Mercurial > repos > mikel-egana-aranguren > oppl
diff OPPL/oppl.xml @ 6:3740505b579c
Added reasoner option: Pellet or HermiT
| author | Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
|---|---|
| date | Sun, 18 Sep 2011 12:35:18 +0200 |
| parents | 68935f90c2db |
| children | 756f1f5798bf |
line wrap: on
line diff
--- a/OPPL/oppl.xml Sat Sep 17 13:41:28 2011 +0200 +++ b/OPPL/oppl.xml Sun Sep 18 12:35:18 2011 +0200 @@ -1,15 +1,17 @@ <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! --> + <!-- 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 --> <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 + #if $import_opts.imports_select==False #java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner > $output 2>/dev/null + #else #java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner > $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>--> + <!-- For big ontologies use something like java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar--> <inputs> <param format="text" name="input" type="data" label="Input ontology file"/> @@ -29,6 +31,10 @@ <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"/> + <param name="reasoner" type="select" label="Choose reasoner"> + <option value="Pellet" selected="true">Pellet</option> + <option value="HermiT">HermiT</option> + </param> </inputs> <outputs> @@ -38,9 +44,10 @@ <test> <param name="input" value="test.owl"/> <param name="OPPL" value="test.oppl"/> + <param name="imports" value="NoImports"/> <param name="format" value="OWL"/> <param name="inferred" value="False"/> - <param name="imports" value="NoImports"/> + <param name="reasoner" value="Pellet"/> <output name="out_file" file="test_new.owl"/> </test> </tests> @@ -48,7 +55,7 @@ **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 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. An OPPL script (See test.oppl) defines a query to be performed against the ontology, and some actions (Adding or removing axioms) 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 an ontology, saving time and effort. **Formats** @@ -70,6 +77,8 @@ The inferred subsumption axioms can be added to the output ontology as asserted axioms. + The reasoner can be Pellet or HermiT. Sometimes, if an execution fails it can be fixed by using a different reasoner. + **More information** http://oppl.sf.net/ @@ -80,6 +89,8 @@ http://clarkparsia.com/pellet + http://hermit-reasoner.com/ + **Contact** Please send any request or comment to mikel.egana.aranguren@gmail.com.