Mercurial > repos > jjkoehorst > sapp

diff conversion/protein2rdf/protein_to_ttl.xml @ 16:74b8ba5e2d5b

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aragorn addition
author jjkoehorst <jasperkoehorst@gmail.com>
date Sat, 21 Feb 2015 17:17:06 +0100
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/conversion/protein2rdf/protein_to_ttl.xml	Sat Feb 21 17:17:06 2015 +0100
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+<tool id="SAPP_protein_rdf" name="Protein FASTA to RDF" version="0.1">
+    <requirements>
+        <requirement type='package' version="3.4">python</requirement>
+        <requirement type='package' version="1.0">rdflib</requirement>
+    </requirements>
+	<description></description>
+	<command interpreter="python3.4">protein_to_ttl.py '-input' '$input' '-output' '$output' '-organism' '$organism' '-ncbi_taxid' '$ncbi_taxid' '-idtag' '$identification_tag' '-diagnosis' '$diagnosis' '-country' '$country' '-location' '$location' '-date' '$date' -sourcedb SAPP 
+		#for $index, $id in enumerate( $ids ) 
+			'-ids' '$id.id_tag'
+		#end for
+			'-id_alternative' '$input.name'
+	</command>
+	<inputs>
+		<param size="60" name="input" type="data" format="fasta,fa" label="File for annotation, file types used fasta,fa"/>
+		<param size="60" name="organism" type="text" format="text" label="organism name"/>
+		<param size="60" name="diagnosis" type="text" format="text" label="Diagnosis of host if applicable"/>
+		<param size="60" name="ncbi_taxid" type="text" format="text" label="NCBI taxonomy ID"/>
+		<param size="60" name="country" type="text" format="text" label="Country of sample"/>
+		<param size="60" name="location" type="text" format="text" label="Location of sample e.g., river, city, hospital"/>
+		<param size="60" name="date" type="text" format="text" label="Sample date"/>
+		<param size="60" name="identification_tag" type="text" format="text" label="An identification tag used for RDF storage !Needs to be very unique!"/>
+		<repeat name="ids" title="Identification tags">	    	
+			<param size="60" name="id_tag" type="text" format="text" label="An identification tag used by other consortiums"/>
+		</repeat>
+	</inputs>
+
+	<outputs>
+		<data format="rdf" name="output" label="proteinTTL: ${input.name}" />
+	</outputs>
+    <tests>
+        <test>
+            <param name="input" value="test-data/NC_017117.faa"/>
+            <output name="$output" file="NC_017117.rdf"/>
+            <output name="$ncbi_taxid" value="634455"/>
+            <output name="$idtag" value="Acetobacter pasteurianus IFO 3283-22"/>
+            <output name="$organism" value="Acetobacter pasteurianus IFO 3283-22"/>
+        </test>
+    </tests>
+	<help>
+		RDF creation from a multi protein fasta file
+	</help>
+</tool>