obotools_02: ontologizer.xml annotate

annotate ontologizer.xml @ 0:028babd7a6c5 draft default tip

Try at a fresh start...

author	kltm
date	Fri, 29 Mar 2013 17:30:07 -0400
parents
children

rev	line source
0 028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	1 <tool id="ontologizer" name="ontologizer" version="0.0.16">
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	2 <description>from http://compbio.charite.de/contao/</description>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	3 <requirements>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	4 <requirement type="package" version="0.0.3">ontologizer-jar</requirement>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	5 </requirements>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	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 $tablefile; echo moved table file to [$tablefile]; mv view-.dot $dotfile; echo moved dot file to [$dotfile]</command>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	7 <inputs>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	8 <param name="go" type="data" format="obo" label="Gene Ontology File" />
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	9 <param name="gaf" type="data" format="gaf" label="Gene Association File" />
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	10 <param name="population" type="data" format="tabular" label="Population Geneset File" />
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	11 <param name="studyset" type="data" format="tabular" label="Study Geneset File" />
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	12 <param name="calc" type="select" format="text" label="Calculation Method">
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	13 <option value="MGSA">MGSA</option>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	14 <option value="Parent-Child-Intersection">Parent-Child-Intersection</option>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	15 <option value="Parent-Child-Union" selected="true">Parent-Child-Union</option>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	16 <option value="Term-For-Term">Term-For-Term</option>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	17 <option value="Topology-Elim">Topology-Elim</option>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	18 <option value="Topology-Weighted">Topology-Weighted</option>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	19 </param>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	20 <param name="mtc" type="select" format="text" label="MTC Method">
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	21 <option value="Benjamini-Hochberg">Benjamini-Hochberg</option>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	22 <option value="Benjamini-Yekutieli">Benjamini-Yekutieli</option>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	23 <option value="Bonferroni">Bonferroni</option>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	24 <option value="Bonferroni-Holm">Bonferroni-Holm</option>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	25 <option value="None" selected="true">None</option>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	26 <option value="Westfall-Young-Single-Step">Westfall-Young-Single-Step</option>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	27 <option value="Westfall-Young-Step-Down">Westfall-Young-Step-Down</option>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	28 </param>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	29 </inputs>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	30 <outputs>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	31 <data format="tabular" name="tablefile" />
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	32 <data format="text" name="dotfile" />
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	33 </outputs>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	34
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	35 <stdio>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	36 <exit_code range="1:" level="fatal" description="Unknown error" />
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	37 </stdio>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	38
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	39 <help>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	40 see http://compbio.charite.de/contao/index.php/ontologizer2.html
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	41 </help>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	42
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	43 </tool>
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	44
028babd7a6c5 Try at a fresh start... kltm parents: diff changeset	45

Mercurial > repos > kltm > obotools_02

annotate ontologizer.xml @ 0:028babd7a6c5 draft default tip