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comparison ontologizer.xml @ 30:f48064da7849

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author jorrit
date Tue, 26 Feb 2013 22:46:52 -0500
parents 8ff260813c5e
children 06e8a43d7d65
comparison
equal deleted inserted replaced
29:11beca20586b 30:f48064da7849
1 <tool id="ontologizer" name="ontologizer" version="0.0.15"> 1 <tool id="ontologizer" name="ontologizer" version="0.0.15">
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="package" version="0.0.2">ontologizer-jar</requirement> 4 <requirement type="package" version="0.0.2">ontologizer-jar</requirement>
5 </requirements> 5 </requirements>
6 <command>java -Xmx2G -jar $ONTOLOGIZER_JAR --go $go --association $gaf --population $pop --studyset $study --dot 0.05 > $output</command> 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>
7 <inputs> 7 <inputs>
8 <param name="go" type="text" label="Gene ontology" /> 8 <param name="go" type="data" format="obo" label="Gene Ontology File" />
9 <param name="gaf" type="text" label="Gene association file" /> 9 <param name="gaf" type="data" format="gaf" label="Gene Association File" />
10 <param name="pop" type="text" label="population gene set" /> 10 <param name="population" type="data" format="tabular" label="Population Geneset File" />
11 <param name="study" type="text" label="study gene set" /> 11 <param name="studyset" type="data" format="tabular" label="Study Geneset File" />
12 </inputs> 12 <param name="calc" type="select" format="text" label="Calculation Method">
13 <outputs> 13 <option value="MGSA">MGSA</option>
14 <!-- need to figure out how to handle multiple outputs --> 14 <option value="Parent-Child-Intersection">Parent-Child-Intersection</option>
15 <data type="text" name="output" /> 15 <option value="Parent-Child-Union" selected="true">Parent-Child-Union</option>
16 </outputs> 16 <option value="Term-For-Term">Term-For-Term</option>
17 <tests> 17 <option value="Topology-Elim">Topology-Elim</option>
18 <!-- see http://wiki.galaxyproject.org/Admin/Tools/Writing%20Tests --> 18 <option value="Topology-Weighted">Topology-Weighted</option>
19 <test> 19 </param>
20 <param name="go" file="ontologizer/test.obo" /> 20 <param name="mtc" type="select" format="text" label="MTC Method">
21 <param name="gaf" file="ontologizer/test.gaf" /> 21 <option value="Benjamini-Hochberg">Benjamini-Hochberg</option>
22 <param name="pop" file="ontologizer/test.gs" /> 22 <option value="Benjamini-Yekutieli">Benjamini-Yekutieli</option>
23 <param name="study" file="ontologizer/test.gs" /> 23 <option value="Bonferroni">Bonferroni</option>
24 <output name="output" file="test.output"/> 24 <option value="Bonferroni-Holm">Bonferroni-Holm</option>
25 </test> 25 <option value="None" selected="true">None</option>
26 </tests> 26 <option value="Westfall-Young-Single-Step">Westfall-Young-Single-Step</option>
27 <option value="Westfall-Young-Step-Down">Westfall-Young-Step-Down</option>
28 </param>
29 </param>
30 </inputs>
31 <outputs>
32 <data format="tabular" name="tablefile" />
33 <data format="text" name="dotfile" />
34 </outputs>
27 35
28 36 <help>
29 <help> 37 see http://compbio.charite.de/contao/index.php/ontologizer2.html
30 see http://compbio.charite.de/contao/index.php/ontologizer2.html 38 </help>
31 </help>
32 39
33 </tool> 40 </tool>
34 41
35 42