diff OPPL/oppl.xml @ 6:3740505b579c

Added reasoner option: Pellet or HermiT

--- a/OPPL/oppl.xml	Sat Sep 17 13:41:28 2011 +0200
+++ b/OPPL/oppl.xml	Sun Sep 18 12:35:18 2011 +0200
@@ -1,15 +1,17 @@
 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.3">
 	<description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description>
 
-	<!-- The conditional is tacky, I think, but it works! -->
+	<!-- The command execution of the conditional is tacky, I think, but it works! -->
+	<!-- Galaxy is not happy with OPPL throwing info into stderr, and I have redirected stderr to /dev/null, which is a bad solution since OPPL galaxy does not inform properly when it fails -->
+	<!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->
 
 	<command>
-		#if $import_opts.imports_select==False #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports > $output 2>/dev/null
-		#else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports > $output 2>/dev/null
+		#if $import_opts.imports_select==False #java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner > $output 2>/dev/null
+		#else #java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner > $output 2>/dev/null
 		#end if
 	</command>
 		
-	<!--<command>java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports > $output 2>/dev/null</command>-->
+	<!-- For big ontologies use something like java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar-->
 
 	<inputs>
 		<param format="text" name="input" type="data" label="Input ontology file"/>
@@ -29,6 +31,10 @@
 			<option value="OBO">OBO</option>
 		</param>
 		<param name="inferred" type="boolean" value="False" truevalue="Add_inferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/>
+		<param name="reasoner" type="select" label="Choose reasoner">
+			<option value="Pellet" selected="true">Pellet</option>
+			<option value="HermiT">HermiT</option>
+		</param>
 
 	</inputs>
 	<outputs>
@@ -38,9 +44,10 @@
 		<test>
 			<param name="input" value="test.owl"/>
 			<param name="OPPL" value="test.oppl"/>
+			<param name="imports" value="NoImports"/>
 			<param name="format" value="OWL"/>
 			<param name="inferred" value="False"/>
-			<param name="imports" value="NoImports"/>
+			<param name="reasoner" value="Pellet"/>
 			<output name="out_file" file="test_new.owl"/>	
 		</test>
 	</tests>
@@ -48,7 +55,7 @@
 
 **About OPPL-Galaxy**
 
-  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.  
+  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. An OPPL script (See test.oppl) defines a query to be performed against the ontology, and some actions (Adding or removing axioms) 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 an ontology, saving time and effort.  
 
 **Formats**
 
@@ -70,6 +77,8 @@
  
   The inferred subsumption axioms can be added to the output ontology as asserted axioms. 
 
+  The reasoner can be Pellet or HermiT. Sometimes, if an execution fails it can be fixed by using a different reasoner. 
+
 **More information**
 
   http://oppl.sf.net/
@@ -80,6 +89,8 @@
 
   http://clarkparsia.com/pellet
 
+  http://hermit-reasoner.com/
+
 **Contact**
 
   Please send any request or comment to [e-mail].