# HG changeset patch
# User iracooke
# Date 1394585516 14400
# Node ID 1ff39c9bd84aee7efdeac4f87a09e0f069a0c5bf
# Parent  89a300fbb1596b5f2c30e6ab183adebd1825ce82
Uploaded

diff -r 89a300fbb159 -r 1ff39c9bd84a peptide_prophet.xml
--- a/peptide_prophet.xml	Tue Mar 11 20:51:34 2014 -0400
+++ b/peptide_prophet.xml	Tue Mar 11 20:51:56 2014 -0400
@@ -1,13 +1,13 @@
 <tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.0.1">
     <requirements>
-        <requirement type="package" version="1.2.2">galaxy_protk</requirement>
-        <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
+        <requirement type="package" version="1.2.6">protk</requirement>
+        <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement>
    </requirements>
    
 	<description>Calculate Peptide Prophet statistics on search results</description>
 
-	<command interpreter="bash">
-        peptide_prophet_wrapper.sh $output $input_file
+	<command>
+        peptide_prophet.rb --galaxy $input_file -o peptide_prophet_output.pep.xml
 
         -r 
         $glyco