# HG changeset patch
# User bgruening
# Date 1450810101 18000
# Node ID f30699e4e9025b9790ee411f00e00ce2fb84c1b7
# Parent  4213153d3b823aa95650926c1f982cd8cbaec70f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 8b9cdb8dc4a8fedd2b2286e7afab6529e49a9d22-dirty

diff -r 4213153d3b82 -r f30699e4e902 deepTools_macros.xml
--- a/deepTools_macros.xml	Mon Dec 21 19:11:03 2015 -0500
+++ b/deepTools_macros.xml	Tue Dec 22 13:48:21 2015 -0500
@@ -40,10 +40,10 @@
     </xml>
 
     <token name="@HEATMAP_OPTIONS@">
-        #if $plotting_type.zMin:
+        #if str($plotting_type.zMin) != "":
             --zMin $plotting_type.zMin
         #end if
-        #if $plotting_type.zMax:
+        #if str($plotting_type.zMax) != "":
             --zMax $plotting_type.zMax
         #end if
         --colorMap '$plotting_type.colorMap'
@@ -107,7 +107,11 @@
                     </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: None)."/>
+                            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])."/>
                     </when>
                     <when value="none" />
                 </conditional>
@@ -408,7 +412,6 @@
             <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>
@@ -456,14 +459,6 @@
     </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 4213153d3b82 -r f30699e4e902 plotProfiler.xml
--- a/plotProfiler.xml	Mon Dec 21 19:11:03 2015 -0500
+++ b/plotProfiler.xml	Tue Dec 22 13:48:21 2015 -0500
@@ -16,10 +16,6 @@
             #if $output.showOutputSettings == "yes"
                 --plotFileFormat $output.outFileFormat
 
-                #if $output.saveData:
-                    --outFileNameData "$outFileNameData"
-                #end if
-
                 #if $output.saveSortedRegions:
                     --outFileSortedRegions '$outFileSortedRegions'
                 #end if
@@ -49,7 +45,7 @@
                     --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
                 #end if
 
-                $advancedOpt.onePlotPerGroup
+                $advancedOpt.perGroup
 
                 #if $advancedOpt.yMin:
                     --yMin $advancedOpt.yMin
@@ -124,7 +120,7 @@
                     <option value="se">add standard error</option>
                     <option value="overlapped_lines">overlapped lines</option>
                 </param>
-                <param argument="--regionsLabel" type="text" value="genes" size="30"
+                <param argument="--regionsLabel" type="text" value="coverage" 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;."/>
@@ -138,11 +134,12 @@
                         message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
                 </param>
 
-                <param argument="--onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
+                <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
                     label="Do one plot per group"
-                    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." />
+                    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." />
 
 
                 <param argument="--yMin" type="float" value="" size="3" optional="true"
@@ -188,7 +185,7 @@
    :alt: Meta-gene profile of Rna Polymerase II
 
 
-You can find more details on the profiler wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-profiler
+You can find more details on the profiler doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/plotProfile.html
 
 
 -----
diff -r 4213153d3b82 -r f30699e4e902 static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed