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annotate OPPL/oppl.xml @ 9:14bfd77f8520

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Interface improved (Imports first) and proper handling of import/merge options added
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Tue, 18 Oct 2011 10:30:16 +0200
parents 40adbcb2a7cc
children 3f31c0eb7539
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14bfd77f8520 Interface improved (Imports first) and proper handling of import/merge options added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 8
diff changeset
1 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.6">
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
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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
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 5
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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
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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
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6 <!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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9 <!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will -->
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
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68935f90c2db Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
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11 <command>
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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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
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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
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14 #end if
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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15 </command>
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parents: 7
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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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
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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 -->
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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21 <!--<command>
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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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 > $output 2>/dev/null
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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23 #else #java -Djava.library.path=${__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
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 4
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24 #end if
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parents: 7
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25 </command>-->
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parents: 7
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parents: 7
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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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 -->
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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30 <!--<command>
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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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
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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
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33 #end if
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parents: 7
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34 </command>-->
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parents: 7
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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37 <!-- EXPERIMENTS AND HOUSE KEEPING-->
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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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
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39 <!--<command>
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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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
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41 #else
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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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
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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
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44 #end if
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parents: 7
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45 #end if
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 7
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46 </command>-->
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47
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48 <inputs>
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49 <conditional name="import_opts">
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50 <param name="imports_select" type="boolean" value="False" truevalue="imports_yes" falsevalue="imports_no" label="Tick the box if the input ontology includes OWL imports"/>
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parents: 7
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52 <!-- EXPERIMENTS AND HOUSE KEEPING-->
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parents: 7
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53 <!--<when value="imports_no"/> -->
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54 <!--<when value="imports_no">
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55 <param type="hidden" name="merged" value="no_merge"/>
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parents: 4
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56 </when>-->
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57
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58 <when value="imports_yes">
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60 <param format="text" name="imports" type="data" label="OWL imports URI mapping file"/>
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parents: 7
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62 <!-- EXPERIMENTS AND HOUSE KEEPING-->
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parents: 7
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63 <!--<conditional name="merge_opts">
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parents: 7
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64 <param name="merge_select" type="boolean" value="False" truevalue="merge_yes" falsevalue="merge_no" label="Tick the box to merge ontologies"/>
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parents: 7
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65 <when value="merge_yes">
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66 <param name="merged" type="text" size="100" value="http://oppl-galaxy/merged" label="Type an URI or use the default URI" />
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parents: 7
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67 </when>
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parents: 7
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68 </conditional>-->
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parents: 7
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69 <!--<param format="text" name="merged" type="data" label="OWL "/>-->
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70
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71 </when>
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72 </conditional>
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73 <param format="text" name="input" type="data" label="Input ontology file"/>
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74 <param format="text" name="OPPL" type="data" label="OPPL file"/>
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75 <param name="format" type="select" label="Choose ontology output format">
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76 <option value="OWL" selected="true">OWL</option>
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77 <option value="OBO">OBO</option>
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78 </param>
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79 <param name="inferred" type="boolean" value="False" truevalue="AddInferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/>
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80 <param name="merged" type="text" size="100" value="NoMerge" label="To merge ontologies (If there are imports), type an URI for the new ontology (Leave NoMerge for not merging)" />
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81 <param name="reasoner" type="select" label="Choose reasoner">
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82 <option value="Pellet" selected="true">Pellet</option>
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83 <option value="HermiT">HermiT</option>
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84 <option value="FaCTPlusPlus">FaCT++</option>
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85 </param>
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86
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87 </inputs>
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88 <outputs>
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89 <data format="text" name="output" />
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90 </outputs>
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91 <tests>
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92 <test>
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93 <param name="input" value="test.owl"/>
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94 <param name="OPPL" value="test.oppl"/>
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95 <param name="imports" value="NoImports"/>
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96 <param name="format" value="OWL"/>
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97 <param name="inferred" value="False"/>
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98 <param name="reasoner" value="Pellet"/>
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99 <param name="merged" value="no_merge"/>
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100 <output name="out_file" file="test_new.owl"/>
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101 </test>
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102 </tests>
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103 <help>
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104
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105 **About OPPL-Galaxy**
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106
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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.
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108
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109 **Formats**
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110
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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).
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112
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113 **Usage**
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114
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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.
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116
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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.
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118
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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:
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120
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121 http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_chebi_ontology /home/pik/UPM/OPPL_galaxy/oppl/OPPL/chebi.owl
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122
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123 http://purl.obolibrary.org/obo/UBERON_uberon /home/pik/UPM/OPPL_galaxy/oppl/OPPL/cell.owl
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124
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125 The output ontology can be OBO or OWL (RDF/XML).
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126
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127 The inferred subsumption axioms can be added to the output ontology as asserted axioms.
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128
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129 The reasoner can be Pellet, HermiT FaCT++. Sometimes, if an execution fails it can be fixed by using a different reasoner.
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130
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131 If OWL imports are used, all the ontologies (Main one and imported ones) can be merged in a single ontology for the output.
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132
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133 **More information**
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134
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135 http://oppl.sf.net/
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136
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137 http://owlapi.sourceforge.net/
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138
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139 http://www.w3.org/TR/owl2-manchester-syntax/
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140
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141 http://clarkparsia.com/pellet
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142
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143 http://hermit-reasoner.com/
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144
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145 http://code.google.com/p/factplusplus/
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146
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147 **Contact**
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148
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149 Please send any request or comment to mikel.egana.aranguren@gmail.com.
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150
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151 </help>
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152
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153 </tool>