# HG changeset patch
# User bgruening
# Date 1450873683 18000
# Node ID f4fb73df60df2362f2e8ae55782b47814924475e
# Parent  71724ff7d329b150711c9f023490c921a7c86d99
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69

diff -r 71724ff7d329 -r f4fb73df60df bigwigCompare.xml
--- a/bigwigCompare.xml	Wed Dec 23 03:53:46 2015 -0500
+++ b/bigwigCompare.xml	Wed Dec 23 07:28:03 2015 -0500
@@ -86,7 +86,7 @@
                     help="Size of the bins in bp for the output of the bigwig/bedgraph file."/>
 
                 <expand macro="skipNAs" />
-                <expand macro="scaleFactor" />
+                <expand macro="scaleFactors" />
                 <expand macro="plotTitle" />
             </when>
         </conditional>
diff -r 71724ff7d329 -r f4fb73df60df deepTools_macros.xml
--- a/deepTools_macros.xml	Wed Dec 23 03:53:46 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 07:28:03 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 71724ff7d329 -r f4fb73df60df static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed
diff -r 71724ff7d329 -r f4fb73df60df test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r 71724ff7d329 -r f4fb73df60df test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r 71724ff7d329 -r f4fb73df60df test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg	Wed Dec 23 03:53:46 2015 -0500
+++ b/test-data/bamCoverage_result3.bg	Wed Dec 23 07:28:03 2015 -0500
@@ -5,4 +5,4 @@
 chrM	220	230	7690304.31
 chrM	230	240	6027535.81
 chrM	240	250	3325537.00
-chrM	250	260	623538.19
+chrM	250	16569	623538.2
diff -r 71724ff7d329 -r f4fb73df60df test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r 71724ff7d329 -r f4fb73df60df test-data/profiler_result2.png
Binary file test-data/profiler_result2.png has changed