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comparison ontologizer.xml @ 35:25c037153c9f

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Uploaded
author jorrit
date Tue, 26 Feb 2013 23:08:53 -0500
parents f475c42e642c
children 2ab168fd30a6
comparison
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34:f475c42e642c 35:25c037153c9f
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--> 4 <requirement type="set_environment">ONTOLOGIZER_JAR</requirement>
5 <requirement type="package" version="0.0.3">ontologizer-jar</requirement> 5 <requirement type="package" version="0.0.3">ontologizer-jar</requirement>
6 </requirements> 6 </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> 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>
8 <inputs> 8 <inputs>
9 <param name="go" type="data" format="obo" label="Gene Ontology File" /> 9 <param name="go" type="data" format="obo" label="Gene Ontology File" />
10 <param name="gaf" type="data" format="gaf" label="Gene Association File" /> 10 <param name="gaf" type="data" format="gaf" label="Gene Association File" />
11 <param name="population" type="data" format="tabular" label="Population Geneset File" /> 11 <param name="population" type="data" format="tabular" label="Population Geneset File" />
12 <param name="studyset" type="data" format="tabular" label="Study Geneset File" /> 12 <param name="studyset" type="data" format="tabular" label="Study Geneset File" />