comparison OPPL/oppl.xml @ 4:4f60202c58d9

Added option to push inferred subsumption axioms into output ontology

3:5255f1333cc4

<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.1">
  <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 > $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>
  </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"/>
      <output name="out_file" file="test_new.owl"/>	
    </test>
  </tests>

  <help>

  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 reasoner (Right now only Pellet is available).

**Contact**

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

4:4f60202c58d9

<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>

  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].