<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>