Mercurial > repos > mikel-egana-aranguren > oppl

annotate OPPL/oppl.xml @ 8:40adbcb2a7cc

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Added merge function and FaCT++ support. Improved OBO render
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Tue, 11 Oct 2011 11:09:52 +0200
parents 756f1f5798bf
children 14bfd77f8520
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
1 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.5">
5
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
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>
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
3
6
3740505b579c Added reasoner option: Pellet or HermiT
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 5
diff changeset
4 <!-- The command execution of the conditional is tacky, I think, but it works! -->
3740505b579c Added reasoner option: Pellet or HermiT
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 5
diff changeset
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 -->
3740505b579c Added reasoner option: Pellet or HermiT
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 5
diff changeset
6 <!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
7
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
9 <!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will -->
5
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
10
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
11 <command>
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
12 #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 $reasoner NoMerge > $output 2>/dev/null
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
13 #else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner $merged > $output 2>/dev/null
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
14 #end if
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
15 </command>
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
16
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
17
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
18 <!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the one 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, ...... -->
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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 -->
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
20
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
21 <!--<command>
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
22 #if $import_opts.imports_select==False #java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner NoMerge > $output 2>/dev/null
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
23 #else #java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner $merged > $output 2>/dev/null
5
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
24 #end if
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
25 </command>-->
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
26
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
27
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
28 <!-- For debugging simply remove 2>/dev/null Or uncomment bellow. It will fail always (Due to OPPL messages) but at least it will be informative -->
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
29
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
30 <!--<command>
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
31 #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 $reasoner no_merge > $output
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
32 #else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner $merged > $output
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
33 #end if
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
34 </command>-->
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
35
5
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
36
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
37 <!-- EXPERIMENTS AND HOUSE KEEPING-->
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
38 <!--<command>java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner $merged > $output 2>/dev/null</command> -->
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
39 <!--<command>
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
40 #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 $reasoner NoMerge > $output 2>/dev/null
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
41 #else
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
42 #if $merge_opts.merge_select==False #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner NoMerge > $output 2>/dev/null
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
43 #else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner $merged > $output 2>/dev/null
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
44 #end if
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
45 #end if
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
46 </command>-->
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
47
5
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
48 <inputs>
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
49 <param format="text" name="input" type="data" label="Input ontology file"/>
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
50 <param format="text" name="OPPL" type="data" label="OPPL file"/>
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
51 <conditional name="import_opts">
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
52 <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"/>
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
53
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
54 <!-- EXPERIMENTS AND HOUSE KEEPING-->
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
55 <!--<when value="imports_no"/> -->
5
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
56 <!--<when value="imports_no">
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
57 <param type="hidden" name="merged" value="no_merge"/>
5
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
58 </when>-->
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
59
5
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
60 <when value="imports_yes">
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
61
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
62 <param format="text" name="imports" type="data" label="OWL imports URI mapping file"/>
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
63
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
64 <!-- EXPERIMENTS AND HOUSE KEEPING-->
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
65 <!--<conditional name="merge_opts">
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
66 <param name="merge_select" type="boolean" value="False" truevalue="merge_yes" falsevalue="merge_no" label="Tick the box to merge ontologies"/>
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
67 <when value="merge_yes">
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
68 <param name="merged" type="text" size="100" value="http://oppl-galaxy/merged" label="Type an URI or use the default URI" />
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
69 </when>
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
70 </conditional>-->
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
71 <!--<param format="text" name="merged" type="data" label="OWL "/>-->
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
72
5
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
73 </when>
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
74 </conditional>
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
75 <param name="format" type="select" label="Choose ontology output format">
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
76 <option value="OWL" selected="true">OWL</option>
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
77 <option value="OBO">OBO</option>
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
78 </param>
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
79 <param name="inferred" type="boolean" value="False" truevalue="AddInferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/>
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
80 <param name="merged" type="text" size="100" value="NoMerge" label="To merge the ontologies, type an URI for the new ontology (Leave NoMerge for not merging)" />
6
3740505b579c Added reasoner option: Pellet or HermiT
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 5
diff changeset
81 <param name="reasoner" type="select" label="Choose reasoner">
3740505b579c Added reasoner option: Pellet or HermiT
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 5
diff changeset
82 <option value="Pellet" selected="true">Pellet</option>
3740505b579c Added reasoner option: Pellet or HermiT
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 5
diff changeset
83 <option value="HermiT">HermiT</option>
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
84 <option value="FaCTPlusPlus">FaCT++</option>
6
3740505b579c Added reasoner option: Pellet or HermiT
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 5
diff changeset
85 </param>
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
86
5
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
87 </inputs>
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
88 <outputs>
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
89 <data format="text" name="output" />
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
90 </outputs>
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
91 <tests>
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
92 <test>
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
93 <param name="input" value="test.owl"/>
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
94 <param name="OPPL" value="test.oppl"/>
6
3740505b579c Added reasoner option: Pellet or HermiT
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 5
diff changeset
95 <param name="imports" value="NoImports"/>
5
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
96 <param name="format" value="OWL"/>
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
97 <param name="inferred" value="False"/>
6
3740505b579c Added reasoner option: Pellet or HermiT
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 5
diff changeset
98 <param name="reasoner" value="Pellet"/>
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
99 <param name="merged" value="no_merge"/>
5
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
100 <output name="out_file" file="test_new.owl"/>
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
101 </test>
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
102 </tests>
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
103 <help>
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
104
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
105 **About OPPL-Galaxy**
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
106
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
107 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.
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
108
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
109 **Formats**
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
110
3
5255f1333cc4 Version 1.0.1
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 0
diff changeset
111 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).
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
112
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
113 **Usage**
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
114
5
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
115 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.
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
116
5
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
117 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.
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
118
5
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
119 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:
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
120
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
121 http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_chebi_ontology /home/pik/UPM/OPPL_galaxy/oppl/OPPL/chebi.owl
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
122
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
123 http://purl.obolibrary.org/obo/UBERON_uberon /home/pik/UPM/OPPL_galaxy/oppl/OPPL/cell.owl
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
124
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
125 The output ontology can be OBO or OWL (RDF/XML).
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
126
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
127 The inferred subsumption axioms can be added to the output ontology as asserted axioms.
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
128
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
129 The reasoner can be Pellet, HermiT FaCT++. Sometimes, if an execution fails it can be fixed by using a different reasoner.
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
130
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
131 If OWL imports are used, all the ontologies (Main one and imported ones) can be merged in a single ontology for the output.
6
3740505b579c Added reasoner option: Pellet or HermiT
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 5
diff changeset
132
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
133 **More information**
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
134
4
4f60202c58d9 Added option to push inferred subsumption axioms into output ontology
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 3
diff changeset
135 http://oppl.sf.net/
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
136
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
137 http://owlapi.sourceforge.net/
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
138
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
139 http://www.w3.org/TR/owl2-manchester-syntax/
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
140
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
141 http://clarkparsia.com/pellet
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
142
6
3740505b579c Added reasoner option: Pellet or HermiT
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 5
diff changeset
143 http://hermit-reasoner.com/
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
144
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
145 http://code.google.com/p/factplusplus/
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
146
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
diff changeset
147 http://code.google.com/p/oboformat/
6
3740505b579c Added reasoner option: Pellet or HermiT
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 5
diff changeset
148
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
149 **Contact**
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
150
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
151 Please send any request or comment to mikel.egana.aranguren@gmail.com.
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
152
5
68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
diff changeset
153 </help>
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
154
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
155 </tool>