<tool id="DFASTA2RDF" name="FASTA to RDF" version="0.1">
	<description></description>
	<requirements>
		<container type="docker">jjkoehorst/sappdocker:FASTA2RDF</container>
	</requirements>
	<command interpreter="docker">java -jar /fasta2rdf/target/FASTA2RDF-0.1-jar-with-dependencies.jar
                '--type' '$source.fastaType' '--ignorestop' '$IgnoreStopCodon'
		'--input' '$input' '--output' '$output' '-organism' '$organism'
		'--ncbi_taxid' '$ncbi_taxid'
		#if len(str($identification_tag))==0
		'--idtag' ${input.name}
		#else
		'--idtag' '$identification_tag'
		#end if
		--source SAPP
		
		#for $index, $id in enumerate( $ids )
		'--id_alternative' '$id.id_tag'
		#end for
		'--id_alternative' '$input.name'
		'--codon' '$table'
	</command>
	<inputs>
		<param size="60" name="input" type="data" format="fasta" label="Fasta file for conversion" />

                <conditional name="source">
                        <param name="fastaType" type="select"
                                label="Select if it is a Genome/Gene/Protein or program wont start!">
                                <option value="">To be chosen</option>
                                <option value="genome"> Genome </option>
                                <option value="gene"> Gene</option>
                                <option value="protein"> Protein </option>
                                <validator type="empty_field"
                                        message="Please select if it is a Genome, Gene or Protein" />
                        </param>
                </conditional>

		<param name="table" type="select" label="Codon table">
			<option value="1"> 1 - UNIVERSAL </option>
			<option value="2"> 2 - VERTEBRATE_MITOCHONDRIAL </option>
			<option value="3"> 3 - YEAST_MITOCHONDRIAL </option>
			<option value="4"> 4 - MOLD_MITOCHONDRIAL </option>
			<option value="5"> 5 - INVERTEBRATE_MITOCHONDRIAL </option>
			<option value="6"> 6 - CILIATE_NUCLEAR </option>
			<option value="9"> 9 - ECHINODERM_MITOCHONDRIAL </option>
			<option value="10"> 10 - EUPLOTID_NUCLEAR </option>
			<option value="11" selected="true"> 11 - BACTERIAL </option>
			<option value="12"> 12 - ALTERNATIVE_YEAST_NUCLEAR </option>
			<option value="13"> 13 - ASCIDIAN_MITOCHONDRIAL </option>
			<option value="14"> 14 - FLATWORM_MITOCHONDRIAL </option>
			<option value="15"> 15 - BLEPHARISMA_MACRONUCLEAR </option>
			<option value="16"> 16 - 2CHLOROPHYCEAN_MITOCHONDRIAL </option>
			<option value="21"> 21 - TREMATODE_MITOCHONDRIAL </option>
			<option value="23"> 23 - SCENEDESMUS_MITOCHONDRIAL </option>
		</param>
		<param size="60" name="organism" type="text" format="text"
			label="organism name" />
		<param name='IgnoreStopCodon' type='boolean'
			label='Ignore if stop codon within protein sequence' truevalue='true'
			falsevalue='false' checked="false" help='' />

		<param size="60" name="ncbi_taxid" type="integer" value="0"
			label="NCBI taxonomy ID" optional="False">
			<validator type="in_range" min="1"
				message="Minimum taxonomy value is 1" />
		</param>
		<param size="60" name="identification_tag" type="text" format="text"
			label="An identification tag used for RDF storage !Needs to be very unique!"
			optional="True" />
		<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="ttl" name="output" label="FASTA2RDF: ${input.name}" />
	</outputs>
	<help>
		RDF creation from a multi (gene/protein/genome) fasta file
	</help>
</tool>