# HG changeset patch
# User bgruening
# Date 1450860988 18000
# Node ID 3bfd8cde1b763517a03e81c7f1c7b951c3f2b4a9
# Parent  9f2b016177e7b2178888d1b04f60dabb62e88003
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 54a10cf268ca9a5399f13458a1b218be7891bd41

diff -r 9f2b016177e7 -r 3bfd8cde1b76 deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Dec 22 13:43:42 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 03:56:28 2015 -0500
@@ -40,10 +40,10 @@
     </xml>
 
     <token name="@HEATMAP_OPTIONS@">
-        #if str($plotting_type.zMin) != "":
+        #if $plotting_type.zMin:
             --zMin $plotting_type.zMin
         #end if
-        #if str($plotting_type.zMax) != "":
+        #if $plotting_type.zMax:
             --zMax $plotting_type.zMax
         #end if
         --colorMap '$plotting_type.colorMap'
@@ -107,11 +107,7 @@
                     </param>
                     <when value="kmeans">
                         <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
-                            help="When this option is set, then the matrix is split into clusters using the kmeans algorithm.
-                            Only works for data that is not grouped, otherwise only the first group will be clustered.
-                            If more specific clustering methods are required it is advisable to save the underlying matrix and
-                            run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault)
-                            if a cluster has very few members compared to the total number or regions. (default: 0 [do not cluster])."/>
+                            help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
                     </when>
                     <when value="none" />
                 </conditional>
@@ -412,6 +408,7 @@
             <when value="no" />
             <when value="yes">
                 <yield />
+                <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
                 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
             </when>
         </conditional>
@@ -459,6 +456,14 @@
     </xml>
 
     <xml name="output_graphic_outputs">
+        <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
+            <filter>
+            ((
+                output['showOutputSettings'] == 'yes' and
+                output['saveData'] is True
+            ))
+            </filter>
+        </data>
         <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
             <filter>
             ((
diff -r 9f2b016177e7 -r 3bfd8cde1b76 plotCoverage.xml
--- a/plotCoverage.xml	Tue Dec 22 13:43:42 2015 -0500
+++ b/plotCoverage.xml	Wed Dec 23 03:56:28 2015 -0500
@@ -1,5 +1,5 @@
 <tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0">
-    <description>plots a histogram of coverage on genomic regions </description>
+    <description>creates a heatmap of correlation scores between different samples </description>
     <macros>
         <token name="@BINARY@">plotCoverage</token>
         <import>deepTools_macros.xml</import>
@@ -22,7 +22,7 @@
             --plotFileFormat "$outFileFormat"
 
             #if $outRawCounts:
-                --outRawCounts '$outFileRawCounts'
+                --outRawCounts '$outFileRawCounts' 
             #end if
 
             #if $advancedOpt.showAdvancedOpt == "yes":
diff -r 9f2b016177e7 -r 3bfd8cde1b76 static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed
diff -r 9f2b016177e7 -r 3bfd8cde1b76 test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r 9f2b016177e7 -r 3bfd8cde1b76 test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r 9f2b016177e7 -r 3bfd8cde1b76 test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg	Tue Dec 22 13:43:42 2015 -0500
+++ b/test-data/bamCoverage_result3.bg	Wed Dec 23 03:56:28 2015 -0500
@@ -5,4 +5,4 @@
 chrM	220	230	7690304.31
 chrM	230	240	6027535.81
 chrM	240	250	3325537.00
-chrM	250	16569	623538.2
+chrM	250	260	623538.19
diff -r 9f2b016177e7 -r 3bfd8cde1b76 test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r 9f2b016177e7 -r 3bfd8cde1b76 test-data/profiler_result2.png
Binary file test-data/profiler_result2.png has changed
diff -r 9f2b016177e7 -r 3bfd8cde1b76 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Dec 22 13:43:42 2015 -0500
+++ b/tool_dependencies.xml	Wed Dec 23 03:56:28 2015 -0500
@@ -4,6 +4,6 @@
         <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="deepTools" version="2.0">
-        <repository changeset_revision="747571992679" name="package_python_2_7_deeptools_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="bd40c0aa7d8e" name="package_python_2_7_deeptools_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>