# HG changeset patch
# User bgruening
# Date 1457564800 18000
# Node ID 10e697ec9bfb36573ebc29bdcfe5bbe1d4bd91f4
# Parent  8145727ba0f0a25bbbe22607031e3e00c7b4f96a
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c

diff -r 8145727ba0f0 -r 10e697ec9bfb bamCoverage.xml
--- a/bamCoverage.xml	Thu Feb 18 11:46:57 2016 -0500
+++ b/bamCoverage.xml	Wed Mar 09 18:06:40 2016 -0500
@@ -46,13 +46,17 @@
                 #if str($advancedOpt.ignoreForNormalization).strip() != '':
                     --ignoreForNormalization $advancedOpt.ignoreForNormalization
                 #end if
+
+                #if str($advancedOpt.filterRNAstrand) != 'no':
+                    --filterRNAstrand '$advancedOpt.filterRNAstrand'
+                #end if
             #end if
 ]]>
     </command>
 
     <inputs>
         <param name="bamInput" format="bam" type="data" label="BAM file"
-            help="The BAM file must be sorted."/>
+            help=""/>
 
         <param name="binSize" type="integer" value="50" min="1"
             label="Bin size in bases"
@@ -105,6 +109,14 @@
                     label="Determine nucleosome positions from MNase-seq data"
                     help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data." />
 
+                <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand." 
+                    help="By default (the no option), all reads are processed, regardless of the strand they originated from. For RNAseq, it can be useful to separately create bigWig files for the forward or reverse strands.
+                          Note that this tools assumes that a dUTP-based method was used, so fragments will be assigned to the reverse strand if the second read in a pair is reverse complemented.">
+                    <option value="no" selected="true">no</option>
+                    <option value="forward">forward</option>
+                    <option value="reverse">reverse</option>
+                </param>
+
             </when>
         </conditional>
     </inputs>
@@ -153,6 +165,14 @@
             <param name="binSize" value="10" />
             <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph" />
         </test>
+        <test>
+            <param name="bamInput" value="phiX.bam" ftype="bam" />
+            <param name="outFileFormat" value="bigwig" />
+            <param name="showAdvancedOpt" value="yes" />
+            <param name="filterRNAstrand" value="reverse" />
+            <param name="binSize" value="10" />
+            <output name="outFileName" file="bamCoverage_result5.bw" ftype="bigwig" />
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r 8145727ba0f0 -r 10e697ec9bfb deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Feb 18 11:46:57 2016 -0500
+++ b/deepTools_macros.xml	Wed Mar 09 18:06:40 2016 -0500
@@ -72,12 +72,12 @@
     </xml>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.1.0</token>
+    <token name="@WRAPPER_VERSION@">2.2.2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.7.10">python</requirement>
             <requirement type="binary">@BINARY@</requirement>
-            <requirement type="package" version="2.1.0">deepTools</requirement>
+            <requirement type="package" version="2.2.2">deepTools</requirement>
             <yield />
         </requirements>
         <expand macro="stdio" />
@@ -310,13 +310,13 @@
     <xml name="multiple_input_bams">
         <param argument="--bamfiles" type="data" format="bam" min="1"
             label="Bam file" multiple="true"
-            help="The BAM file must be sorted."/>
+            help=""/>
     </xml>
 
     <xml name="multiple_input_bams_min2">
         <param argument="--bamfiles" type="data" format="bam" min="2"
             label="Bam file" multiple="true"
-            help="The BAM file must be sorted."/>
+            help=""/>
     </xml>
 
     <xml name="multiple_input_bigwigs">
diff -r 8145727ba0f0 -r 10e697ec9bfb test-data/bamCoverage_result5.bw
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diff -r 8145727ba0f0 -r 10e697ec9bfb test-data/computeMatrix_result1.gz
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diff -r 8145727ba0f0 -r 10e697ec9bfb test-data/computeMatrix_result2.gz
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diff -r 8145727ba0f0 -r 10e697ec9bfb test-data/computeMatrix_result3.gz
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diff -r 8145727ba0f0 -r 10e697ec9bfb test-data/heatmapper_result1.png
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diff -r 8145727ba0f0 -r 10e697ec9bfb test-data/heatmapper_result2.png
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diff -r 8145727ba0f0 -r 10e697ec9bfb test-data/heatmapper_result2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/heatmapper_result2.tabular	Wed Mar 09 18:06:40 2016 -0500
@@ -0,0 +1,3 @@
+bin labels		-0.0Kb	0.0Kb
+bins		1	2
+file_0	genes	2477942.34473	2610259.65234
diff -r 8145727ba0f0 -r 10e697ec9bfb test-data/plotCorrelation_result1.png
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diff -r 8145727ba0f0 -r 10e697ec9bfb test-data/plotCoverage_result1.png
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diff -r 8145727ba0f0 -r 10e697ec9bfb test-data/plotPCA_result1.png
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diff -r 8145727ba0f0 -r 10e697ec9bfb test-data/plotPCA_result2.png
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diff -r 8145727ba0f0 -r 10e697ec9bfb test-data/plotPCA_result2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotPCA_result2.tabular	Wed Mar 09 18:06:40 2016 -0500
@@ -0,0 +1,3 @@
+Component	bowtie2-test1.bam	bowtie2-test1.bam	Eigenvalue
+1	-0.707106781187	-0.707106781187	6.0
+2	-0.707106781187	0.707106781187	1.23259516441e-32
diff -r 8145727ba0f0 -r 10e697ec9bfb test-data/profiler_result1.png
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diff -r 8145727ba0f0 -r 10e697ec9bfb test-data/profiler_result2.png
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diff -r 8145727ba0f0 -r 10e697ec9bfb test-data/profiler_result2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/profiler_result2.tabular	Wed Mar 09 18:06:40 2016 -0500
@@ -0,0 +1,3 @@
+bin labels		-0.0Kb	0.0Kb
+bins		1	2
+file_0	genes	2477942.34473	2610259.65234