--- a/bigwigCompare.xml	Tue Dec 10 11:03:36 2013 -0500
+++ b/bigwigCompare.xml	Thu Dec 12 18:11:46 2013 -0500
@@ -1,6 +1,7 @@
 <tool id="deeptools_bigwigCompare" name="bigwigCompare" version="1.0">
     <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference</description>
     <expand macro="requirements"/>
+    <expand macro="stdio" />
     <macros>
         <import>deepTools_macros.xml</import>
     </macros>
@@ -29,10 +30,6 @@
 
         #end if
     </command>
-    <stdio>
-        <regex match="Error:" />
-        <regex match="EXception:" />
-    </stdio>
     <inputs>
         <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" />
         <param name="bigwigFile2" format="bigwig" type="data" label="bigWig file" />