annotate OPPL/README @ 4:4f60202c58d9

Added option to push inferred subsumption axioms into output ontology

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			OPPL-GALAXY
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INSTALLATION
============

1.- Stop galaxy.

2.- Copy oppl_galaxy_tool.jar and oppl_galaxy_tool_lib/ to 
/galaxy-dist/tool-data/shared/jars/.

3.- Create directory /galaxy-dist/tools/OPPL/.

4.- Copy oppl.xml to /galaxy-dist/tools/OPPL/.

5.- Add the following lines to /galaxy-dist/tool_conf.xml:

  <section name="Ontology Pre Processor Language" id="oppl">
    <tool file="OPPL/oppl.xml"/>
  </section>

6.- Start galaxy.

Note that if you want you can use any java parameter by editing oppl.xml
, eg: <command>java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 
-jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL 
$format > $output </command>



USAGE
=====

An ontology and an OPPL file are needed (test.owl and test.oppl can be 
used as samples). Load both:

Get Data 
	>> Upload File from your computer 

Then execute the OPPL file against the OWL file: 

Ontology Pre Processor Language
	>> Execute an OPPL file against an OWL file 


FORESEEN FEATURES
=================

OWL import closure.

Choose which inferred axioms to add to the output ontology (Right now 
only subsumption is available).

Choose reasoner (Right now only Pellet is available).



TESTS
=====

To run the functional test, first complete installation and then:

1.- Copy test.owl and test.oppl to /galaxy-dist/test-data/

2.- Add the following lines to /galaxy-dist/tool_conf.xml.sample

  <section name="Ontology Pre Processor Language" id="oppl">
    <tool file="OPPL/oppl.xml"/>
  </section>

3.- Execute /galaxy-dist/run_functional_tests.sh -id oppl



CONTACT
=======

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



ACKNOWLEDGEMENTS
================

This work is funded by the Marie Curie Cofund program of the EU, FP7.



COPYRIGHT AND LICENSE
=====================

Copyright (c) 2011 Mikel Egaña Aranguren. 

OPPL-Galaxy is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

OPPL, OWL API and Pellet have their own licenses.

Galaxy is distributed as open source under the conditions of the 
Academic Free License (http://www.opensource.org/licenses/academic.php).