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+++ b/rnammer.xml	Mon Jul 04 10:37:59 2016 -0400
@@ -0,0 +1,87 @@
+<tool id="DRnammer" name="rRNA detection" version="1.0.0">
+	<description/>
+	<requirements>
+		<container type="docker">jjkoehorst/sappdocker:RNAMMER</container>
+	</requirements>
+	<command interpreter="docker">java -jar /rnammer/rnammer-0.0.1-SNAPSHOT-jar-with-dependencies.jar
+		'-input' '$input' -output '$output' -format TURTLE
+	</command>
+	<inputs>
+		<param format="ttl" label="genome ttl file" name="input" type="data"/>
+	</inputs>
+	<outputs>
+		<data format="ttl" label="RNA: ${input.name}" name="output"/>
+	</outputs>
+	<help>Be aware that this can only be used for academic users; other
+		users are
+		requested to contact CBS Software Package Manager at
+		software@cbs.dtu.dk.
+		We are investigating alternative prediction
+		applications, please contact
+		us if you are aware of such method.
+	</help>
+	<citations>
+		<citation type="bibtex">@article{Lagesen2007,
+			abstract = {The
+			publication of a complete genome sequence is usually
+			accompanied by
+			annotations of its genes. In contrast to protein
+			coding genes, genes
+			for ribosomal RNA (rRNA) are often poorly or
+			inconsistently annotated.
+			This makes comparative studies based on
+			rRNA genes difficult. We have
+			therefore created computational
+			predictors for the major rRNA species
+			from all kingdoms of life and
+			compiled them into a program called
+			RNAmmer. The program uses hidden
+			Markov models trained on data from
+			the 5S ribosomal RNA database and
+			the European ribosomal RNA database
+			project. A pre-screening step
+			makes the method fast with little loss
+			of sensitivity, enabling the
+			analysis of a complete bacterial genome
+			in less than a minute.
+			Results from running RNAmmer on a large set of
+			genomes indicate that
+			the location of rRNAs can be predicted with a
+			very high level of
+			accuracy. Novel, unannotated rRNAs are also
+			predicted in many
+			genomes. The software as well as the genome analysis
+			results are
+			available at the CBS web server.},
+			author = {Lagesen, Karin
+			and Hallin, Peter and R\o dland, Einar Andreas and
+			Staerfeldt,
+			Hans-Henrik and Rognes, Torbj\o rn and Ussery, David W},
+			doi =
+			{10.1093/nar/gkm160},
+			file = {:Users/koeho006/Library/Application
+			Support/Mendeley
+			Desktop/Downloaded/Lagesen et al. - 2007 - RNAmmer
+			consistent and
+			rapid annotation of ribosomal RNA genes.pdf:pdf},
+			issn =
+			{1362-4962},
+			journal = {Nucleic acids research},
+			keywords =
+			{Computational Biology,Computational Biology: methods,Genes,
+			rRNA,Genome, Bacterial,Genomics,Genomics: methods,Markov
+			Chains,Software},
+			mendeley-groups = {Dump/VAPP Paper,VAPP Application
+			note},
+			month = jan,
+			number = {9},
+			pages = {3100--8},
+			pmid = {17452365},
+			title = {{RNAmmer: consistent and rapid annotation of ribosomal RNA
+			genes.}},
+			volume = {35},
+			year = {2007}
+			}
+		</citation>
+	</citations>
+</tool>
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