view gbk2rdf/gbktordf.xml @ 9:3f4f1cd22a6a

FASTA 2 RDF code cleanup

<tool id="SAPP_genbank_to_ttl" name="EMBL/GBK to RDF" version="0.1">
	<requirements>
    	<requirement type='package' version="3.4">python</requirement>
    	<requirement type='package' version="1.0">rdflib</requirement>
	</requirements>
	<description>Genbank to RDF conversion</description>
	<command interpreter="python3.4">gbktordf.py '-input' '$input' -output '$output' -sourcedb "$format" -format "$format"</command>
	<inputs>
		<param name="input" type="data" format="gbk,gb,genbank,embl" label="Genbank file"/>
		<param name="format" type="select" label="EMBL/GBK">
			<option value="genbank" selected="true"> Genbank</option>
			<option value="embl"> EMBL </option>
		</param>
	</inputs>

	<outputs>
		<data format="rdf" name="output" label="GBKttl: ${input.name}" />
	</outputs>

	<tests>
    	<test>
      		<param name="input" value="test-data/NC_010067.gbk"/>
      		<output name="$output" file="NC_010067.rdf"/>
      		<output name="$format" value="genbank"/>
      		<output name="$sourcedb" value="genbank"/>
    	</test>
    	<test>
      		<param name="input" value="test-data/CP009049.embl"/>
      		<output name="$output" file="CP009049.rdf"/>
      		<output name="$format" value="embl"/>
      		<output name="$sourcedb" value="embl"/>
    	</test>
  </tests>
  
	<help>
		Genbank or EMBL to RDF conversion
	</help>
</tool>