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comparison ontologizer.xml @ 34:f475c42e642c

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author jorrit
date Tue, 26 Feb 2013 23:02:45 -0500
parents b277bb358960
children 25c037153c9f
comparison
equal deleted inserted replaced
33:b277bb358960 34:f475c42e642c
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" />
25 <option value="Bonferroni-Holm">Bonferroni-Holm</option> 25 <option value="Bonferroni-Holm">Bonferroni-Holm</option>
26 <option value="None" selected="true">None</option> 26 <option value="None" selected="true">None</option>
27 <option value="Westfall-Young-Single-Step">Westfall-Young-Single-Step</option> 27 <option value="Westfall-Young-Single-Step">Westfall-Young-Single-Step</option>
28 <option value="Westfall-Young-Step-Down">Westfall-Young-Step-Down</option> 28 <option value="Westfall-Young-Step-Down">Westfall-Young-Step-Down</option>
29 </param> 29 </param>
30 </inputs> 30 </inputs>
31 <outputs> 31 <outputs>
32 <data format="tabular" name="tablefile" /> 32 <data format="tabular" name="tablefile" />
33 <data format="text" name="dotfile" /> 33 <data format="text" name="dotfile" />
34 </outputs> 34 </outputs>
35 35
36 <help> 36 <help>
37 see http://compbio.charite.de/contao/index.php/ontologizer2.html 37 see http://compbio.charite.de/contao/index.php/ontologizer2.html
38 </help> 38 </help>
39 39
40 </tool> 40 </tool>
41 41
42 42