# HG changeset patch
# User bgruening
# Date 1457566401 18000
# Node ID a842285199d9daa3cec507be4aa33f358678fa4e
# Parent  df1ee352b23b7e7d4de033252959c2531c390246
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c

diff -r df1ee352b23b -r a842285199d9 computeMatrix.xml
--- a/computeMatrix.xml	Thu Feb 18 11:53:52 2016 -0500
+++ b/computeMatrix.xml	Wed Mar 09 18:33:21 2016 -0500
@@ -51,7 +51,12 @@
                 #if $mode.regionStartLength.regionStartLength_select == "yes":
                     --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength
                     --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength
+
+                    --unscaled5prime $mode.regionStartLength.unscaled5prime
+                    --unscaled3prime $mode.regionStartLength.unscaled3prime
+
                 #end if
+
             #end if
 
             #if $advancedOpt.showAdvancedOpt == "yes":
@@ -71,7 +76,6 @@
                 #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '':
                     --scale $advancedOpt.scale
                 #end if
-
             #end if
 ]]>
     </command>
@@ -118,6 +122,14 @@
                             label="Distance downstream of the region end position"
                             help="If the regions are genes, this would be the
                             distance downstream of the transcription end site."/>
+                        <param argument="--unscaled5prime" type="integer" min="0" value="0"
+                            label="Number of bases within the gene body at the 5-prime end to exclude from scaling."
+                            help="By default, each region is scaled to a given length (see the --regionBodyLength
+                             option). In some cases it is useful to look at unscaled signals around region boundaries, so this
+                             setting specifies the number of unscaled bases on the 5-prime end of each boundary." />
+                        <param argument="--unscaled3prime" type="integer" min="0" value="0"
+                            label="Number of bases within the gene body at the 3-prime end to exclude from scaling."
+                            help="As with --unscaled5prime, but for the 3-prime end." />
                     </when>
                 </conditional>
             </when>
@@ -202,9 +214,6 @@
         <expand macro="output_graphic_outputs" />
         <expand macro="output_save_matrix_values" />
     </outputs>
-    <!--
-    computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1
-    -->
     <tests>
         <test>
             <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" />
diff -r df1ee352b23b -r a842285199d9 deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Feb 18 11:53:52 2016 -0500
+++ b/deepTools_macros.xml	Wed Mar 09 18:33:21 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 df1ee352b23b -r a842285199d9 test-data/bamCoverage_result5.bw
Binary file test-data/bamCoverage_result5.bw has changed
diff -r df1ee352b23b -r a842285199d9 test-data/computeMatrix_result1.gz
Binary file test-data/computeMatrix_result1.gz has changed
diff -r df1ee352b23b -r a842285199d9 test-data/computeMatrix_result2.gz
Binary file test-data/computeMatrix_result2.gz has changed
diff -r df1ee352b23b -r a842285199d9 test-data/computeMatrix_result3.gz
Binary file test-data/computeMatrix_result3.gz has changed
diff -r df1ee352b23b -r a842285199d9 test-data/heatmapper_result1.png
Binary file test-data/heatmapper_result1.png has changed
diff -r df1ee352b23b -r a842285199d9 test-data/heatmapper_result2.png
Binary file test-data/heatmapper_result2.png has changed
diff -r df1ee352b23b -r a842285199d9 test-data/heatmapper_result2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/heatmapper_result2.tabular	Wed Mar 09 18:33:21 2016 -0500
@@ -0,0 +1,3 @@
+bin labels		-0.0Kb	0.0Kb
+bins		1	2
+file_0	genes	2477942.34473	2610259.65234
diff -r df1ee352b23b -r a842285199d9 test-data/plotCorrelation_result1.png
Binary file test-data/plotCorrelation_result1.png has changed
diff -r df1ee352b23b -r a842285199d9 test-data/plotCoverage_result1.png
Binary file test-data/plotCoverage_result1.png has changed
diff -r df1ee352b23b -r a842285199d9 test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r df1ee352b23b -r a842285199d9 test-data/plotPCA_result2.png
Binary file test-data/plotPCA_result2.png has changed
diff -r df1ee352b23b -r a842285199d9 test-data/plotPCA_result2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotPCA_result2.tabular	Wed Mar 09 18:33:21 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 df1ee352b23b -r a842285199d9 test-data/profiler_result1.png
Binary file test-data/profiler_result1.png has changed
diff -r df1ee352b23b -r a842285199d9 test-data/profiler_result2.png
Binary file test-data/profiler_result2.png has changed
diff -r df1ee352b23b -r a842285199d9 test-data/profiler_result2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/profiler_result2.tabular	Wed Mar 09 18:33:21 2016 -0500
@@ -0,0 +1,3 @@
+bin labels		-0.0Kb	0.0Kb
+bins		1	2
+file_0	genes	2477942.34473	2610259.65234