# HG changeset patch
# User jorrit
# Date 1361936812 18000
# Node ID f48064da784905d176430a46a847e5c149fc1f99
# Parent  11beca20586bf7e6b7767ec3ed3058cfee175cd7
Uploaded

diff -r 11beca20586b -r f48064da7849 ontologizer.xml
--- a/ontologizer.xml	Tue Feb 26 20:53:34 2013 -0500
+++ b/ontologizer.xml	Tue Feb 26 22:46:52 2013 -0500
@@ -3,32 +3,39 @@
   <requirements>
     <requirement type="package" version="0.0.2">ontologizer-jar</requirement>
   </requirements>
-  <command>java -Xmx2G -jar $ONTOLOGIZER_JAR --go $go --association $gaf --population $pop --studyset $study --dot 0.05 > $output</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="text" label="Gene ontology" />
-    <param name="gaf" type="text" label="Gene association file" />
-    <param name="pop" type="text" label="population gene set" />
-    <param name="study" type="text" label="study gene set" />
-  </inputs>
-  <outputs>
-    <!-- need to figure out how to handle multiple outputs -->
-    <data type="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>
+    <param name="go" type="data" format="obo" label="Gene Ontology File" />
+    <param name="gaf" type="data" format="gaf" label="Gene Association File" />
+    <param name="population" type="data" format="tabular" label="Population Geneset File" />
+    <param name="studyset" type="data" format="tabular" label="Study Geneset File" />
+    <param name="calc" type="select" format="text" label="Calculation Method">
+      <option value="MGSA">MGSA</option>
+      <option value="Parent-Child-Intersection">Parent-Child-Intersection</option>
+      <option value="Parent-Child-Union" selected="true">Parent-Child-Union</option>
+      <option value="Term-For-Term">Term-For-Term</option>
+      <option value="Topology-Elim">Topology-Elim</option>
+      <option value="Topology-Weighted">Topology-Weighted</option>
+    </param>
+    <param name="mtc" type="select" format="text" label="MTC Method">
+      <option value="Benjamini-Hochberg">Benjamini-Hochberg</option>
+      <option value="Benjamini-Yekutieli">Benjamini-Yekutieli</option>
+      <option value="Bonferroni">Bonferroni</option>
+      <option value="Bonferroni-Holm">Bonferroni-Holm</option>
+      <option value="None" selected="true">None</option>
+      <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" />
+  <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>