# HG changeset patch
# User Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
# Date 1316343442 -7200
# Node ID 756f1f5798bfee10dcf9a684033a5d1e611224e0
# Parent  3740505b579cc41df170ab489b4221f1e99defef
Added (Properly) reasoner option (Pellet or HermiT)

diff -r 3740505b579c -r 756f1f5798bf OPPL/Tool.java
--- a/OPPL/Tool.java	Sun Sep 18 12:35:18 2011 +0200
+++ b/OPPL/Tool.java	Sun Sep 18 12:57:22 2011 +0200
@@ -125,7 +125,7 @@
 		// Parse the OPPL script
 		ParserFactory parserFactory = new ParserFactory(manager, OWL_ontology, reasoner); 
 		Logger logger = Logger.getLogger(Tool.class.getName());
-		Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy (Fixed in Galaxy by 2 > /dev/null)
+//		Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy (Fixed in Galaxy by 2 > /dev/null)
 		ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger);
 		OPPLParser opplparser = parserFactory.build(errorListener);
 		OPPLScript OPPLscript = opplparser.parse(OPPL_script_source);
diff -r 3740505b579c -r 756f1f5798bf OPPL/oppl.xml
--- a/OPPL/oppl.xml	Sun Sep 18 12:35:18 2011 +0200
+++ b/OPPL/oppl.xml	Sun Sep 18 12:57:22 2011 +0200
@@ -1,4 +1,4 @@
-<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.3">
+<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.4">
 	<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 command execution of the conditional is tacky, I think, but it works! -->
@@ -6,12 +6,12 @@
 	<!-- 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 -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
+		#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 $reasoner > $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 $reasoner > $output 2>/dev/null
 		#end if
 	</command>
 		
-	<!-- For big ontologies use something like java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar-->
+	<!-- For big ontologies use something like java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar -->
 
 	<inputs>
 		<param format="text" name="input" type="data" label="Input ontology file"/>
diff -r 3740505b579c -r 756f1f5798bf OPPL/oppl_galaxy_tool.jar
Binary file OPPL/oppl_galaxy_tool.jar has changed
diff -r 3740505b579c -r 756f1f5798bf OPPL/oppl_galaxy_tool_lib/HermiT.jar
Binary file OPPL/oppl_galaxy_tool_lib/HermiT.jar has changed