# HG changeset patch
# User jorrit
# Date 1361937201 18000
# Node ID b277bb358960d01a1de9c39b2da3ac7a6ea5fcb9
# Parent  f0048a544d61a291b451312b1374aa1f768ccd6f
Uploaded

diff -r f0048a544d61 -r b277bb358960 ontologizer.xml
--- a/ontologizer.xml	Tue Feb 26 22:50:29 2013 -0500
+++ b/ontologizer.xml	Tue Feb 26 22:53:21 2013 -0500
@@ -1,6 +1,7 @@
 <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="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>
@@ -26,7 +27,6 @@
       <option value="Westfall-Young-Single-Step">Westfall-Young-Single-Step</option>
       <option value="Westfall-Young-Step-Down">Westfall-Young-Step-Down</option>
     </param>
-  </param>
 </inputs>
 <outputs>
   <data format="tabular" name="tablefile" />