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changeset 0:fa6a9fd0889e draft

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Uploaded
author enios
date Wed, 21 Apr 2021 10:52:43 +0000
parents
children 17a9bf6ca902
files biotranslator.xml
diffstat 1 files changed, 74 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/biotranslator.xml	Wed Apr 21 10:52:43 2021 +0000
@@ -0,0 +1,74 @@
+<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>