<tool id="DGBK2RDF" name="EMBL/GBK to RDF" version="0.1">
	<description>Converts GenBank/EMBL files to RDF</description>
	<requirements>
		<container type="docker">jjkoehorst/sappdocker:GBK2RDF</container>
  	</requirements>
	<command>java -jar /genbank2rdf/target/GenBank2RDF-0.0.1-SNAPSHOT-jar-with-dependencies.jar '-input' '$input' -output '$output' -source "$source" -format "$format" -identifier "${input.name}" -codon "$codon" </command>
	<inputs>
		<param format="gbk,gb,genbank" label="Genbank file" name="input" type="data"/>
		<param label="EMBL/GBK" name="format" type="select">
			<option value="gbk">Genbank</option>
			<option selected="true" value="embl">EMBL</option>
		</param>
		<param label="11/4" name="codon" type="select">
			<option selected="true" value="11">11</option>
			<option value="4">4</option>
		</param>
		<param label="Source of annotation eg. RAST/NCBI/EBI" name="source" optional="false" type="text"/>
	</inputs>
	<outputs>
		<data format="ttl" label="GBKttl: ${input.name}" name="output"/>
	</outputs>
	<help>Java Genbank or EMBL to RDF conversion
	</help>
</tool>