# HG changeset patch
# User bgruening
# Date 1450809624 18000
# Node ID ef75ff1815d96e2be4446ca4b4df743007fd6177
# Parent  386f947de774e9931343b6ccf37f8fbce6f3c126
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 8b9cdb8dc4a8fedd2b2286e7afab6529e49a9d22-dirty

diff -r 386f947de774 -r ef75ff1815d9 bamPEFragmentSize.xml
--- a/bamPEFragmentSize.xml	Mon Dec 21 19:02:15 2015 -0500
+++ b/bamPEFragmentSize.xml	Tue Dec 22 13:40:24 2015 -0500
@@ -15,7 +15,7 @@
             #if $histogram:
                 --histogram ./hist.png
             #end if
-
+            --plotTitle "$plotTitle"
             one.bam
             > $outfile
 ]]>
@@ -24,8 +24,9 @@
         <param name="bamInput" format="bam" type="data" label="BAM file"
             help="The BAM file must be sorted."/>
         <param argument="--histogram" type="boolean" truevalue="--histogram" falsevalue=""
-            label="Get the distribion of fragment length as histogram"
+            label="Get the distribution of fragment length as a histogram"
             help=""/>
+        <expand macro="plotTitle" />
     </inputs>
     <outputs>
         <data name="outfile" format="txt"/>
@@ -37,6 +38,7 @@
         <test>
             <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
             <param name="histogram" value="True" />
+            <param name="plotTitle" value="Test Plot" />
             <output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" />
             <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" compare="sim_size" />
         </test>
@@ -45,7 +47,8 @@
 <![CDATA[
 **What it does**
 
-Given a BAM file it samples several regions to estimate the paird-end fragment length.
+Given a BAM file, several regions are sampled depending on the size of the genome to estimate the paired-end fragment length.
+Properly paired reads are preferred for computation. The output can be obtained as a histogram.
 
 -----
 
diff -r 386f947de774 -r ef75ff1815d9 deepTools_macros.xml
--- a/deepTools_macros.xml	Mon Dec 21 19:02:15 2015 -0500
+++ b/deepTools_macros.xml	Tue Dec 22 13:40:24 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 386f947de774 -r ef75ff1815d9 static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed