Mercurial > repos > enios > nc_rna
view biotranslator.xml @ 12:b612b035a493 draft
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author | enios |
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date | Sat, 22 May 2021 07:29:26 +0000 |
parents | fa6a9fd0889e |
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<tool id="biotranslator" name="biotranslator" > <requirements> <container type="docker">eniosorg/bim:biotranslator_</container> </requirements> <description>** Biotranslator **</description> <command><![CDATA[ python /code/wrapper.py --authtoken $authtoken --dataset $dataset --project $project --idtype '$id_type' --organism '$organism' --terms '$terms' --foldchange '$fold_change' --correctedpvalue '$correctedpvalue' --title '$exp_title' --description '$description' && cp *.html $html && tar -cvf $results * ]]></command> <inputs> <param type="text" name="authtoken" value="7dajfghfhjs7fgh" label="Give your bionfominer authentication token "/> <param type="float" name="correctedpvalue" value="0.05" label="correctedpvalue"/> <param type="data" name="dataset" format="csv,txt,tabular,semicolon" label="gene list file"/> <param type="text" name="description" value="description" label="description"/> <param type="text" name="exp_title" value="exp_title" label="exp_title"/> <param type="select" name="fold_change" value="None" label="foldchange"> <option value="None">None</option> <option value="Log">Log</option> <option value="Linear">Linear</option> </param> <param type="select" name="organism" value="Homo sapiens" label="organism"> <option value="Homo sapiens">Homo sapiens</option> <option value="Mus musculus">Mus musculus</option> <option value="Rattus novergicus">Rattus novergicus</option> <option value="Bos taurus">Bos taurus</option> <option value="Sus scrofa">Sus scrofa</option> <option value="Gallus gallus">Gallus gallus</option> <option value="Danio rerio">Danio rerio</option> <option value="Drosophila melanogaster">Drosophila melanogaster</option> <option value="Caenorhabditis elegans">Caenorhabditis elegans</option> <option value="Saccharomyses serevisiae">Saccharomyses serevisiae</option> <option value="Schizosaccharomyses pombe">Schizosaccharomyses pombe</option> <option value="Aspergillus nidulans">Aspergillus nidulans</option> <option value="Magnaporthe grisea">Magnaporthe grisea</option> <option value="Arabidopsis thaliana">Arabidopsis thaliana</option> <option value="Oryza sativa Japonica">Oryza sativa Japonica</option> <option value="Glycine max">Glycine max</option> <option value="Hellanthus annuus">Hellanthus annuus</option> <option value="Sorghum bicolor">Sorghum bicolor</option> <option value="Zea mays">Zea mays</option> <option value="Beta vulgaris">Beta vulgaris</option> </param> <param type="select" name="id_type" value="Gene Symbol" label="Id type"> <option value="Gene Symbol">Gene Symbol</option> <option value="Entrez Gene id">Entrez Gene id</option> <option value="Ensembl Gene id">Ensembl Gene id</option> </param> <param type="text" name="project" value="hgjahgdf7886sjhfg" label="Provide a bioinfominer project ID"/> <param type="select" name="terms" value="Gene Ontology" label="terms"> <option value="Gene Ontology">Gene Ontology</option> <option value="MGI Mammalian Phenotype">MGI Mammalian Phenotype</option> <option value="Human Phenotype Ontology">Human Phenotype Ontology</option> <option value="Plant Ontology">Plant Ontology</option> <option value="Zebrafish Ontology">Zebrafish Ontology</option> </param> </inputs> <outputs> <data name="html" format="html" /> <data name="results" format="tar" /> <!--data name="analysis" format="tsv" /> <data name="extended_analysis" format="txt" /> <data name="visualization" format="html" /--> </outputs> </tool>