--- a/bam_to_bigwig/bam_to_bigwig.xml	Tue Jun 07 16:26:46 2011 -0400
+++ b/bam_to_bigwig/bam_to_bigwig.xml	Wed Sep 05 21:14:54 2012 -0400
@@ -1,17 +1,23 @@
-<tool id="bam_to_bigwig" name="BAM to BigWig" version="0.0.2">
+<tool id="bam_to_bigwig" name="BAM to BigWig" version="0.1.0">
   <description>Calculates coverage from a BAM alignment file</description>
-  <command interpreter="python">bam_to_wiggle.py $align --outfile=$out</command>
+  <command interpreter="python">bam_to_bigwig.py $align --outfile=$out</command>
   <inputs>
     <param format="bam" name="align" type="data" label="BAM alignment file"/>
   </inputs>
   <outputs>
     <data format="bigwig" name="out" />
   </outputs>
-
+  <requirements>
+        <requirement type="python-module">pysam</requirement>
+        <requirement type="binary">genomeCoverageBed</requirement>
+        <requirement type="binary">bedGraphToBigWig</requirement>
+  </requirements>
 <help>
 **What it does**
 
-Creates a coverage file in BigWig format, given a BAM alignment file. 
+Creates a coverage file in BigWig format, given a BAM alignment file.
+
+Gaps or skips (CIGAR D or N operators) are not counted towards the coverage calculation, which is important when mapping RNA Seq reads to genes with introns.
 
 **Input**
 
@@ -21,5 +27,4 @@
 
 BigWig files can be loaded directly from Galaxy into the UCSC browser. They can be loaded incrementally by UCSC, so a single file can be used to represent the entire genome without having to upload the entire thing as a custom track.
 </help>
-
 </tool>