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<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
		[e-mail].
		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>