--- a/protein_prophet.xml	Tue Mar 05 00:28:22 2013 -0500
+++ b/protein_prophet.xml	Sun Jun 09 08:19:01 2013 -0500
@@ -1,6 +1,6 @@
 <tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.0.1">
 	<requirements>
-	    <requirement type="package" version="1.2.0">galaxy_protk</requirement>
+	    <requirement type="package" version="1.2.2">galaxy_protk</requirement>
 	    <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
    </requirements>
 
@@ -8,7 +8,27 @@
 
 
 <!-- Note .. the input file is assumed to be the first argument -->
-  <command interpreter="ruby">protein_prophet_wrapper.rb --galaxy $input_file -r $iproph $nooccam $groupwts $normprotlen $logprobs $confem $allpeps $unmapped $instances $delude --minprob=$minprob --minindep=$minindep </command>
+  <command interpreter="bash">
+  	protein_prophet_wrapper.sh 
+
+  	--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"/>