Mercurial > repos > mikel-egana-aranguren > oppl

comparison OPPL/oppl.xml @ 17:c9e01f86b07c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Mon, 20 Aug 2012 11:39:56 +0200
parents 68c4ae500a13
children d3616fac4ca5
comparison
equal deleted inserted replaced
16:6c25e717c896 17:c9e01f86b07c
7 7
8 8
9 9
10 <!-- DEFAULT SETTINGS --> 10 <!-- DEFAULT SETTINGS -->
11 11
12 <!-- For big ontologies I use -Xmx7000M -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 --> 12 <!-- 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 -->
13 13
14 <command> 14 <command>
15 java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null 15 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null
16 </command> 16 </command>
17 17
18 18
19 19
20 <!-- FACT++ --> 20 <!-- FACT++ -->
21 21
22 <!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... --> 22 <!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... -->
23 <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT --> 23 <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT -->
24 24
25 <!--<command> 25 <!--<command>
26 java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null 26 java -Djava.library.path=${__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
27 </commadn>--> 27 </commadn>-->
28 28
29 29
30 30
31 31
32 <!-- DEBUGGING --> 32 <!-- DEBUGGING -->
33 33
34 <!-- 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 --> 34 <!-- 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 -->
35 35
36 <!--<command> 36 <!--<command>
37 java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 37 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output
38 </command>--> 38 </command>-->
39 39
40 40
41 41
42 42
54 </param> 54 </param>
55 </inputs> 55 </inputs>
56 <outputs> 56 <outputs>
57 <data format="text" name="output" /> 57 <data format="text" name="output" />
58 </outputs> 58 </outputs>
59 <tests> 59 <!--<tests>
60 <test> 60 <test>
61 <param name="input" value="test.owl"/> 61 <param name="input" value="test.owl"/>
62 <param name="OPPL" value="test.oppl"/> 62 <param name="OPPL" value="test.oppl"/>
63 <param name="format" value="OWL"/> 63 <param name="format" value="OWL"/>
64 <param name="reasoner" value="Pellet"/> 64 <param name="reasoner" value="Pellet"/>
65 <output name="out_file" file="test_new.owl"/> 65 <output name="out_file" file="test_new.owl"/>
66 </test> 66 </test>
67 </tests> 67 </tests>-->
68 <help> 68 <help>
69 69
70 **About OPPL-Galaxy** 70 **About OPPL-Galaxy**
71 71
72 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 efforts. 72 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 efforts.