--- a/OPPL/oppl.xml	Tue Sep 06 14:55:49 2011 -0400
+++ b/OPPL/oppl.xml	Wed Sep 07 10:46:29 2011 +0200
@@ -1,9 +1,13 @@
-<tool id="oppl" name="Execute an OPPL file against an OWL file" version="1.0.0">
+<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.1">
   <description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description>
-  <command>java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL > $output </command>
+  <command>java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format > $output </command>
   <inputs>
-    <param format="text" name="input" type="data" label="Source OWL file"/>
+    <param format="text" name="input" type="data" label="Input ontology file"/>
     <param format="text" name="OPPL" type="data" label="OPPL file"/>
+    <param name="format" type="select" label="Choose ontology output format">
+        <option value="OWL" selected="true">OWL</option>
+	<option value="OBO">OBO</option>
+    </param>
   </inputs>
   <outputs>
     <data format="text" name="output" />
@@ -13,6 +17,7 @@
     <test>
       <param name="input" value="test.owl"/>
       <param name="OPPL" value="test.oppl"/>
+      <param name="format" value="OWL"/>
       <output name="out_file" file="test_new.owl"/>	
     </test>
   </tests>
@@ -21,11 +26,11 @@
 
 **About OPPL-Galaxy**
 
-  OPPL-Galaxy can be used to execute an OPPL script against an (OWL) ontology, generating a new ontology. OPPL (Ontology Pre Processor Language) is a high level scripting language, based in the Manchester OWL Syntax, to automate the manipulation of an ontology (Adding or removing axioms). An OPPL script (See bellow or test.oppl) defines a query to be performed against the ontology, and some actions that affect the entities that will be retrieved. Those entities can be named or defined by a variable. OPPL is a powerful method for defining and executing modelling patterns that are repeated in a given ontology, saving time and effort.  
+  OPPL-Galaxy can be used to execute an OPPL script against an ontology, generating a new ontology. OPPL (Ontology Pre Processor Language) is a high level scripting language, based in the Manchester OWL Syntax, to automate the manipulation of an ontology (Adding or removing axioms). An OPPL script (See bellow or test.oppl) defines a query to be performed against the ontology, and some actions that affect the entities that will be retrieved. Those entities can be named or defined by a variable. OPPL is a powerful method for defining and executing modelling patterns that are repeated in a given ontology, saving time and effort.  
 
 **Formats**
 
-  OPPL-Galaxy uses the OWL API, and therefore can work with any ontology format that such API is able to load. That includes: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS.
+  OPPL-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. The available output formats are OBO flat file and OWL (RDF/XML).
 
 **Usage**
 
@@ -33,7 +38,7 @@
 
   Then execute the OPPL file against the OWL file with Ontology Pre Processor Language >> Execute an OPPL file against an OWL file.
 
-  This is the OPPL script provided in the bundle, test.oppl. Variables start with ?: 
+  This is the OPPL script provided in the bundle, test.oppl (Variables start with ?): 
 
   ?whole:CLASS,
   ?part:CLASS
@@ -55,11 +60,9 @@
 
 **Features that will be implemented soon**
 
-  OWL import closure
+  OWL import closure.
 
-  Choose output format (Right now only OWL RDF/XML is available)
-
-  Choose reasoner (Right now only Pellet is available)
+  Choose reasoner (Right now only Pellet is available).
 
 **Contact**