--- a/CoverageReport.xml	Mon Nov 17 07:10:11 2014 -0500
+++ b/CoverageReport.xml	Thu Feb 12 08:51:06 2015 -0500
@@ -16,6 +16,7 @@
       $PositionLevel
       -m $threshold
       -f $frac 
+      $trim
       ## sample name
       #if $namefromselect.namesource == "typed" :
           -n "${namefromselect.typedname}"
@@ -26,6 +27,7 @@
       #else:
           -n "Unspecified"
       #end if
+      
   </command>
   <requirements>
     <requirement type="package" version="3.0.3">R</requirement>
@@ -35,6 +37,10 @@
   <inputs>
         <param name="input1" type="data" format="bam" label="BAM file" help="BAM file of mapped reads" />
         <param name="input2" type="data" format="bed" label="Target Regions BED" help="BED file containing regions of interest. See below for format" />
+	<param name="trim" type="select" label="Collapse overlapping regions in targets">
+		<option value='-T' selected="TRUE">Yes</option>
+		<option value=''>No</option>
+	</param>    
         <param name="threshold" type="integer" value="40" label="Minimal Coverage Threshold" help="Default: 40" />   
         <param name="frac" type="float" value="0.2" label="Fraction of Average Coverage for usage in plot" help="Default: 0.2" />
 	<param name="perGene" type="select" label="Plot exon coverages for all genes in targets">