Mercurial > repos > mikel-egana-aranguren > oppl
view oppl.xml @ 22:8d4bbaa99b4a draft
Minor changes for JBS paper
author | Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
---|---|
date | Sun, 14 Oct 2012 17:21:51 +0200 |
parents | cc270db37d33 |
children | 707c3654df66 |
line wrap: on
line source
<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.8"> <description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description> <!-- 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 --> <!-- Testing with wrapper.sh but no success so far --> <!-- DEFAULT SETTINGS --> <!-- For big ontologies I use -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory --> <!--<command> java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null </command>--> <!-- FACT++ --> <!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... --> <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT --> <command> java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null </command> <!-- DEBUGGING --> <!-- For debugging simply remove 2>/dev/null Or uncomment bellow (And comment the default settings above). It will fail always (Due to OPPL messages) but at least it will be informative --> <!--<command> java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output </command>--> <inputs> <param name="input" type="data" label="Input ontology file"/> <param format="text" name="OPPL" type="data" label="OPPL file"/> <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> <option value="Elk">Elk (Not all axioms supported)</option> </param> <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"/> <param name="reasoner" value="Pellet"/> <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. 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 energy. **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, or redirect from another Galaxy tool. 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. In case the loaded ontology includes OWL imports, OPPL-Galaxy will try to resolve them. The reasoner can be Pellet, HermiT, FaCT++ or Elk. The output ontology can be OBO or OWL (RDF/XML). **More information** Galaxy public instance with OPPL-Galaxy pre-installed: http://biordf.org:8080/ OPPL-Galaxy Examples: http://biordf.org/OPPL-Galaxy/ OPPL examples: http://oppl2.sourceforge.net/taggedexamples/ Links of interest: http://oppl.sf.net/ http://www.w3.org/TR/owl2-manchester-syntax/ http://clarkparsia.com/pellet http://hermit-reasoner.com/ http://code.google.com/p/factplusplus/ http://code.google.com/p/elk-reasoner/ http://owlapi.sourceforge.net/ **Citation** Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Erick Antezana. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL. In Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences, SWAT4LS 2011, pages 12–19, ACM 2012. **Contact** Please send any request or comment to mikel.egana.aranguren@gmail.com. </help> </tool>