--- a/protein_prophet.xml	Mon Mar 04 19:04:16 2013 -0500
+++ b/protein_prophet.xml	Mon Mar 04 19:09:54 2013 -0500
@@ -3,12 +3,12 @@
 	    <requirement type="package" version="1.1.9">galaxy_protk</requirement>
 	    <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
    </requirements>
-   
+
   <description>Calculate Protein Prophet statistics on search results</description>
 
 
 <!-- Note .. the input file is assumed to be the first argument -->
-  <command>protein_prophet.rb --galaxy $input_file -r $iproph $nooccam $groupwts $normprotlen $logprobs $confem $allpeps $unmapped $instances $delude --minprob=$minprob --minindep=$minindep </command>
+  <command>protein_prophet_wrapper.rb --galaxy $input_file -r $iproph $nooccam $groupwts $normprotlen $logprobs $confem $allpeps $unmapped $instances $delude --minprob=$minprob --minindep=$minindep </command>
   <inputs>
 	
     <param name="input_file" type="data" format="peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Peptide Prophet Results" help="These files will typically be outputs from peptide prophet or interprophet"/>