Mercurial > repos > jorrit > obotools
comparison ontologizer.xml @ 36:2ab168fd30a6
Uploaded
| author | jorrit |
|---|---|
| date | Tue, 26 Feb 2013 23:25:57 -0500 |
| parents | 25c037153c9f |
| children | 2633a06624e4 |
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| 35:25c037153c9f | 36:2ab168fd30a6 |
|---|---|
| 1 <tool id="ontologizer" name="ontologizer" version="0.0.16"> | 1 <tool id="ontologizer" name="ontologizer" version="0.0.16"> |
| 2 <description>from http://compbio.charite.de/contao/</description> | 2 <description>from http://compbio.charite.de/contao/</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="set_environment">ONTOLOGIZER_JAR</requirement> | |
| 5 <requirement type="package" version="0.0.3">ontologizer-jar</requirement> | 4 <requirement type="package" version="0.0.3">ontologizer-jar</requirement> |
| 6 </requirements> | 5 </requirements> |
| 7 <command>java -Xmx2G -jar \$ONTOLOGIZER_JAR --go $go --association $gaf --population $population --studyset $studyset --dot 0.05 --mtc "$mtc" --calculation "$calc"; mv table-*.txt $tablefile; mv view-*.dot $dotfile</command> | 6 <command>java -Xmx2G -jar \$ONTOLOGIZER_JAR --go $go --association $gaf --population $population --studyset $studyset --dot 0.05 --mtc "$mtc" --calculation "$calc"; echo moving files; mv table-*.txt $tablefile; mv view-*.dot $dotfile; echo moving files to $dotfile</command> |
| 8 <inputs> | 7 <inputs> |
| 9 <param name="go" type="data" format="obo" label="Gene Ontology File" /> | 8 <param name="go" type="data" format="obo" label="Gene Ontology File" /> |
| 10 <param name="gaf" type="data" format="gaf" label="Gene Association File" /> | 9 <param name="gaf" type="data" format="gaf" label="Gene Association File" /> |
| 11 <param name="population" type="data" format="tabular" label="Population Geneset File" /> | 10 <param name="population" type="data" format="tabular" label="Population Geneset File" /> |
| 12 <param name="studyset" type="data" format="tabular" label="Study Geneset File" /> | 11 <param name="studyset" type="data" format="tabular" label="Study Geneset File" /> |