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+++ b/aragorn.xml	Mon Jul 04 10:37:59 2016 -0400
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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>
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