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+++ b/genecaller.xml	Mon Jul 04 10:37:59 2016 -0400
@@ -0,0 +1,103 @@
+<tool id="DGenes" name="Gene prediction" version="1.0.0">
+	<description/>
+	<requirements>
+		<container type="docker">jjkoehorst/sappdocker:GENECALLER</container>
+	</requirements>
+	<command interpreter="docker">java -jar /genecaller/genecaller-0.0.1-SNAPSHOT-jar-with-dependencies.jar
+		'-runtype' '$runtype' -input $input -output $output -codon $codon -format TURTLE
+	</command>
+	<inputs>
+		<param format="ttl" label="ttl genome file" name="input" type="data"/>
+		<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="single or meta genome" name="runtype" type="select">
+			<option value="single">Single genome analysis</option>
+			<option value="meta">Metagenome analysis</option>
+		</param>
+	</inputs>
+	<outputs>
+		<data format="ttl" label="ORF: ${input.name}" name="output"/>
+	</outputs>
+	<help>Prodigal gene prediction requires an RDF file from either a
+		Genome FASTA or
+		Genbank/EMBL format.
+	</help>
+	<citations>
+		<citation type="bibtex">@article{Hyatt2010,
+			abstract = {BACKGROUND: The
+			quality of automated gene prediction in microbial
+			organisms has
+			improved steadily over the past decade, but there is
+			still room for
+			improvement. Increasing the number of correct
+			identifications, both of
+			genes and of the translation initiation
+			sites for each gene, and
+			reducing the overall number of false
+			positives, are all desirable
+			goals.
+
+			RESULTS: With our years of experience in manually curating
+			genomes for the
+			Joint Genome Institute, we developed a new gene
+			prediction algorithm
+			called Prodigal (PROkaryotic DYnamic programming
+			Gene-finding
+			ALgorithm). With Prodigal, we focused specifically on the
+			three goals
+			of improved gene structure prediction, improved
+			translation
+			initiation site recognition, and reduced false positives.
+			We compared
+			the results of Prodigal to existing gene-finding methods
+			to
+			demonstrate that it met each of these objectives.
+
+			CONCLUSION: We
+			built a fast, lightweight, open source gene prediction program
+			called
+			Prodigal http://compbio.ornl.gov/prodigal/. Prodigal achieved
+			good
+			results compared to existing methods, and we believe it will be
+			a
+			valuable asset to automated microbial annotation pipelines.},
+			author =
+			{Hyatt, Doug and Chen, Gwo-Liang and Locascio, Philip F and
+			Land,
+			Miriam L and Larimer, Frank W and Hauser, Loren J},
+			doi =
+			{10.1186/1471-2105-11-119},
+			file =
+			{:Users/koeho006/Library/Application Support/Mendeley
+			Desktop/Downloaded/Hyatt et al. - 2010 - Prodigal prokaryotic gene
+			recognition and translation initiation site identification.pdf:pdf},
+			issn = {1471-2105},
+			journal = {BMC bioinformatics},
+			keywords =
+			{Algorithms,Databases, Genetic,Genome, Bacterial,Peptide Chain
+			Initiation, Translational,Peptide Chain Initiation, Translational:
+			genetics,Prokaryotic Cells,Software},
+			mendeley-groups = {Dump/VAPP
+			Paper},
+			month = jan,
+			number = {1},
+			pages = {119},
+			pmid = {20211023},
+			title = {{Prodigal: prokaryotic gene recognition and translation
+			initiation site identification.}},
+			url =
+			{http://www.biomedcentral.com/1471-2105/11/119},
+			volume = {11},
+			year =
+			{2010}
+			}
+
+		</citation>
+	</citations>
+</tool>
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