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<tool id="DRDF2EMBL" name="EMBL/GenBank creation" version="0.1">
	<description/>
	<requirements>
		<container type="docker">jjkoehorst/sappdocker:RDF2EMBL</container>
	</requirements>
	<command interpreter="docker">java -jar /rdf2embl/rdf2embl-0.0.1-SNAPSHOT-jar-with-dependencies.jar
		'-input' '$input' -output '$output' -format 'TURTLE' '-organism'
		'$organism' '-strain' '$strain' '-substrain' '$substrain' '-keywords'
		'$keywords' '-taxon' '$taxon' -codon '$codon'
		-locus '$prefix' '-title'
		'$title' '-authors' '$authors' '-consortium' '$consortium' '-journal'
		'$journal' '-dataclass' '$dataclass' '-writer' '$writer' '-projectid'
		'$projectid' '$pathwaytools' '-note' '$note' '-scaffold' '$scaffold'
		'$gapprotein'
	</command>
	<inputs>
		<param format="ttl" label="TTL / RDF file" multiple="False" name="input" type="data"/>
		<param label="Organism name" name="organism" optional="false" type="text"/>
		<param label="Strain name" name="strain" optional="false" type="text"/>
		<param label="Substrain name" name="substrain" optional="false" type="text"/>
		<param label="Keywords" name="keywords" optional="false" type="text"/>
		<param label="Project identifier" name="projectid" optional="false" type="text"/>
		<param label="Taxon number" name="taxon" optional="false" type="text"/>
		<param label="Locus prefix (FZH_)" name="prefix" optional="false" type="text"/>
		<param label="Scaffold prefix (SCAF_)" name="scaffold" optional="false" type="text"/>
		<param label="Journal" name="journal" optional="false" type="text" value="journal vol:pp-pp(year)"/>
		<param label="Authors" name="authors" optional="false" type="text"/>
		<param label="Title" name="title" optional="false" type="text"/>
		<param label="Consortium" name="consortium" optional="false" type="text"/>
		<param area="True" label="Note for each record" name="note" optional="false" size="10" type="text" value="Annotation was performed using the Semantic Annotation Platform for Prokaryotes (SAPP) and the sha384 key is $shakey and the FASTA header name is: $header"/>
		<param label="codon table selection" name="codon" type="select">
			<option value="11">The Bacterial, Archaeal and Plant Plastid Code
				(transl_table=11)
			</option>
			<option value="4">The Mold, Protozoan, Coelenterate Mitochondrial
				and Mycoplasma/Spiroplasma Code (transl_table=4)
			</option>
		</param>
		<param label="Output format" name="writer" type="select">
			<option selected="true" value="embl">EMBL format</option>
			<option value="genbank">Genbank format</option>
		</param>
		<param label="Data class selection" name="dataclass" type="select">
			<option value="PAT">Patent</option>
			<option value="EST">Expressed Sequence Tag</option>
			<option value="GSS">Genome Survey Sequence</option>
			<option value="HTC">High Thoughput CDNA sequencing</option>
			<option value="HTG">High Thoughput Genome sequencing</option>
			<option value="MGA">Mass Genome Annotation</option>
			<option selected="true" value="WGS">Whole Genome Shotgun</option>
			<option value="TSA">Transcriptome Shotgun Assembly</option>
			<option value="STS">Sequence Tagged Site</option>
			<option value="STD">Standard (all entries not classified as above)
			</option>
		</param>
		<param label="Remove gap spanning proteins (contains more than 50% of XXX in sequence)" name="gapprotein" type="select">
			<option selected="true" value="">No</option>
			<option selected="false" value="-gapprotein">Yes</option>
		</param>
		<param label="Pathway tools compatible? WARNING: Each contig needs to be loaded individually into Pathway tools (V19.0)" name="pathwaytools" type="select">
			<option selected="true" value="">No</option>
			<option selected="false" value="-pathwaytools">Yes</option>
		</param>
	</inputs>
	<outputs>
		<data format="embl" label="EMBL: ${input.name}" name="output"/>
	</outputs>
	<help>RDF to EMBL conversion. Locus tags are automatically generated unless locus tags have been inferred or generated through the locus module.
	</help>
</tool>