|
0
|
1 <tool id="biotranslator" name="biotranslator" >
|
|
|
2 <requirements>
|
|
|
3 <container type="docker">eniosorg/bim:biotranslator_</container>
|
|
|
4 </requirements>
|
|
|
5 <description>** Biotranslator **</description>
|
|
|
6 <command><![CDATA[ python /code/wrapper.py
|
|
|
7 --authtoken $authtoken
|
|
|
8 --dataset $dataset
|
|
|
9 --project $project
|
|
|
10 --idtype '$id_type'
|
|
|
11 --organism '$organism'
|
|
|
12 --terms '$terms'
|
|
|
13 --foldchange '$fold_change'
|
|
|
14 --correctedpvalue '$correctedpvalue'
|
|
|
15 --title '$exp_title'
|
|
|
16 --description '$description'
|
|
|
17 && cp *.html $html
|
|
|
18 && tar -cvf $results *
|
|
|
19 ]]></command>
|
|
|
20 <inputs>
|
|
|
21 <param type="text" name="authtoken" value="7dajfghfhjs7fgh" label="Give your bionfominer authentication token "/>
|
|
|
22 <param type="float" name="correctedpvalue" value="0.05" label="correctedpvalue"/>
|
|
|
23 <param type="data" name="dataset" format="csv,txt,tabular,semicolon" label="gene list file"/>
|
|
|
24 <param type="text" name="description" value="description" label="description"/>
|
|
|
25 <param type="text" name="exp_title" value="exp_title" label="exp_title"/>
|
|
|
26 <param type="select" name="fold_change" value="None" label="foldchange">
|
|
|
27 <option value="None">None</option>
|
|
|
28 <option value="Log">Log</option>
|
|
|
29 <option value="Linear">Linear</option>
|
|
|
30 </param>
|
|
|
31 <param type="select" name="organism" value="Homo sapiens" label="organism">
|
|
|
32 <option value="Homo sapiens">Homo sapiens</option>
|
|
|
33 <option value="Mus musculus">Mus musculus</option>
|
|
|
34 <option value="Rattus novergicus">Rattus novergicus</option>
|
|
|
35 <option value="Bos taurus">Bos taurus</option>
|
|
|
36 <option value="Sus scrofa">Sus scrofa</option>
|
|
|
37 <option value="Gallus gallus">Gallus gallus</option>
|
|
|
38 <option value="Danio rerio">Danio rerio</option>
|
|
|
39 <option value="Drosophila melanogaster">Drosophila melanogaster</option>
|
|
|
40 <option value="Caenorhabditis elegans">Caenorhabditis elegans</option>
|
|
|
41 <option value="Saccharomyses serevisiae">Saccharomyses serevisiae</option>
|
|
|
42 <option value="Schizosaccharomyses pombe">Schizosaccharomyses pombe</option>
|
|
|
43 <option value="Aspergillus nidulans">Aspergillus nidulans</option>
|
|
|
44 <option value="Magnaporthe grisea">Magnaporthe grisea</option>
|
|
|
45 <option value="Arabidopsis thaliana">Arabidopsis thaliana</option>
|
|
|
46 <option value="Oryza sativa Japonica">Oryza sativa Japonica</option>
|
|
|
47 <option value="Glycine max">Glycine max</option>
|
|
|
48 <option value="Hellanthus annuus">Hellanthus annuus</option>
|
|
|
49 <option value="Sorghum bicolor">Sorghum bicolor</option>
|
|
|
50 <option value="Zea mays">Zea mays</option>
|
|
|
51 <option value="Beta vulgaris">Beta vulgaris</option>
|
|
|
52 </param>
|
|
|
53 <param type="select" name="id_type" value="Gene Symbol" label="Id type">
|
|
|
54 <option value="Gene Symbol">Gene Symbol</option>
|
|
|
55 <option value="Entrez Gene id">Entrez Gene id</option>
|
|
|
56 <option value="Ensembl Gene id">Ensembl Gene id</option>
|
|
|
57 </param>
|
|
|
58 <param type="text" name="project" value="hgjahgdf7886sjhfg" label="Provide a bioinfominer project ID"/>
|
|
|
59 <param type="select" name="terms" value="Gene Ontology" label="terms">
|
|
|
60 <option value="Gene Ontology">Gene Ontology</option>
|
|
|
61 <option value="MGI Mammalian Phenotype">MGI Mammalian Phenotype</option>
|
|
|
62 <option value="Human Phenotype Ontology">Human Phenotype Ontology</option>
|
|
|
63 <option value="Plant Ontology">Plant Ontology</option>
|
|
|
64 <option value="Zebrafish Ontology">Zebrafish Ontology</option>
|
|
|
65 </param>
|
|
|
66 </inputs>
|
|
|
67 <outputs>
|
|
|
68 <data name="html" format="html" />
|
|
|
69 <data name="results" format="tar" />
|
|
|
70 <!--data name="analysis" format="tsv" />
|
|
|
71 <data name="extended_analysis" format="txt" />
|
|
|
72 <data name="visualization" format="html" /-->
|
|
|
73 </outputs>
|
|
|
74 </tool>
|
