Mercurial > repos > jorrit > obotools

changeset 37:2633a06624e4

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Uploaded
author jorrit
date Tue, 26 Feb 2013 23:36:00 -0500
parents 2ab168fd30a6
children 7e92c084e223
files ontologizer.xml
diffstat 1 files changed, 5 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/ontologizer.xml	Tue Feb 26 23:25:57 2013 -0500
+++ b/ontologizer.xml	Tue Feb 26 23:36:00 2013 -0500
@@ -3,7 +3,7 @@
   <requirements>
     <requirement type="package" version="0.0.3">ontologizer-jar</requirement>
   </requirements>
-  <command>java -Xmx2G -jar \$ONTOLOGIZER_JAR --go $go --association $gaf --population $population --studyset $studyset --dot 0.05 --mtc "$mtc" --calculation "$calc"; echo moving files; mv table-*.txt $tablefile; mv view-*.dot $dotfile; echo moving files to $dotfile</command>
+  <command>java -Xmx2G -jar \$ONTOLOGIZER_JAR --go $go --association $gaf --population $population --studyset $studyset --dot 0.05 --mtc "$mtc" --calculation "$calc"; mv table-*.txt $tablefile; echo moved table file to [$tablefile]; mv view-*.dot $dotfile; echo moved dot file to [$dotfile]</command>
   <inputs>
     <param name="go" type="data" format="obo" label="Gene Ontology File" />
     <param name="gaf" type="data" format="gaf" label="Gene Association File" />
@@ -32,6 +32,10 @@
     <data format="text" name="dotfile" />
   </outputs>
 
+  <stdio>
+    <exit_code range="1:"   level="fatal"   description="Unknown error" />
+  </stdio>
+
   <help>
     see http://compbio.charite.de/contao/index.php/ontologizer2.html
   </help>