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comparison biotranslator.xml @ 0:fa6a9fd0889e draft

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author enios
date Wed, 21 Apr 2021 10:52:43 +0000
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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>