Mercurial > repos > mikel-egana-aranguren > oppl
comparison 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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18:d3616fac4ca5 | 19:cc270db37d33 |
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1 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.8"> | |
2 <description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description> | |
3 | |
4 <!-- 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 --> | |
5 <!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr --> | |
6 <!-- Testing with wrapper.sh but no success so far --> | |
7 | |
8 | |
9 | |
10 <!-- DEFAULT SETTINGS --> | |
11 | |
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 | |
14 <!--<command> | |
15 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null | |
16 </command>--> | |
17 | |
18 <!-- FACT++ --> | |
19 | |
20 <!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... --> | |
21 <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT --> | |
22 | |
23 <command> | |
24 java -Djava.library.path=${__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 | |
25 </command> | |
26 | |
27 | |
28 | |
29 | |
30 <!-- DEBUGGING --> | |
31 | |
32 <!-- 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 --> | |
33 | |
34 <!--<command> | |
35 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output | |
36 </command>--> | |
37 | |
38 | |
39 | |
40 | |
41 <inputs> | |
42 <param name="input" type="data" label="Input ontology file"/> | |
43 <param format="text" name="OPPL" type="data" label="OPPL file"/> | |
44 <param name="reasoner" type="select" label="Choose reasoner"> | |
45 <option value="Pellet" selected="true">Pellet</option> | |
46 <option value="HermiT">HermiT</option> | |
47 <option value="FaCTPlusPlus">FaCT++</option> | |
48 <option value="Elk">Elk (Not all axioms supported)</option> | |
49 </param> | |
50 <param name="format" type="select" label="Choose ontology output format"> | |
51 <option value="OWL" selected="true">OWL</option> | |
52 <option value="OBO">OBO</option> | |
53 </param> | |
54 </inputs> | |
55 <outputs> | |
56 <data format="text" name="output" /> | |
57 </outputs> | |
58 <!--<tests> | |
59 <test> | |
60 <param name="input" value="test.owl"/> | |
61 <param name="OPPL" value="test.oppl"/> | |
62 <param name="format" value="OWL"/> | |
63 <param name="reasoner" value="Pellet"/> | |
64 <output name="out_file" file="test_new.owl"/> | |
65 </test> | |
66 </tests>--> | |
67 <help> | |
68 | |
69 **About OPPL-Galaxy** | |
70 | |
71 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. | |
72 | |
73 **Usage** | |
74 | |
75 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. | |
76 | |
77 The reasoner can be Pellet, HermiT, FaCT++ or Elk. | |
78 | |
79 The output ontology can be OBO or OWL (RDF/XML). | |
80 | |
81 **More information** | |
82 | |
83 Galaxy public instances with OPPL-Galaxy pre-installed: | |
84 | |
85 http://sele.inf.um.es:9080/ | |
86 | |
87 http://linkeddata2.dia.fi.upm.es:8080 | |
88 | |
89 OPPL-Galaxy Examples: | |
90 | |
91 http://miuras.inf.um.es/OPPL-Galaxy/ | |
92 | |
93 OPPL examples: | |
94 | |
95 http://oppl2.sourceforge.net/taggedexamples/ | |
96 | |
97 Links of interest: | |
98 | |
99 http://oppl.sf.net/ | |
100 | |
101 http://www.w3.org/TR/owl2-manchester-syntax/ | |
102 | |
103 http://clarkparsia.com/pellet | |
104 | |
105 http://hermit-reasoner.com/ | |
106 | |
107 http://code.google.com/p/factplusplus/ | |
108 | |
109 http://code.google.com/p/elk-reasoner/ | |
110 | |
111 http://owlapi.sourceforge.net/ | |
112 | |
113 **Citation** | |
114 | |
115 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. | |
116 | |
117 **Contact** | |
118 | |
119 Please send any request or comment to mikel.egana.aranguren@gmail.com. | |
120 | |
121 </help> | |
122 | |
123 </tool> |