diff bamPEFragmentSize.xml @ 8:0f93005471ac draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69

--- 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.
 
 -----