diff ontologizer.xml @ 0:028babd7a6c5 draft default tip

Try at a fresh start...

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ontologizer.xml	Fri Mar 29 17:30:07 2013 -0400
@@ -0,0 +1,45 @@
+<tool id="ontologizer" name="ontologizer" version="0.0.16">
+  <description>from http://compbio.charite.de/contao/</description>
+  <requirements>
+    <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 $tablefile; echo moved table file to [$tablefile]; mv view-*.dot $dotfile; echo moved dot file to [$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" />
+    <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>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="tablefile" />
+    <data format="text" name="dotfile" />
+  </outputs>
+
+  <stdio>
+    <exit_code range="1:"   level="fatal"   description="Unknown error" />
+  </stdio>
+
+  <help>
+    see http://compbio.charite.de/contao/index.php/ontologizer2.html
+  </help>
+
+</tool>
+
+