r 6b592142ce93 -r babca70c3586 test-data/computeMatrixOperations_result2.mat.gz
Binary file test-data/computeMatrixOperations_result2.mat.gz has changed
diff -r 6b592142ce93 -r babca70c3586 test-data/computeMatrix_result1.gz
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diff -r 6b592142ce93 -r babca70c3586 test-data/computeMatrix_result2.gz
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diff -r 6b592142ce93 -r babca70c3586 test-data/computeMatrix_result3.gz
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diff -r 6b592142ce93 -r babca70c3586 test-data/correctGCBias_result1.bam
Binary file test-data/correctGCBias_result1.bam has changed
diff -r 6b592142ce93 -r babca70c3586 test-data/heatmapper_result1.png
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diff -r 6b592142ce93 -r babca70c3586 test-data/heatmapper_result2.png
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diff -r 6b592142ce93 -r babca70c3586 test-data/multiBamSummary_result1.npz
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diff -r 6b592142ce93 -r babca70c3586 test-data/multiBamSummary_result2.npz
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diff -r 6b592142ce93 -r babca70c3586 test-data/multiBamSummary_result2b.npz
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diff -r 6b592142ce93 -r babca70c3586 test-data/multiBigwigSummary_result1.npz
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diff -r 6b592142ce93 -r babca70c3586 test-data/plotCorrelation_result1.png
Binary file test-data/plotCorrelation_result1.png has changed
diff -r 6b592142ce93 -r babca70c3586 test-data/plotCorrelation_result1.tabular
--- a/test-data/plotCorrelation_result1.tabular	Tue Jan 24 04:59:41 2017 -0500
+++ b/test-data/plotCorrelation_result1.tabular	Fri Mar 31 09:28:45 2017 -0400
@@ -1,3 +1,3 @@
-	'bowtie2-test1.bam'	'bowtie2-test1.bam'
-'bowtie2-test1.bam'	1.0000	1.0000
-'bowtie2-test1.bam'	1.0000	1.0000
+	'bowtie2 test1.bam'	'bowtie2 test1.bam'
+'bowtie2 test1.bam'	1.0000	1.0000
+'bowtie2 test1.bam'	1.0000	1.0000
diff -r 6b592142ce93 -r babca70c3586 test-data/plotCorrelation_result2.png
Binary file test-data/plotCorrelation_result2.png has changed
diff -r 6b592142ce93 -r babca70c3586 test-data/plotCoverage_result1.png
Binary file test-data/plotCoverage_result1.png has changed
diff -r 6b592142ce93 -r babca70c3586 test-data/plotEnrichment_output.png
Binary file test-data/plotEnrichment_output.png has changed
diff -r 6b592142ce93 -r babca70c3586 test-data/plotFingerprint_quality_metrics.tabular
--- a/test-data/plotFingerprint_quality_metrics.tabular	Tue Jan 24 04:59:41 2017 -0500
+++ b/test-data/plotFingerprint_quality_metrics.tabular	Fri Mar 31 09:28:45 2017 -0400
@@ -1,3 +1,3 @@
 Sample	AUC	Synthetic AUC	X-intercept	Synthetic X-intercept	Elbow Point	Synthetic Elbow Point	JS Distance	Synthetic JS Distance	% genome enriched	diff. enrichment	CHANCE divergence
-bowtie2 test1.bam	0.00493632029864	0.481650684758	0.984443061605	1.15310443503e-24	0.984940883634	0.523268829811	NA	0.269861238192	NA	NA	NA
-bowtie2 test1.bam	0.00493632029864	0.481650684758	0.984443061605	1.15310443503e-24	0.984940883634	0.523268829811	NA	0.269861238192	NA	NA	NA
+bowtie2 test1.bam	0.00493632029864	0.481650684758	0.984443061605	1.15310443503e-24	0.984940883634	0.523268829811	NA	0.269004498068	NA	NA	NA
+bowtie2 test1.bam	0.00493632029864	0.481650684758	0.984443061605	1.15310443503e-24	0.984940883634	0.523268829811	NA	0.269004498068	NA	NA	NA
diff -r 6b592142ce93 -r babca70c3586 test-data/plotFingerprint_result1.png
Binary file test-data/plotFingerprint_result1.png has changed
diff -r 6b592142ce93 -r babca70c3586 test-data/plotFingerprint_result2.png
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diff -r 6b592142ce93 -r babca70c3586 test-data/profiler_result1.png
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diff -r 6b592142ce93 -r babca70c3586 test-data/profiler_result2.png
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diff -r 6b592142ce93 -r babca70c3586 test-data/profiler_result2.tabular
--- a/test-data/profiler_result2.tabular	Tue Jan 24 04:59:41 2017 -0500
+++ b/test-data/profiler_result2.tabular	Fri Mar 31 09:28:45 2017 -0400
@@ -1,3 +1,3 @@
 bin labels		-0.0Kb	0.0Kb
 bins		1	2
-file_0	genes	2477942.34473	2610259.65234
+bamCoverage_result4_bw_0	genes	2477942.875	2610260.125
diff -r 6b592142ce93 -r babca70c3586 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jan 24 04:59:41 2017 -0500
+++ b/tool_dependencies.xml	Fri Mar 31 09:28:45 2017 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="python" version="2.7.10">
-        <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="bd7165ea6526" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="deeptools" version="2.4.2">
         <repository changeset_revision="efc55c226f11" name="package_python_2_7_deeptools_2_4_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />