--- a/peptide_prophet.xml	Tue Mar 05 00:28:22 2013 -0500
+++ b/peptide_prophet.xml	Sun Jun 09 08:19:01 2013 -0500
@@ -1,12 +1,29 @@
 <tool id="proteomics_search_peptide_prophet_1" name="Peptide 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>
    
 	<description>Calculate Peptide Prophet statistics on search results</description>
 
-	<command interpreter="ruby">peptide_prophet_wrapper.rb ${output} ${input_file}  -r $glyco $useicat $phospho $usepi $usert $accurate_mass $no_ntt $no_nmc $use_gamma $use_only_expect $force_fit $allow_alt_instruments $maldi
+	<command interpreter="bash">
+        peptide_prophet_wrapper.sh $output $input_file
+
+        -r 
+        $glyco 
+        $useicat 
+        $phospho 
+        $usepi 
+        $usert 
+        $accurate_mass 
+        $no_ntt 
+        $no_nmc 
+        $use_gamma 
+        $use_only_expect 
+        $force_fit 
+        $allow_alt_instruments 
+        $maldi
+
 	</command>
 
 	<inputs>