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comparison OPPL/oppl.xml @ 6:3740505b579c

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Added reasoner option: Pellet or HermiT
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Sun, 18 Sep 2011 12:35:18 +0200
parents 68935f90c2db
children 756f1f5798bf
comparison
equal deleted inserted replaced
5:68935f90c2db 6:3740505b579c
1 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.3"> 1 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.3">
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> 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 3
4 <!-- The conditional is tacky, I think, but it works! --> 4 <!-- The command execution of the conditional is tacky, I think, but it works! -->
5 <!-- 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 -->
6 <!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->
5 7
6 <command> 8 <command>
7 #if $import_opts.imports_select==False #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports > $output 2>/dev/null 9 #if $import_opts.imports_select==False #java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner > $output 2>/dev/null
8 #else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports > $output 2>/dev/null 10 #else #java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner > $output 2>/dev/null
9 #end if 11 #end if
10 </command> 12 </command>
11 13
12 <!--<command>java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports > $output 2>/dev/null</command>--> 14 <!-- For big ontologies use something like java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar-->
13 15
14 <inputs> 16 <inputs>
15 <param format="text" name="input" type="data" label="Input ontology file"/> 17 <param format="text" name="input" type="data" label="Input ontology file"/>
16 <param format="text" name="OPPL" type="data" label="OPPL file"/> 18 <param format="text" name="OPPL" type="data" label="OPPL file"/>
17 <conditional name="import_opts"> 19 <conditional name="import_opts">
27 <param name="format" type="select" label="Choose ontology output format"> 29 <param name="format" type="select" label="Choose ontology output format">
28 <option value="OWL" selected="true">OWL</option> 30 <option value="OWL" selected="true">OWL</option>
29 <option value="OBO">OBO</option> 31 <option value="OBO">OBO</option>
30 </param> 32 </param>
31 <param name="inferred" type="boolean" value="False" truevalue="Add_inferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/> 33 <param name="inferred" type="boolean" value="False" truevalue="Add_inferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/>
34 <param name="reasoner" type="select" label="Choose reasoner">
35 <option value="Pellet" selected="true">Pellet</option>
36 <option value="HermiT">HermiT</option>
37 </param>
32 38
33 </inputs> 39 </inputs>
34 <outputs> 40 <outputs>
35 <data format="text" name="output" /> 41 <data format="text" name="output" />
36 </outputs> 42 </outputs>
37 <tests> 43 <tests>
38 <test> 44 <test>
39 <param name="input" value="test.owl"/> 45 <param name="input" value="test.owl"/>
40 <param name="OPPL" value="test.oppl"/> 46 <param name="OPPL" value="test.oppl"/>
47 <param name="imports" value="NoImports"/>
41 <param name="format" value="OWL"/> 48 <param name="format" value="OWL"/>
42 <param name="inferred" value="False"/> 49 <param name="inferred" value="False"/>
43 <param name="imports" value="NoImports"/> 50 <param name="reasoner" value="Pellet"/>
44 <output name="out_file" file="test_new.owl"/> 51 <output name="out_file" file="test_new.owl"/>
45 </test> 52 </test>
46 </tests> 53 </tests>
47 <help> 54 <help>
48 55
49 **About OPPL-Galaxy** 56 **About OPPL-Galaxy**
50 57
51 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 (Adding or removing axioms). An OPPL script (See bellow or test.oppl) defines a query to be performed against the ontology, and some actions 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 a given ontology, saving time and effort. 58 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 effort.
52 59
53 **Formats** 60 **Formats**
54 61
55 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. The available output formats are OBO flat file and OWL (RDF/XML). 62 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. The available output formats are OBO flat file and OWL (RDF/XML).
56 63
68 75
69 The output ontology can be OBO or OWL (RDF/XML). 76 The output ontology can be OBO or OWL (RDF/XML).
70 77
71 The inferred subsumption axioms can be added to the output ontology as asserted axioms. 78 The inferred subsumption axioms can be added to the output ontology as asserted axioms.
72 79
80 The reasoner can be Pellet or HermiT. Sometimes, if an execution fails it can be fixed by using a different reasoner.
81
73 **More information** 82 **More information**
74 83
75 http://oppl.sf.net/ 84 http://oppl.sf.net/
76 85
77 http://owlapi.sourceforge.net/ 86 http://owlapi.sourceforge.net/
78 87
79 http://www.w3.org/TR/owl2-manchester-syntax/ 88 http://www.w3.org/TR/owl2-manchester-syntax/
80 89
81 http://clarkparsia.com/pellet 90 http://clarkparsia.com/pellet
82 91
92 http://hermit-reasoner.com/
93
83 **Contact** 94 **Contact**
84 95
85 Please send any request or comment to mikel.egana.aranguren@gmail.com. 96 Please send any request or comment to mikel.egana.aranguren@gmail.com.
86 97
87 </help> 98 </help>