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comparison OPPL/oppl.xml @ 5:68935f90c2db

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Added OWL imports closure
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Sat, 17 Sep 2011 13:41:28 +0200
parents 4f60202c58d9
children 3740505b579c
comparison
equal deleted inserted replaced
4:4f60202c58d9 5:68935f90c2db
1 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.2"> 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 <command>java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred > $output </command>
4 <!--<command>java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format > $output </command>-->
5 <inputs>
6 <param format="text" name="input" type="data" label="Input ontology file"/>
7 <param format="text" name="OPPL" type="data" label="OPPL file"/>
8 <param name="format" type="select" label="Choose ontology output format">
9 <option value="OWL" selected="true">OWL</option>
10 <option value="OBO">OBO</option>
11 </param>
12 <param name="inferred" type="boolean" value="False" truevalue="Add_inferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/>
13 </inputs>
14 <outputs>
15 <data format="text" name="output" />
16 </outputs>
17 3
18 <tests> 4 <!-- The conditional is tacky, I think, but it works! -->
19 <test>
20 <param name="input" value="test.owl"/>
21 <param name="OPPL" value="test.oppl"/>
22 <param name="format" value="OWL"/>
23 <param name="inferred" value="False"/>
24 <output name="out_file" file="test_new.owl"/>
25 </test>
26 </tests>
27 5
28 <help> 6 <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
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
9 #end if
10 </command>
11
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>-->
13
14 <inputs>
15 <param format="text" name="input" type="data" label="Input ontology file"/>
16 <param format="text" name="OPPL" type="data" label="OPPL file"/>
17 <conditional name="import_opts">
18 <param name="imports_select" type="boolean" value="False" truevalue="imports_yes" falsevalue="imports_no" label="Tick the box if the loaded ontology includes OWL imports"/>
19 <when value="imports_no"/>
20 <!--<when value="imports_no">
21 <param type="hidden" name="imports" value="NoImports"/>
22 </when>-->
23 <when value="imports_yes">
24 <param format="text" name="imports" type="data" label="OWL imports URI mapping file"/>
25 </when>
26 </conditional>
27 <param name="format" type="select" label="Choose ontology output format">
28 <option value="OWL" selected="true">OWL</option>
29 <option value="OBO">OBO</option>
30 </param>
31 <param name="inferred" type="boolean" value="False" truevalue="Add_inferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/>
32
33 </inputs>
34 <outputs>
35 <data format="text" name="output" />
36 </outputs>
37 <tests>
38 <test>
39 <param name="input" value="test.owl"/>
40 <param name="OPPL" value="test.oppl"/>
41 <param name="format" value="OWL"/>
42 <param name="inferred" value="False"/>
43 <param name="imports" value="NoImports"/>
44 <output name="out_file" file="test_new.owl"/>
45 </test>
46 </tests>
47 <help>
29 48
30 **About OPPL-Galaxy** 49 **About OPPL-Galaxy**
31 50
32 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. 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.
33 52
35 54
36 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). 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).
37 56
38 **Usage** 57 **Usage**
39 58
40 An ontology and an OPPL file are needed (test.owl and test.oppl can be used as samples). Load both with Get Data >> Upload File from your computer. 59 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.
41 60
42 Then execute the OPPL file against the OWL file with Ontology Pre Processor Language >> Execute an OPPL file against an OWL file. 61 Then execute the OPPL file against the OWL file with Ontology Pre Processor Language >> Execute an OPPL file against an OWL file. A new output ontology will be generated.
43 62
44 This is the OPPL script provided in the bundle, test.oppl (Variables start with ?): 63 In case the loaded ontology includes OWL imports, a file that maps the imported ontologies' URIs to actual physical URIs is needed. The file (See the file test_URI_mappings provided in the bundle) follows the convention URI-tab-physical URI:
64
65 http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_chebi_ontology /home/pik/UPM/OPPL_galaxy/oppl/OPPL/chebi.owl
45 66
46 ?whole:CLASS, 67 http://purl.obolibrary.org/obo/UBERON_uberon /home/pik/UPM/OPPL_galaxy/oppl/OPPL/cell.owl
47 ?part:CLASS 68
48 SELECT 69 The output ontology can be OBO or OWL (RDF/XML).
49 ?part SubClassOf part_of some ?whole WHERE ?part != Nothing 70
50 BEGIN 71 The inferred subsumption axioms can be added to the output ontology as asserted axioms.
51 ADD ?part SubClassOf part_of only ?whole
52 END;
53 72
54 **More information** 73 **More information**
55 74
56 http://oppl.sf.net/ 75 http://oppl.sf.net/
57 76
63 82
64 **Contact** 83 **Contact**
65 84
66 Please send any request or comment to mikel.egana.aranguren@gmail.com. 85 Please send any request or comment to mikel.egana.aranguren@gmail.com.
67 86
68 </help> 87 </help>
69 88
70 </tool> 89 </tool>