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annotate ontologizer.xml @ 32:f0048a544d61

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author jorrit
date Tue, 26 Feb 2013 22:50:29 -0500
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1 <tool id="ontologizer" name="ontologizer" version="0.0.16">
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2 <description>from http://compbio.charite.de/contao/</description>
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3 <requirements>
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4 <requirement type="package" version="0.0.3">ontologizer-jar</requirement>
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5 </requirements>
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6 <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>
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7 <inputs>
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8 <param name="go" type="data" format="obo" label="Gene Ontology File" />
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9 <param name="gaf" type="data" format="gaf" label="Gene Association File" />
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10 <param name="population" type="data" format="tabular" label="Population Geneset File" />
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11 <param name="studyset" type="data" format="tabular" label="Study Geneset File" />
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12 <param name="calc" type="select" format="text" label="Calculation Method">
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13 <option value="MGSA">MGSA</option>
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14 <option value="Parent-Child-Intersection">Parent-Child-Intersection</option>
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15 <option value="Parent-Child-Union" selected="true">Parent-Child-Union</option>
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16 <option value="Term-For-Term">Term-For-Term</option>
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17 <option value="Topology-Elim">Topology-Elim</option>
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18 <option value="Topology-Weighted">Topology-Weighted</option>
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19 </param>
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20 <param name="mtc" type="select" format="text" label="MTC Method">
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21 <option value="Benjamini-Hochberg">Benjamini-Hochberg</option>
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22 <option value="Benjamini-Yekutieli">Benjamini-Yekutieli</option>
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23 <option value="Bonferroni">Bonferroni</option>
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24 <option value="Bonferroni-Holm">Bonferroni-Holm</option>
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25 <option value="None" selected="true">None</option>
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26 <option value="Westfall-Young-Single-Step">Westfall-Young-Single-Step</option>
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27 <option value="Westfall-Young-Step-Down">Westfall-Young-Step-Down</option>
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28 </param>
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29 </param>
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30 </inputs>
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31 <outputs>
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32 <data format="tabular" name="tablefile" />
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33 <data format="text" name="dotfile" />
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34 </outputs>
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35
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36 <help>
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37 see http://compbio.charite.de/contao/index.php/ontologizer2.html
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38 </help>
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40 </tool>
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