# HG changeset patch
# User jorrit
# Date 1361938133 18000
# Node ID 25c037153c9fe8858d0fda94bcf5e3d26b730595
# Parent  f475c42e642cb1a4c926b88a665056dde62637a7
Uploaded

diff -r f475c42e642c -r 25c037153c9f ontologizer.xml
--- a/ontologizer.xml	Tue Feb 26 23:02:45 2013 -0500
+++ b/ontologizer.xml	Tue Feb 26 23:08:53 2013 -0500
@@ -1,10 +1,10 @@
 <tool id="ontologizer" name="ontologizer" version="0.0.16">
   <description>from http://compbio.charite.de/contao/</description>
   <requirements>
-    <!--requirement type="set_environment">ONTOLOGIZER_JAR</requirement-->
+    <requirement type="set_environment">ONTOLOGIZER_JAR</requirement>
     <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"; mv table-*.txt $tablefile; mv view-*.dot $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; mv view-*.dot $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" />