Mercurial > repos > mikel-egana-aranguren > oppl
diff oppl.xml @ 19:cc270db37d33 draft
Directories re-arranged
author | Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
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date | Sat, 06 Oct 2012 21:50:39 +0200 |
parents | OPPL/oppl.xml@d3616fac4ca5 |
children | 8d4bbaa99b4a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/oppl.xml Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,123 @@ +<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 instances with OPPL-Galaxy pre-installed: + + http://sele.inf.um.es:9080/ + + http://linkeddata2.dia.fi.upm.es:8080 + + OPPL-Galaxy Examples: + + http://miuras.inf.um.es/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>