# HG changeset patch
# User bgruening
# Date 1450809822 18000
# Node ID 9f2b016177e7b2178888d1b04f60dabb62e88003
# Parent  fd4a79e7e5f06cdc8be09931be970829aff9d096
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 8b9cdb8dc4a8fedd2b2286e7afab6529e49a9d22-dirty

diff -r fd4a79e7e5f0 -r 9f2b016177e7 deepTools_macros.xml
--- a/deepTools_macros.xml	Mon Dec 21 19:06:15 2015 -0500
+++ b/deepTools_macros.xml	Tue Dec 22 13:43:42 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 ${on_string}: sorted/filtered regions">
             <filter>
             ((
diff -r fd4a79e7e5f0 -r 9f2b016177e7 plotCoverage.xml
--- a/plotCoverage.xml	Mon Dec 21 19:06:15 2015 -0500
+++ b/plotCoverage.xml	Tue Dec 22 13:43:42 2015 -0500
@@ -1,5 +1,5 @@
 <tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0">
-    <description>creates a heatmap of correlation scores between different samples </description>
+    <description>plots a histogram of coverage on genomic regions </description>
     <macros>
         <token name="@BINARY@">plotCoverage</token>
         <import>deepTools_macros.xml</import>
@@ -22,7 +22,7 @@
             --plotFileFormat "$outFileFormat"
 
             #if $outRawCounts:
-                --outRawCounts '$outFileRawCounts' 
+                --outRawCounts '$outFileRawCounts'
             #end if
 
             #if $advancedOpt.showAdvancedOpt == "yes":
diff -r fd4a79e7e5f0 -r 9f2b016177e7 static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed