diff OPPL/README @ 11:6ca67b155e32

Imports simplified, new tool for inference added

--- a/OPPL/README	Thu Jan 12 10:20:00 2012 +0100
+++ b/OPPL/README	Fri Mar 09 16:15:27 2012 +0100
@@ -1,9 +1,3 @@
-
-
-
-			===========
-			OPPL-GALAXY
-			===========
 
 
 
@@ -12,60 +6,52 @@
 
 1.- Stop Galaxy.
 
-2.- Copy oppl_galaxy_tool.jar, FaCT++-linux-v1.5.2/ FaCT++-OSX-v1.5.2/ 
-and oppl_galaxy_tool_lib/ to /galaxy-dist/tool-data/shared/jars/
+2.- Copy the following files and dirs to
+/galaxy-dist/tool-data/shared/jars/:
+
+oppl_galaxy_tool.jar
+oppl_galax_lib/
+FaCT++-linux-v1.5.2/ 
+FaCT++-OSX-v1.5.2/
+inference.jar
+inference_lib/ 
 
 3.- Create directory /galaxy-dist/tools/OPPL/
 
-4.- Copy oppl.xml to /galaxy-dist/tools/OPPL/
+4.- Copy oppl.xml and inference.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"/>
+    <tool file="OPPL/inference.xml"/>
   </section>
 
 6.- Start Galaxy.
 
 
 
-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 
-
-An ontology produced by another galaxy tool can also be used.
-
-Test.oppl and test.owl can be used as examples. More OPPL-Galaxy 
-examples can be obtained at http://miuras.inf.um.es/OPPL-Galaxy/, and 
-general OPPL script that may be useful to use with OPPL-Galaxy can be 
-obtained at http://oppl2.sourceforge.net/taggedexamples/.
-
-A public instance of Galaxy with pre-installed OPPL-Galaxy can be used 
-at http://sele.inf.um.es:8080/.
-
-
-
 FORESEEN FEATURES
 =================
 
-Choose which inferred axioms to add to the output ontology (Right now 
-only subsumption between named classes is available).
+OPPL:
+
+- Support for processing ontologies that import other ontologies loaded
+in galaxy.
+
+- Rendering definition (URI fragment, label, etc).
 
-Rendering definition (URI fragment, label, etc).
+- Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf
+cell).
+
+- OWLLink and Racer support.
+
 
-XML catalog support for imported URIs.
+Inference:
 
-OWLLink and Racer support.
+- DataPropertyAssertion, DataPropertyHierarchy, DifferentIndividuals,
+...
+
 
 
 
@@ -74,31 +60,14 @@
 
 Currently Galaxy interprets any information thrown to stderr as a tool
 error, which is bad since OPPL (And many other tools) throw info to 
-sdterr even if working properly. In OPPL Galaxy, stderr is redirected to 
-/dev/null to avoid the problem, but that means that OPPL Galaxy does not 
-fail gracefully (It simply stops). A wrapper will be implemented.
+sdterr even if working properly. In OPPL Galaxy, stderr is redirected
+to /dev/null to avoid the problem, but that means that OPPL Galaxy does
+not fail gracefully (It simply stops). A wrapper will be implemented.
 
 http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr
 
 
 
-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
 =======
 
@@ -118,10 +87,10 @@
 
 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.
+(OPPL|Inference)-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