# HG changeset patch
# User bgruening
# Date 1450860788 18000
# Node ID 62d522914d1d382f63c8b049278e606571ce05e0
# Parent  ef75ff1815d96e2be4446ca4b4df743007fd6177
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 54a10cf268ca9a5399f13458a1b218be7891bd41

diff -r ef75ff1815d9 -r 62d522914d1d bamPEFragmentSize.xml
--- a/bamPEFragmentSize.xml	Tue Dec 22 13:40:24 2015 -0500
+++ b/bamPEFragmentSize.xml	Wed Dec 23 03:53:08 2015 -0500
@@ -15,7 +15,7 @@
             #if $histogram:
                 --histogram ./hist.png
             #end if
-            --plotTitle "$plotTitle"
+
             one.bam
             > $outfile
 ]]>
@@ -24,9 +24,8 @@
         <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 distribution of fragment length as a histogram"
+            label="Get the distribion of fragment length as histogram"
             help=""/>
-        <expand macro="plotTitle" />
     </inputs>
     <outputs>
         <data name="outfile" format="txt"/>
@@ -38,7 +37,6 @@
         <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>
@@ -47,8 +45,7 @@
 <![CDATA[
 **What it does**
 
-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.
+Given a BAM file it samples several regions to estimate the paird-end fragment length.
 
 -----
 
diff -r ef75ff1815d9 -r 62d522914d1d deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Dec 22 13:40:24 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 03:53:08 2015 -0500
@@ -40,10 +40,10 @@
     </xml>
 
     <token name="@HEATMAP_OPTIONS@">
-        #if str($plotting_type.zMin) != "":
+        #if $plotting_type.zMin:
             --zMin $plotting_type.zMin
         #end if
-        #if str($plotting_type.zMax) != "":
+        #if $plotting_type.zMax:
             --zMax $plotting_type.zMax
         #end if
         --colorMap '$plotting_type.colorMap'
@@ -107,11 +107,7 @@
                     </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: 0 [do not cluster])."/>
+                            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)."/>
                     </when>
                     <when value="none" />
                 </conditional>
@@ -412,6 +408,7 @@
             <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>
@@ -459,6 +456,14 @@
     </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 ef75ff1815d9 -r 62d522914d1d static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed
diff -r ef75ff1815d9 -r 62d522914d1d test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r ef75ff1815d9 -r 62d522914d1d test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r ef75ff1815d9 -r 62d522914d1d test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg	Tue Dec 22 13:40:24 2015 -0500
+++ b/test-data/bamCoverage_result3.bg	Wed Dec 23 03:53:08 2015 -0500
@@ -5,4 +5,4 @@
 chrM	220	230	7690304.31
 chrM	230	240	6027535.81
 chrM	240	250	3325537.00
-chrM	250	16569	623538.2
+chrM	250	260	623538.19
diff -r ef75ff1815d9 -r 62d522914d1d test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r ef75ff1815d9 -r 62d522914d1d test-data/profiler_result2.png
Binary file test-data/profiler_result2.png has changed
diff -r ef75ff1815d9 -r 62d522914d1d tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Dec 22 13:40:24 2015 -0500
+++ b/tool_dependencies.xml	Wed Dec 23 03:53:08 2015 -0500
@@ -4,6 +4,6 @@
         <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="deepTools" version="2.0">
-        <repository changeset_revision="747571992679" name="package_python_2_7_deeptools_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="bd40c0aa7d8e" name="package_python_2_7_deeptools_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>