# HG changeset patch
# User jorrit
# Date 1361937765 18000
# Node ID f475c42e642cb1a4c926b88a665056dde62637a7
# Parent  b277bb358960d01a1de9c39b2da3ac7a6ea5fcb9
Uploaded

diff -r b277bb358960 -r f475c42e642c ontologizer.xml
--- a/ontologizer.xml	Tue Feb 26 22:53:21 2013 -0500
+++ b/ontologizer.xml	Tue Feb 26 23:02:45 2013 -0500
@@ -1,7 +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="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>
@@ -27,15 +27,15 @@
       <option value="Westfall-Young-Single-Step">Westfall-Young-Single-Step</option>
       <option value="Westfall-Young-Step-Down">Westfall-Young-Step-Down</option>
     </param>
-</inputs>
-<outputs>
-  <data format="tabular" name="tablefile" />
-  <data format="text" name="dotfile" />
-</outputs>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="tablefile" />
+    <data format="text" name="dotfile" />
+  </outputs>
 
-<help>
-  see http://compbio.charite.de/contao/index.php/ontologizer2.html
-</help>
+  <help>
+    see http://compbio.charite.de/contao/index.php/ontologizer2.html
+  </help>
 
 </tool>