diff OPPL/oppl.xml @ 18:d3616fac4ca5 draft

Elk support added

--- a/OPPL/oppl.xml	Mon Aug 20 11:39:56 2012 +0200
+++ b/OPPL/oppl.xml	Thu Sep 20 12:46:36 2012 +0200
@@ -11,20 +11,18 @@
 	
 	<!-- 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 -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null
-	</command>
-	
-	
+	<!--<command>
+	  java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null 
+	</command>-->
 	
 	<!-- FACT++ -->
 	
 	<!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... -->
 	<!-- 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>
+	<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_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null
-	</commadn>-->
+	</command>
 
 	
 	
@@ -42,12 +40,13 @@
 
 	<inputs>
 		<param name="input" type="data" label="Input ontology file"/>
+		<param format="text" name="OPPL" type="data" label="OPPL file"/>
 		<param name="reasoner" type="select" label="Choose reasoner">
 			<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 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>
@@ -69,29 +68,21 @@
 
 **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. 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 efforts.  
-
-**Formats**
-
-  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).
+  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 energy.  
 
 **Usage**
 
-  An ontology and an OPPL file are needed (test.owl and test.oppl can be used as samples, both available in the bundle). Load both with Get Data >> Upload File from your computer, or redirect from another Galaxy tool.
-
-  Then execute the OPPL file against the OWL file with Ontology Pre Processor Language >> Execute an OPPL file against an OWL file. A new output ontology will be generated.
+  An ontology and an OPPL file are needed (test.owl and test.oppl can be used as samples, both available in the bundle). Load both with Get Data >> Upload File from your computer, or redirect from another Galaxy tool. 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. In case the loaded ontology includes OWL imports, OPPL-Galaxy will try to resolve them.
+  
+  The reasoner can be Pellet, HermiT, FaCT++ or Elk.
 
-  In case the loaded ontology includes OWL imports, OPPL-Galaxy will try to resolve them. 
-
-  The output ontology can be OBO or OWL (RDF/XML).
-   
-  The reasoner can be Pellet, HermiT FaCT++. Sometimes, if an execution fails it can be fixed by using a different reasoner. 
+  The output ontology can be OBO or OWL (RDF/XML). 
 
 **More information**
 
   Galaxy public instances with OPPL-Galaxy pre-installed:
   
-  http://sele.inf.um.es:8080/
+  http://sele.inf.um.es:9080/
   
   http://linkeddata2.dia.fi.upm.es:8080
   
@@ -107,8 +98,6 @@
 
   http://oppl.sf.net/
 
-  http://owlapi.sourceforge.net/
-
   http://www.w3.org/TR/owl2-manchester-syntax/
 
   http://clarkparsia.com/pellet
@@ -117,9 +106,13 @@
   
   http://code.google.com/p/factplusplus/
   
+  http://code.google.com/p/elk-reasoner/
+  
+  http://owlapi.sourceforge.net/
+  
 **Citation**
 
-  Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis and Erick Antezana. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL. SWAT4LS 2011.
+  Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Erick Antezana. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL. In Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences, SWAT4LS 2011, pages 12–19, ACM 2012.
 
 **Contact**