annotate OPPL/oppl.xml @ 4:4f60202c58d9

Added option to push inferred subsumption axioms into output ontology

<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.2">
  <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 $format $inferred > $output </command>
  <!--<command>java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format > $output </command>-->
  <inputs>
    <param format="text" name="input" type="data" label="Input ontology file"/>
    <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>
    </param>
    <param name="inferred" type="boolean" value="False" truevalue="Add_inferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/>
  </inputs>
  <outputs>
    <data format="text" name="output" />
  </outputs>

  <tests>
    <test>
      <param name="input" value="test.owl"/>
      <param name="OPPL" value="test.oppl"/>
      <param name="format" value="OWL"/>
      <param name="inferred" value="False"/>
      <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 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 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).

**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://oppl.sf.net/

  http://owlapi.sourceforge.net/

  http://www.w3.org/TR/owl2-manchester-syntax/

  http://clarkparsia.com/pellet

**Contact**

  Please send any request or comment to [e-mail].

  </help>

</tool>