comparison OPPL/oppl.xml @ 5:68935f90c2db

Added OWL imports closure

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>

**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.  

  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/

**Contact**

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

  </help>

</tool>

5:68935f90c2db

<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.3">
	<description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description>

	<!-- The conditional is tacky, I think, but it works! -->

	<command>
		#if $import_opts.imports_select==False #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports > $output 2>/dev/null
		#else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports > $output 2>/dev/null
		#end if
	</command>
		
	<!--<command>java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports > $output 2>/dev/null</command>-->

	<inputs>
		<param format="text" name="input" type="data" label="Input ontology file"/>
		<param format="text" name="OPPL" type="data" label="OPPL file"/>
		<conditional name="import_opts">
			<param name="imports_select" type="boolean" value="False" truevalue="imports_yes" falsevalue="imports_no" label="Tick the box if the loaded ontology includes OWL imports"/>
			<when value="imports_no"/>
			<!--<when value="imports_no">
				<param type="hidden" name="imports" value="NoImports"/>
	    		</when>-->
			<when value="imports_yes">
                		<param format="text" name="imports" type="data" label="OWL imports URI mapping file"/>
            		</when>
		</conditional>
		<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"/>
			<param name="imports" value="NoImports"/>
			<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.  

  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, both available in the bundle). 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. A new output ontology will be generated.

  In case the loaded ontology includes OWL imports, a file that maps the imported ontologies' URIs to actual physical URIs is needed. The file (See the file test_URI_mappings provided in the bundle) follows the convention URI-tab-physical URI:
  
  http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_chebi_ontology	/home/pik/UPM/OPPL_galaxy/oppl/OPPL/chebi.owl

  http://purl.obolibrary.org/obo/UBERON_uberon	/home/pik/UPM/OPPL_galaxy/oppl/OPPL/cell.owl

  The output ontology can be OBO or OWL (RDF/XML).
 
  The inferred subsumption axioms can be added to the output ontology as asserted axioms. 

**More information**

  http://oppl.sf.net/

**Contact**

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

	</help>

</tool>