# HG changeset patch
# User iracooke
# Date 1403644146 14400
# Node ID 05f020f19ef688d9f809d5842272697ae2257afb
# Parent  22babad2d8f2d1bcb077f84a70ce85062784fbbe
Uploaded

diff -r 22babad2d8f2 -r 05f020f19ef6 peptide_shaker.xml
--- a/peptide_shaker.xml	Fri Jun 20 15:42:17 2014 -0400
+++ b/peptide_shaker.xml	Tue Jun 24 17:09:06 2014 -0400
@@ -1,15 +1,16 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="1.19.4.0">
+<tool id="peptide_shaker" name="Peptide Shaker" version="1.19.5.0">
     <description>
         Perform protein identification using various search engines (using SearchGUI) and combine results with PeptideShaker.
     </description>
     <requirements>
-        <requirement type="package" version="0.31.3">peptide_shaker</requirement>
-        <requirement type="package" version="1.19.4">searchgui</requirement>
+        <requirement type="package" version="0.31.4">peptide_shaker</requirement>
+        <requirement type="package" version="1.19.5">searchgui</requirement>
         <!--<requirement type="package" version="2.2.29">blast+</requirement>-->
     </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" description="Job Failed" />
-        <regex match="Error" level="fatal" description="Error encounterd!"/> 
+        <regex match="java.*Exception" level="fatal" description="Java Exception"/> 
+        <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
     </stdio>
     <command>
 
@@ -154,7 +155,10 @@
                     -ms_amanda 0
                 #end if
 
+            #else
+                -ms_amanda 0
             #end if
+            
         2>> $temp_stderr)
         &amp;&amp;
 
@@ -241,13 +245,14 @@
             -temp_folder `pwd`
             -in \$cwd/peptide_shaker_output.cps
             -out_reports \$cwd/output_reports
-            #if 'cps' in str($outputs).split(','):
-                #set $cleaned_list = str($outputs).split(',')
+            #set $cleaned_list = str($outputs).split(',')
+            #if 'cps' in $cleaned_list:
                 #silent $cleaned_list.remove('cps')
-                -reports #echo ','.join($cleaned_list)#
-            #else:
-                -reports #echo str($outputs)#
             #end if
+            #if 'mzidentML' in $cleaned_list:
+                #silent $cleaned_list.remove('mzidentML')
+            #end if
+            -reports #echo ','.join($cleaned_list)#
 
         2>> $temp_stderr)
         &amp;&amp;
@@ -793,7 +798,7 @@
     <help>
 **What it does**
 
-Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the results.
+Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI application and combines the results.
 
 https://code.google.com/p/peptide-shaker/