# HG changeset patch
# User jorrit
# Date 1361919300 18000
# Node ID aebf24eea33887e5e931ad20efdaa0f630a1fed8
# Parent  00a5ede354a088e3cf2eda8ce30df5602b6160c7
Uploaded

diff -r 00a5ede354a0 -r aebf24eea338 ontologizer.xml
--- a/ontologizer.xml	Tue Feb 26 17:45:58 2013 -0500
+++ b/ontologizer.xml	Tue Feb 26 17:55:00 2013 -0500
@@ -1,18 +1,18 @@
 <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>
+    <requirement type="package" version="0.0.1">ontologizer-jar</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" />
+    <param name="go" type="obo" label="Gene ontology" />
+    <param name="gaf" type="gaf" label="Gene association file" />
+    <param name="pop" format="gs" label="population gene set" />
+    <param name="study" format="gs" label="study gene set" />
   </inputs>
   <outputs>
     <!-- need to figure out how to handle multiple outputs -->
-    <data format="text" name="output" />
+    <data type="text" name="output" />
   </outputs>
   <tests>
     <!-- see http://wiki.galaxyproject.org/Admin/Tools/Writing%20Tests -->
diff -r 00a5ede354a0 -r aebf24eea338 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Feb 26 17:45:58 2013 -0500
+++ b/tool_dependencies.xml	Tue Feb 26 17:55:00 2013 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="ontologizer" version="0.0.1">
+    <package name="ontologizer-jar" version="0.0.1">
         <install version="1.0">
             <actions>
                 <action type="shell_command">curl http://compbio.charite.de/contao/index.php/cmdlineOntologizer.html?file=tl_files/ontologizer/cmdline/Ontologizer.jar > ontologizer.jar</action>