view biotranslator.xml @ 12:b612b035a493 draft

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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>