comparison OPPL/oppl.xml @ 9:14bfd77f8520

Interface improved (Imports first) and proper handling of import/merge options added

8:40adbcb2a7cc

<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.5">
	<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 command execution of the conditional is tacky, I think, but it works! -->
	<!-- Galaxy is not happy with OPPL throwing info into stderr, and I have redirected stderr to /dev/null, which is a bad solution since OPPL galaxy does not inform properly when it fails -->
	<!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->

		  #end if
		#end if
	</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"/>

			<!-- EXPERIMENTS AND HOUSE KEEPING-->
			<!--<when value="imports_no"/> -->
			<!--<when value="imports_no">
				<param type="hidden" name="merged" value="no_merge"/>

				</conditional>-->  
				<!--<param format="text" name="merged" type="data" label="OWL "/>-->
				
            		</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="AddInferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/>
		<param name="merged" type="text" size="100" value="NoMerge" label="To merge the ontologies, type an URI for the new ontology (Leave NoMerge for not merging)" />
		<param name="reasoner" type="select" label="Choose reasoner">
			<option value="Pellet" selected="true">Pellet</option>
			<option value="HermiT">HermiT</option>
			<option value="FaCTPlusPlus">FaCT++</option>
		</param>

  http://clarkparsia.com/pellet

  http://hermit-reasoner.com/
  
  http://code.google.com/p/factplusplus/
  
  http://code.google.com/p/oboformat/

**Contact**

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

9:14bfd77f8520

<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.6">
	<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 command execution of the conditional is tacky, I think, but it works! -->
	<!-- Galaxy is not happy with OPPL throwing info into stderr, and I have redirected stderr to /dev/null, which is a bad solution since OPPL galaxy does not inform properly when it fails -->
	<!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->

		  #end if
		#end if
	</command>-->

	<inputs>
		<conditional name="import_opts">
			<param name="imports_select" type="boolean" value="False" truevalue="imports_yes" falsevalue="imports_no" label="Tick the box if the input ontology includes OWL imports"/>

			<!-- EXPERIMENTS AND HOUSE KEEPING-->
			<!--<when value="imports_no"/> -->
			<!--<when value="imports_no">
				<param type="hidden" name="merged" value="no_merge"/>

				</conditional>-->  
				<!--<param format="text" name="merged" type="data" label="OWL "/>-->
				
            		</when>
		</conditional>
		<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="AddInferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/>
		<param name="merged" type="text" size="100" value="NoMerge" label="To merge ontologies (If there are imports), type an URI for the new ontology (Leave NoMerge for not merging)" />
		<param name="reasoner" type="select" label="Choose reasoner">
			<option value="Pellet" selected="true">Pellet</option>
			<option value="HermiT">HermiT</option>
			<option value="FaCTPlusPlus">FaCT++</option>
		</param>

  http://clarkparsia.com/pellet

  http://hermit-reasoner.com/
  
  http://code.google.com/p/factplusplus/

**Contact**

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