Mercurial > repos > mikel-egana-aranguren > oppl
comparison OPPL/oppl.xml @ 7:756f1f5798bf
Added (Properly) reasoner option (Pellet or HermiT)
| author | Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
|---|---|
| date | Sun, 18 Sep 2011 12:57:22 +0200 |
| parents | 3740505b579c |
| children | 40adbcb2a7cc |
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| 6:3740505b579c | 7:756f1f5798bf |
|---|---|
| 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="1.0.4"> |
| 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 command execution of 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 --> | 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 --> | 6 <!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr --> |
| 7 | 7 |
| 8 <command> | 8 <command> |
| 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 | 9 #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 > $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 | 10 #else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner > $output 2>/dev/null |
| 11 #end if | 11 #end if |
| 12 </command> | 12 </command> |
| 13 | 13 |
| 14 <!-- For big ontologies use something like java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar--> | 14 <!-- For big ontologies use something like java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar --> |
| 15 | 15 |
| 16 <inputs> | 16 <inputs> |
| 17 <param format="text" name="input" type="data" label="Input ontology file"/> | 17 <param format="text" name="input" type="data" label="Input ontology file"/> |
| 18 <param format="text" name="OPPL" type="data" label="OPPL file"/> | 18 <param format="text" name="OPPL" type="data" label="OPPL file"/> |
| 19 <conditional name="import_opts"> | 19 <conditional name="import_opts"> |