# HG changeset patch
# User bgruening
# Date 1450873644 18000
# Node ID 0f93005471ac89bf36b8736412e90794f8dc60ec
# Parent  62d522914d1d382f63c8b049278e606571ce05e0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69

diff -r 62d522914d1d -r 0f93005471ac bamPEFragmentSize.xml
--- a/bamPEFragmentSize.xml	Wed Dec 23 03:53:08 2015 -0500
+++ b/bamPEFragmentSize.xml	Wed Dec 23 07:27:24 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 62d522914d1d -r 0f93005471ac deepTools_macros.xml
--- a/deepTools_macros.xml	Wed Dec 23 03:53:08 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 07:27:24 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 62d522914d1d -r 0f93005471ac static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed
diff -r 62d522914d1d -r 0f93005471ac test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r 62d522914d1d -r 0f93005471ac test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r 62d522914d1d -r 0f93005471ac test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg	Wed Dec 23 03:53:08 2015 -0500
+++ b/test-data/bamCoverage_result3.bg	Wed Dec 23 07:27:24 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 62d522914d1d -r 0f93005471ac test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r 62d522914d1d -r 0f93005471ac test-data/profiler_result2.png
Binary file test-data/profiler_result2.png has changed