diff OPPL/oppl.xml @ 0:46b9d13a44fc

First commit (1.0.0)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/oppl.xml	Tue Sep 06 14:53:59 2011 -0400
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+<tool id="oppl" name="Execute an OPPL file against an OWL file" version="1.0.0">
+  <description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description>
+  <command>java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL > $output </command>
+  <inputs>
+    <param format="text" name="input" type="data" label="Source OWL file"/>
+    <param format="text" name="OPPL" type="data" label="OPPL file"/>
+  </inputs>
+  <outputs>
+    <data format="text" name="output" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input" value="test.owl"/>
+      <param name="OPPL" value="test.oppl"/>
+      <output name="out_file" file="test_new.owl"/>	
+    </test>
+  </tests>
+
+  <help>
+
+**About OPPL-Galaxy**
+
+  OPPL-Galaxy can be used to execute an OPPL script against an (OWL) 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.  
+
+**Formats**
+
+  OPPL-Galaxy uses the OWL API, and therefore can work with any ontology format that such API is able to load. That includes: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS.
+
+**Usage**
+
+  An ontology and an OPPL file are needed (test.owl and test.oppl can be used as samples). Load both with Get Data >> Upload File from your computer. 
+
+  Then execute the OPPL file against the OWL file with Ontology Pre Processor Language >> Execute an OPPL file against an OWL file.
+
+  This is the OPPL script provided in the bundle, test.oppl. Variables start with ?: 
+
+  ?whole:CLASS,
+  ?part:CLASS
+  SELECT
+  ?part SubClassOf part_of some ?whole WHERE ?part != Nothing
+  BEGIN
+  ADD ?part SubClassOf part_of only ?whole
+  END;
+
+**More information**
+
+  http://oppl2.sourceforge.net/
+
+  http://owlapi.sourceforge.net/
+
+  http://www.w3.org/TR/owl2-manchester-syntax/
+
+  http://clarkparsia.com/pellet
+
+**Features that will be implemented soon**
+
+  OWL import closure
+
+  Choose output format (Right now only OWL RDF/XML is available)
+
+  Choose reasoner (Right now only Pellet is available)
+
+**Contact**
+
+  Please send any request or comment to [e-mail].
+
+  </help>
+
+</tool>