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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>