# HG changeset patch
# User iracooke
# Date 1403292719 14400
# Node ID 25d57c17e7d5a12c8d07e950682c96547f083054
# Parent  ba73c62f13c4e36165d6f016bd1c609e52d5cf2a
Uploaded

diff -r ba73c62f13c4 -r 25d57c17e7d5 peptide_shaker.xml
--- a/peptide_shaker.xml	Fri Jun 20 15:30:58 2014 -0400
+++ b/peptide_shaker.xml	Fri Jun 20 15:31:59 2014 -0400
@@ -1,10 +1,10 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="1.19.1.0">
+<tool id="peptide_shaker" name="Peptide Shaker" version="1.19.4.0">
     <description>
         Perform protein identification using various search engines (using SearchGUI) and combine results with PeptideShaker.
     </description>
     <requirements>
-        <requirement type="package" version="0.30.1">peptide_shaker</requirement>
-        <requirement type="package" version="1.19.1">searchgui</requirement>
+        <requirement type="package" version="0.30.3">peptide_shaker</requirement>
+        <requirement type="package" version="1.19.4">searchgui</requirement>
         <!--<requirement type="package" version="2.2.29">blast+</requirement>-->
     </requirements>
     <stdio>
@@ -253,7 +253,7 @@
         &amp;&amp;
 
         #if 'mzidentML' in str($outputs).split(','):
-            java -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.MzidCLI
+            java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.MzidCLI
                 -in \$cwd/peptide_shaker_output.cps
                 -output_file output.mzid
                 -contact_first_name 'Proteomics'