# HG changeset patch
# User bgruening
# Date 1457566605 18000
# Node ID c73c5d2c94b3b24247e044bd703a54b8eb9b0e5e
# Parent  0b9bc8b4d0c19014cc3c8a24b3f11482c25e8e34
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c

diff -r 0b9bc8b4d0c1 -r c73c5d2c94b3 deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Feb 18 11:54:57 2016 -0500
+++ b/deepTools_macros.xml	Wed Mar 09 18:36:45 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 0b9bc8b4d0c1 -r c73c5d2c94b3 plotProfiler.xml
--- a/plotProfiler.xml	Thu Feb 18 11:54:57 2016 -0500
+++ b/plotProfiler.xml	Wed Mar 09 18:36:45 2016 -0500
@@ -60,6 +60,10 @@
                     --yMax $advancedOpt.yMax
                 #end if
 
+                #if $advancedOpt.outFileNameData:
+                    --outFileNameData "$output_outFileNameData"
+                #end if
+
                 @KMEANS_CLUSTERING@
 
             #end if
@@ -154,6 +158,8 @@
                     label="Make one plot per group of regions"
                     help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions. " />
 
+                <param argument="--outFileNameData" type="boolean" label="Save the data underlying the average profile"
+                    help="This option will create an additional output file." />
 
                 <param argument="--yMin" type="float" value="" size="3" optional="true"
                     label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/>
@@ -168,6 +174,11 @@
     <outputs>
         <expand macro="output_image_file_format" />
         <expand macro="output_graphic_outputs" />
+
+        <data format="tabular" name="output_outFileNameData" label="${tool.name} on ${on_string}: Underlying data">
+            <filter>outFileNameData</filter>
+        </data>
+
     </outputs>
     <tests>
         <test>
@@ -178,7 +189,9 @@
             <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="showScaleRegionsOpt" value="yes" />
+            <param name="outFileNameData" value="True" />
             <output name="outFileName" file="profiler_result2.png" ftype="png" compare="sim_size" delta="4000" />
+            <output name="output_outFileNameData" file="profiler_result2.tabular" ftype="tabular" />
         </test>
     </tests>
     <help>
diff -r 0b9bc8b4d0c1 -r c73c5d2c94b3 test-data/bamCoverage_result5.bw
Binary file test-data/bamCoverage_result5.bw has changed
diff -r 0b9bc8b4d0c1 -r c73c5d2c94b3 test-data/computeMatrix_result1.gz
Binary file test-data/computeMatrix_result1.gz has changed
diff -r 0b9bc8b4d0c1 -r c73c5d2c94b3 test-data/computeMatrix_result2.gz
Binary file test-data/computeMatrix_result2.gz has changed
diff -r 0b9bc8b4d0c1 -r c73c5d2c94b3 test-data/computeMatrix_result3.gz
Binary file test-data/computeMatrix_result3.gz has changed
diff -r 0b9bc8b4d0c1 -r c73c5d2c94b3 test-data/heatmapper_result1.png
Binary file test-data/heatmapper_result1.png has changed
diff -r 0b9bc8b4d0c1 -r c73c5d2c94b3 test-data/heatmapper_result2.png
Binary file test-data/heatmapper_result2.png has changed
diff -r 0b9bc8b4d0c1 -r c73c5d2c94b3 test-data/heatmapper_result2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/heatmapper_result2.tabular	Wed Mar 09 18:36:45 2016 -0500
@@ -0,0 +1,3 @@
+bin labels		-0.0Kb	0.0Kb
+bins		1	2
+file_0	genes	2477942.34473	2610259.65234
diff -r 0b9bc8b4d0c1 -r c73c5d2c94b3 test-data/plotCorrelation_result1.png
Binary file test-data/plotCorrelation_result1.png has changed
diff -r 0b9bc8b4d0c1 -r c73c5d2c94b3 test-data/plotCoverage_result1.png
Binary file test-data/plotCoverage_result1.png has changed
diff -r 0b9bc8b4d0c1 -r c73c5d2c94b3 test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r 0b9bc8b4d0c1 -r c73c5d2c94b3 test-data/plotPCA_result2.png
Binary file test-data/plotPCA_result2.png has changed
diff -r 0b9bc8b4d0c1 -r c73c5d2c94b3 test-data/plotPCA_result2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotPCA_result2.tabular	Wed Mar 09 18:36:45 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 0b9bc8b4d0c1 -r c73c5d2c94b3 test-data/profiler_result1.png
Binary file test-data/profiler_result1.png has changed
diff -r 0b9bc8b4d0c1 -r c73c5d2c94b3 test-data/profiler_result2.png
Binary file test-data/profiler_result2.png has changed
diff -r 0b9bc8b4d0c1 -r c73c5d2c94b3 test-data/profiler_result2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/profiler_result2.tabular	Wed Mar 09 18:36:45 2016 -0500
@@ -0,0 +1,3 @@
+bin labels		-0.0Kb	0.0Kb
+bins		1	2
+file_0	genes	2477942.34473	2610259.65234