# HG changeset patch
# User bgruening
# Date 1490962132 14400
# Node ID 22bfbb186bf1f5deed29d12c5ed9bcaaa81dbd7d
# Parent  41b3f35b75635cfd2c2e2b369ac5cebcc3b35401
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289

diff -r 41b3f35b7563 -r 22bfbb186bf1 bamCoverage.xml
--- a/bamCoverage.xml	Tue Jan 24 04:53:33 2017 -0500
+++ b/bamCoverage.xml	Fri Mar 31 08:08:52 2017 -0400
@@ -21,14 +21,12 @@
 
             #if $scaling.type=='rpkm':
                 --normalizeUsingRPKM
-                --scaleFactor $scaling.scaleFactor
             #elif $scaling.type=='1x':
                 #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
                     --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize
                 #else:
                     --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt
                 #end if
-                --scaleFactor $scaling.scaleFactor
             #end if
 
             #if str($region).strip() != '':
@@ -36,6 +34,10 @@
             #end if
 
             #if $advancedOpt.showAdvancedOpt == "yes":
+                #if str($advancedOpt.scaleFactor).strip() != '':
+                    --scaleFactor $advancedOpt.scaleFactor
+                #end if
+
                 #if $advancedOpt.smoothLength:
                     --smoothLength '$advancedOpt.smoothLength'
                 #end if
@@ -74,13 +76,10 @@
                 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option>
                 <option value="no">Do not normalize or scale</option>
             </param>
-            <when value="rpkm">
-                <expand macro="scaleFactor" />
-            </when>
+            <when value="rpkm"/>
             <when value="no"/>
             <when value="1x">
                 <expand macro="effectiveGenomeSize" />
-                <expand macro="scaleFactor" />
             </when>
         </conditional>
 
@@ -98,6 +97,7 @@
             </param>
             <when value="no" />
             <when value="yes">
+                <expand macro="scaleFactor" />
                 <expand macro="smoothLength" />
 
                 <param argument="ignoreForNormalization" type="text" value=""
diff -r 41b3f35b7563 -r 22bfbb186bf1 deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Jan 24 04:53:33 2017 -0500
+++ b/deepTools_macros.xml	Fri Mar 31 08:08:52 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 41b3f35b7563 -r 22bfbb186bf1 test-data/bamCompare_result2.bw
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/bamCoverage_result1.bw
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/bamCoverage_result2.bw
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/bamCoverage_result6.bw
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/bamPEFragmentSize_histogram_result1.png
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/bigwigCompare_result1.bw
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/computeMatrixOperations.txt
--- a/test-data/computeMatrixOperations.txt	Tue Jan 24 04:53:33 2017 -0500
+++ b/test-data/computeMatrixOperations.txt	Fri Mar 31 08:08:52 2017 -0400
@@ -1,4 +1,4 @@
 Groups:
 	genes
 Samples:
-	file_0
+	bamCoverage_result4_bw_0
diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/computeMatrixOperations_result2.mat.gz
Binary file test-data/computeMatrixOperations_result2.mat.gz has changed
diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/computeMatrix_result1.gz
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/computeMatrix_result2.gz
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/computeMatrix_result3.gz
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/correctGCBias_result1.bam
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/heatmapper_result1.png
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/heatmapper_result2.png
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/multiBamSummary_result1.npz
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/multiBamSummary_result2.npz
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/multiBamSummary_result2b.npz
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/multiBigwigSummary_result1.npz
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/plotCorrelation_result1.png
Binary file test-data/plotCorrelation_result1.png has changed
diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/plotCorrelation_result1.tabular
--- a/test-data/plotCorrelation_result1.tabular	Tue Jan 24 04:53:33 2017 -0500
+++ b/test-data/plotCorrelation_result1.tabular	Fri Mar 31 08:08:52 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 41b3f35b7563 -r 22bfbb186bf1 test-data/plotCorrelation_result2.png
Binary file test-data/plotCorrelation_result2.png has changed
diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/plotCoverage_result1.png
Binary file test-data/plotCoverage_result1.png has changed
diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/plotEnrichment_output.png
Binary file test-data/plotEnrichment_output.png has changed
diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/plotFingerprint_quality_metrics.tabular
--- a/test-data/plotFingerprint_quality_metrics.tabular	Tue Jan 24 04:53:33 2017 -0500
+++ b/test-data/plotFingerprint_quality_metrics.tabular	Fri Mar 31 08:08:52 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 41b3f35b7563 -r 22bfbb186bf1 test-data/plotFingerprint_result1.png
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/plotFingerprint_result2.png
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/profiler_result1.png
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/profiler_result2.png
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diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/profiler_result2.tabular
--- a/test-data/profiler_result2.tabular	Tue Jan 24 04:53:33 2017 -0500
+++ b/test-data/profiler_result2.tabular	Fri Mar 31 08:08:52 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 41b3f35b7563 -r 22bfbb186bf1 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jan 24 04:53:33 2017 -0500
+++ b/tool_dependencies.xml	Fri Mar 31 08:08:52 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" />