# HG changeset patch
# User bgruening
# Date 1450861264 18000
# Node ID e6dbb616211e62d56d5d9af2eb58ab8a9c3a2315
# Parent  f30699e4e9025b9790ee411f00e00ce2fb84c1b7
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 54a10cf268ca9a5399f13458a1b218be7891bd41

diff -r f30699e4e902 -r e6dbb616211e deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Dec 22 13:48:21 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 04:01:04 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 f30699e4e902 -r e6dbb616211e plotProfiler.xml
--- a/plotProfiler.xml	Tue Dec 22 13:48:21 2015 -0500
+++ b/plotProfiler.xml	Wed Dec 23 04:01:04 2015 -0500
@@ -16,6 +16,10 @@
             #if $output.showOutputSettings == "yes"
                 --plotFileFormat $output.outFileFormat
 
+                #if $output.saveData:
+                    --outFileNameData "$outFileNameData"
+                #end if
+
                 #if $output.saveSortedRegions:
                     --outFileSortedRegions '$outFileSortedRegions'
                 #end if
@@ -45,7 +49,7 @@
                     --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
                 #end if
 
-                $advancedOpt.perGroup
+                $advancedOpt.onePlotPerGroup
 
                 #if $advancedOpt.yMin:
                     --yMin $advancedOpt.yMin
@@ -120,7 +124,7 @@
                     <option value="se">add standard error</option>
                     <option value="overlapped_lines">overlapped lines</option>
                 </param>
-                <param argument="--regionsLabel" type="text" value="coverage" size="30"
+                <param argument="--regionsLabel" type="text" value="genes" size="30"
                     label="Labels for the regions plotted in the heatmap"
                     help="If more than one region is being plotted a list of labels separated
                     by comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>
@@ -134,12 +138,11 @@
                         message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
                 </param>
 
-                <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
+                <param argument="--onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
                     label="Do one plot per group"
-                    help="When clustering is applied to the data, or the region file contains groups separated by &quot;#&quot;,
-                    plot the groups next to each other. The default is to plot the samples next to each other.
-                    If this option is set, each group (or cluster) will get its own plot, with different samples
-                    stacked on top of each other." />
+                    help="When the region file contains groups separated by &quot;#&quot;, the default is
+                    to plot the averages for the distinct plots in one plot. If this option is set, each group
+                    will get its own plot, stacked on top of each other." />
 
 
                 <param argument="--yMin" type="float" value="" size="3" optional="true"
@@ -185,7 +188,7 @@
    :alt: Meta-gene profile of Rna Polymerase II
 
 
-You can find more details on the profiler doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/plotProfile.html
+You can find more details on the profiler wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-profiler
 
 
 -----
diff -r f30699e4e902 -r e6dbb616211e static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed
diff -r f30699e4e902 -r e6dbb616211e test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r f30699e4e902 -r e6dbb616211e test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r f30699e4e902 -r e6dbb616211e test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg	Tue Dec 22 13:48:21 2015 -0500
+++ b/test-data/bamCoverage_result3.bg	Wed Dec 23 04:01:04 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 f30699e4e902 -r e6dbb616211e test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r f30699e4e902 -r e6dbb616211e test-data/profiler_result2.png
Binary file test-data/profiler_result2.png has changed
diff -r f30699e4e902 -r e6dbb616211e tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Dec 22 13:48:21 2015 -0500
+++ b/tool_dependencies.xml	Wed Dec 23 04:01:04 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>