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<tool id="DAragorn" name="tRNA and tmRNA prediction" version="0.3">
	<description>SAPP - Aragorn tRNA and tmRNA prediction</description>
	<requirements>
		<container type="docker">jjkoehorst/sappdocker:ARAGORN</container>
	</requirements>
	<command interpreter="docker">java -jar /aragorn/aragorn-0.0.1-SNAPSHOT-jar-with-dependencies.jar
		'-input' '$input' '-output' '$output' '-gc' $genbank_gencode
		'$tmRNA' '$tRNA' '$topology' -format TURTLE
	</command>
	<inputs>
		<param format="ttl" label="RDF Genome" name="input" type="data"/>
		<param label="Genetic code" name="genbank_gencode" type="select">
			<option select="True" value="1">1. Standard</option>
			<option value="2">2. Vertebrate Mitochondrial</option>
			<option value="3">3. Yeast Mitochondrial</option>
			<option value="4">4. Mold, Protozoan, and Coelenterate
				Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
			<option value="5">5. Invertebrate Mitochondrial</option>
			<option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear
				Code</option>
			<option value="9">9. Echinoderm Mitochondrial</option>
			<option value="10">10. Euplotid Nuclear</option>
			<option value="11">11. Bacteria and Archaea</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. Chlorophycean Mitochondrial</option>
			<option value="21">21. Trematode Mitochondrial</option>
			<option value="22">22. Scenedesmus obliquus mitochondrial</option>
			<option value="23">23. Thraustochytrium Mitochondrial</option>
			<option value="24">24. Pterobranchia mitochondrial</option>
		</param>
		<param label="Topology" name="topology" type="select">
			<option value="-c">Assume that each sequence has a circular
				topology</option>
			<option value="-l">Assume that each sequence has a linear topology
			</option>
		</param>
		<param checked="true" falsevalue="" help="" label="Search for tmRNA genes (-m)" name="tmRNA" truevalue="-m" type="boolean"/>
		<param checked="true" falsevalue="" help="" label="Search for tRNA genes (-t)" name="tRNA" truevalue="-t" type="boolean"/>
	</inputs>
	<outputs>
		<data format="ttl" label="Aragorn: ${input.name}" name="output"/>
	</outputs>
	<citations>
		<citation type="bibtex">@article{Laslett2004,
			abstract = {A computer program, ARAGORN, identifies tRNA and tmRNA genes. The
			program employs heuristic algorithms to predict tRNA secondary
			structure, based on homology with recognized tRNA consensus sequences
			and ability to form a base-paired cloverleaf. tmRNA genes are
			identified using a modified version of the BRUCE program. ARAGORN
			achieves a detection sensitivity of 99\% from a set of 1290
			eubacterial, eukaryotic and archaeal tRNA genes and detects all
			complete tmRNA sequences in the tmRNA database, improving on the
			performance of the BRUCE program. Recently discovered tmRNA genes in
			the chloroplasts of two species from the 'green' algae lineage are
			detected. The output of the program reports the proposed tRNA
			secondary structure and, for tmRNA genes, the secondary structure of
			the tRNA domain, the tmRNA gene sequence, the tag peptide and a list
			of organisms with matching tmRNA peptide tags.},
			author = {Laslett, Dean and Canback, Bjorn},
			doi = {10.1093/nar/gkh152},
			file = {:Users/koeho006/Library/Application Support/Mendeley
			Desktop/Downloaded/Laslett, Canback - 2004 - ARAGORN, a program to
			detect tRNA genes and tmRNA genes in nucleotide sequences.pdf:pdf},
			isbn = {1362-4962 (Electronic)$\backslash$n1362-4962 (Linking)},
			issn = {03051048},
			journal = {Nucleic Acids Research},
			mendeley-groups = {VAPP Application note},
			pages = {11--16},
			pmid = {14704338},
			title = {{ARAGORN, a program to detect tRNA genes and tmRNA genes in
			nucleotide sequences}},
			volume = {32},
			year = {2004}
			}
		</citation>
	</citations>
</tool>