diff OPPL/oppl_query.xml @ 18:d3616fac4ca5 draft

Elk support added

--- a/OPPL/oppl_query.xml	Mon Aug 20 11:39:56 2012 +0200
+++ b/OPPL/oppl_query.xml	Thu Sep 20 12:46:36 2012 +0200
@@ -20,7 +20,7 @@
 	
 	<!--<command>
 		java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_query.jar $ontology $reasoner $answer_format "$query" > $output 2>/dev/null
-	</commadn>-->
+	</command>-->
 	
 
 	<inputs>
@@ -30,6 +30,7 @@
 			<option value="Pellet" selected="true">Pellet</option>
 			<option value="HermiT">HermiT</option>
 			<option value="FaCTPlusPlus">FaCT++</option>
+			<option value="Elk">Elk (Not all axioms supported)</option>
 		</param>
 		<param name="answer_format" type="select" label="Choose how to render the retrieved entities">
 			<option value="URI" selected="true">URI</option>
@@ -53,11 +54,17 @@
 
 **About OPPL-Query-Galaxy**
 
-  OPPL-Query-Galaxy can be used to execute an OPPL query against an OWL ontology (?whole:CLASS, ?part:CLASS SELECT ?part SubClassOf part_of some ?whole WHERE ?part != Nothing). The result is a two column table with the entities that have been bound by the variables. 
+  OPPL-Query-Galaxy can be used to execute an OPPL query against an OWL ontology. The result is a two column table with the entities that have been bound by the variables. 
+  
+**Usage**
+ 
+  An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. OPPL-Query-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. In case the loaded ontology includes OWL imports, OPPL-Query-Galaxy will try to resolve them.
   
-**Formats**
-
-  OPPL-Query-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 output is a list of terms.
+  An OPPL query must be provided, e.g. ?whole:CLASS, ?part:CLASS SELECT ?part SubClassOf part_of some ?whole WHERE ?part != Nothing.
+  
+  The reasoner can be Pellet, HermiT, FaCT++ or Elk.  
+   
+  The returned entities can be rendered using their URI, their URI fragment, or OBO type URI fragment (e.g. GO_0000022 to GO:0000022).
 
 **Contact**