diff ontologizer.xml @ 8:00a5ede354a0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ontologizer.xml	Tue Feb 26 17:45:58 2013 -0500
@@ -0,0 +1,35 @@
+<tool id="ontologizer" name="ontologizer" version="0.0.14">
+  <description>from http://compbio.charite.de/contao/</description>
+  <requirements>
+    <requirement type="package" version="0.0.1">ontologizer</requirement>
+  </requirements>
+  <command>java -Xmx2G -jar $ONTOLOGIZER_JAR --go $go --association $gaf --population $pop --studyset $study --dot 0.05 > $output</command>
+  <inputs>
+    <param name="go" format="obo" label="Gene ontology" />
+    <param name="gaf" format="gaf" label="Gene association file" />
+    <param name="pop" format="text" label="population gene set" />
+    <param name="study" format="text" label="study gene set" />
+  </inputs>
+  <outputs>
+    <!-- need to figure out how to handle multiple outputs -->
+    <data format="text" name="output" />
+  </outputs>
+  <tests>
+    <!-- see http://wiki.galaxyproject.org/Admin/Tools/Writing%20Tests -->
+    <test>
+     <param name="go" file="ontologizer/test.obo" />
+     <param name="gaf" file="ontologizer/test.gaf" />
+     <param name="pop" file="ontologizer/test.gs" />
+     <param name="study" file="ontologizer/test.gs" />
+     <output name="output" file="test.output"/>
+    </test>
+  </tests>
+
+
+  <help>
+    see http://compbio.charite.de/contao/index.php/ontologizer2.html
+  </help>
+
+</tool>
+
+