|
32
|
1 <tool id="ontologizer" name="ontologizer" version="0.0.16">
|
|
8
|
2 <description>from http://compbio.charite.de/contao/</description>
|
|
|
3 <requirements>
|
|
35
|
4 <requirement type="set_environment">ONTOLOGIZER_JAR</requirement>
|
|
31
|
5 <requirement type="package" version="0.0.3">ontologizer-jar</requirement>
|
|
8
|
6 </requirements>
|
|
35
|
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
|
8 <inputs>
|
|
30
|
9 <param name="go" type="data" format="obo" label="Gene Ontology 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" />
|
|
|
12 <param name="studyset" type="data" format="tabular" label="Study Geneset File" />
|
|
|
13 <param name="calc" type="select" format="text" label="Calculation Method">
|
|
|
14 <option value="MGSA">MGSA</option>
|
|
|
15 <option value="Parent-Child-Intersection">Parent-Child-Intersection</option>
|
|
|
16 <option value="Parent-Child-Union" selected="true">Parent-Child-Union</option>
|
|
|
17 <option value="Term-For-Term">Term-For-Term</option>
|
|
|
18 <option value="Topology-Elim">Topology-Elim</option>
|
|
|
19 <option value="Topology-Weighted">Topology-Weighted</option>
|
|
|
20 </param>
|
|
|
21 <param name="mtc" type="select" format="text" label="MTC Method">
|
|
|
22 <option value="Benjamini-Hochberg">Benjamini-Hochberg</option>
|
|
|
23 <option value="Benjamini-Yekutieli">Benjamini-Yekutieli</option>
|
|
|
24 <option value="Bonferroni">Bonferroni</option>
|
|
|
25 <option value="Bonferroni-Holm">Bonferroni-Holm</option>
|
|
|
26 <option value="None" selected="true">None</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>
|
|
|
29 </param>
|
|
34
|
30 </inputs>
|
|
|
31 <outputs>
|
|
|
32 <data format="tabular" name="tablefile" />
|
|
|
33 <data format="text" name="dotfile" />
|
|
|
34 </outputs>
|
|
8
|
35
|
|
34
|
36 <help>
|
|
|
37 see http://compbio.charite.de/contao/index.php/ontologizer2.html
|
|
|
38 </help>
|
|
8
|
39
|
|
|
40 </tool>
|
|
|
41
|
|
|
42
|
