diff fasta2rdf/fastatordf.xml @ 6:ec73c34af97b

FASTA2RDF

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta2rdf/fastatordf.xml	Sat Feb 21 15:19:42 2015 +0100
@@ -0,0 +1,34 @@
+<tool id="SAPP_genome_to_ttl" name="FASTA to RDF" version="0.1">
+	<description></description>
+	<command interpreter="python3">fastatordf.py '-input' '$input' '-output' '$output' '-organism' '$organism' '-ncbi_taxid' '$ncbi_taxid' '-idtag' '$identification_tag' -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" optional="false"/>
+		<param size="60" name="ncbi_taxid" type="text" format="text" label="NCBI taxonomy ID"/>
+		<param size="60" name="identification_tag" type="text" format="text" label="An identification tag used for RDF storage !Needs to be very unique!" optional="false"/>
+		<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="genomeTTL: ${input.name}" />
+	</outputs>
+    
+    <tests>
+        <test>
+            <param name="input" value="test-data/NC_017117.fna"/>
+            <output name="$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> Genome FASTA file to RDF</help>
+</tool>