diff macros.xml @ 49:58a3e6cb2598 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4

--- a/macros.xml	Thu Sep 27 04:31:53 2018 -0400
+++ b/macros.xml	Fri Oct 12 08:56:06 2018 -0400
@@ -2,12 +2,14 @@
     <xml name="stdio">
         <stdio>
             <exit_code range="1:" level="fatal" description="Job Failed" />
-	    <regex match="java.lang.OutOfMemoryError" level="fatal_oom" description="Java memory Exception"/>
+	    <!--	    <regex match="java.lang.OutOfMemoryError" level="fatal_oom" description="Java memory Exception"/>
 	    <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/>
 	    <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/>
+	    <regex match="Native memory allocation (malloc) failed" level="fatal_oom" description="Java memory Exception"/>-->
 	    <regex match="java.*Exception" level="fatal" description="Java Exception"/>
             <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
-            <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
+	    <regex match="PeptideShaker ran out of memory" level="fatal" description="JVM Error"/>
+	    <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
         </stdio>
     </xml>
     <token name="@GENERAL_PARAMETERS@">
@@ -52,7 +54,8 @@
 
     </token>
     <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
-    <token name="@SEARCHGUI_VERSION@">3.3.3</token>
+    <token name="@SEARCHGUI_VERSION@">3.3.5</token>
+    <token name="@PEPTIDESHAKER_VERSION@">1.16.31</token>
     <xml name="general_options">
 
         <section name="protein_digest_options" expanded="false" title="Protein Digestion Options">