Mercurial > repos > mikel-egana-aranguren > oppl

annotate oppl_query.xml @ 22:8d4bbaa99b4a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Minor changes for JBS paper
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Sun, 14 Oct 2012 17:21:51 +0200
parents cc270db37d33
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
1 <tool id="oppl_query" name="Perform an OPPL query against an ontology" version="1.0.1">
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
2 <description>It performs a query, expressed in OPPL Syntax, against an OWL ontology</description>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
3
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
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 -->
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
5 <!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
6 <!-- Testing with wrapper.sh but no success so far -->
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
7
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
8 <!-- DEFAULT SETTINGS -->
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
9
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
10 <!-- 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 -->
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
11
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
12 <command>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
13 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_query.jar $ontology $reasoner $answer_format $query > $output 2>/dev/null
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
14 </command>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
15
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
16 <!-- FACT++ -->
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
17
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
18 <!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... -->
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
19 <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT -->
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
20
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
21 <!--<command>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
22 java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_query.jar $ontology $reasoner $answer_format $query > $output 2>/dev/null
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
23 </command>-->
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
24
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
25
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
26 <inputs>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
27 <param name="ontology" type="data" label="Input ontology file"/>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
28 <param name="query" type="data" format="text" label="OPPL query file" />
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
29 <param name="reasoner" type="select" label="Choose reasoner">
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
30 <option value="Pellet" selected="true">Pellet</option>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
31 <option value="HermiT">HermiT</option>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
32 <option value="FaCTPlusPlus">FaCT++</option>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
33 <option value="Elk">Elk (Not all axioms supported)</option>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
34 </param>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
35 <param name="answer_format" type="select" label="Choose how to render the retrieved entities">
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
36 <option value="URI" selected="true">URI</option>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
37 <option value="URIfragment">URI fragment</option>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
38 <option value="URIfragment2OBO">OBO type URI fragment (e.g. GO_0000022 to GO:0000022)</option>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
39 </param>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
40 </inputs>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
41 <outputs>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
42 <data type="data" format="text" name="output" />
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
43 </outputs>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
44 <!--<tests>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
45 <test>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
46 <param name="input" value="test.owl"/>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
47 <param name="query" value="?p:OBJECTPROPERTY SELECT Transitive ?p "/>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
48 <param name="reasoner" value="Pellet"/>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
49 <param name="answer_format" value="URIfragment"/>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
50 <output name="out_file" file="query_result"/>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
51 </test>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
52 </tests>-->
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
53 <help>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
54
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
55 **About OPPL-Query-Galaxy**
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
56
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
57 OPPL-Query-Galaxy can be used to execute an OPPL query against an OWL ontology. The result is a two column table with the entities that have been bound by the variables.
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
58
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
59 **Usage**
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
60
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
61 An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. OPPL-Query-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-Query-Galaxy will try to resolve them.
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
62
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
63 An OPPL query must be provided in a file: an OPPL query is an OPPL script without the actions part, e.g. ?whole:CLASS, ?part:CLASS SELECT ?part SubClassOf part_of some ?whole WHERE ?part != Nothing.
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
64
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
65 The reasoner can be Pellet, HermiT, FaCT++ or Elk.
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
66
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
67 The returned entities can be rendered using their URI, their URI fragment, or OBO type URI fragment (e.g. GO_0000022 to GO:0000022).
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
68
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
69 **Contact**
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
70
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
71 Please send any request or comment to mikel.egana.aranguren@gmail.com.
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
72
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
73 </help>
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
74
cc270db37d33 Directories re-arranged
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
75 </tool>