diff OPPL/query.xml @ 17:c9e01f86b07c draft

New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files

--- a/OPPL/query.xml	Thu Aug 02 09:22:57 2012 +0200
+++ b/OPPL/query.xml	Mon Aug 20 11:39:56 2012 +0200
@@ -3,10 +3,10 @@
 
 	<!-- DEFAULT SETTINGS -->
 	
-	<!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory -->
+	<!-- For big ontologies I use -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory -->
 
 	<command>
-		java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output 
+		java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output 
 	</command>
 	
 	<!-- FACT++ -->
@@ -15,7 +15,7 @@
 	<!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT -->
 	
 	<!--<command>
-		java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output 
+		java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output 
 	</commadn>-->
 	
 
@@ -44,7 +44,7 @@
 	<outputs>
 		<data type="data" format="text" name="output" />
 	</outputs>
-	<tests>
+	<!--<tests>
 		<test>
 			<param name="input" value="OWLQueryGalaxyTest.owl"/>
 			<param name="query" value="p some d"/>
@@ -53,7 +53,7 @@
 			<param name="answer_format" value="URIfragment"/>
 			<output name="out_file" file="query_result"/>	
 		</test>
-	</tests>
+	</tests>-->
 	<help>
 
 **About Query-Galaxy**
@@ -62,7 +62,7 @@
 
 **Formats**
 
-  Inference-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.
+  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.
 
 **Contact**