<tool id="DCRT" name="CRISPR detection" version="0.1">
	<description></description>
	<requirements>
		<container type="docker">jjkoehorst/sappdocker:CRT</container>
	</requirements>
	<command interpreter="docker">java -jar /crt/CRT-0.0.1-SNAPSHOT-jar-with-dependencies.jar
		'-input' '$input' -output '$output' -format TURTLE
	</command>
	<inputs>
		<param name="input" type="data" format="ttl" label="genome ttl file" />
	</inputs>

	<outputs>
		<data format="ttl" name="output" label="CRISPR: ${input.name}" />
	</outputs>
	<help>
		CIRSPR prediction using CRT. Requires a converted
		FASTA/EMBL/GenBank file.
	</help>
	<citations>
		<citation type="bibtex">
			@article{Bland2007,
			abstract = {BACKGROUND:
			Clustered Regularly Interspaced Palindromic Repeats
			(CRISPRs) are a
			novel type of direct repeat found in a wide range of
			bacteria and
			archaea. CRISPRs are beginning to attract attention
			because of their
			proposed mechanism; that is, defending their hosts
			against invading
			extrachromosomal elements such as viruses. Existing
			repeat detection
			tools do a poor job of identifying CRISPRs due to
			the presence of
			unique spacer sequences separating the repeats. In
			this study, a new
			tool, CRT, is introduced that rapidly and
			accurately identifies
			CRISPRs in large DNA strings, such as genomes
			and metagenomes.
			RESULTS: CRT was compared to CRISPR detection tools,
			Patscan and
			Pilercr. In terms of correctness, CRT was shown to be
			very reliable,
			demonstrating significant improvements over Patscan
			for measures
			precision, recall and quality. When compared to Pilercr,
			CRT showed
			improved performance for recall and quality. In terms of
			speed, CRT
			proved to be a huge improvement over Patscan. Both CRT and
			Pilercr
			were comparable in speed, however CRT was faster for genomes
			containing large numbers of repeats. CONCLUSION: In this paper a new
			tool was introduced for the automatic detection of CRISPR elements.
			This tool, CRT, showed some important improvements over current
			techniques for CRISPR identification. CRT's approach to detecting
			repetitive sequences is straightforward. It uses a simple sequential
			scan of a DNA sequence and detects repeats directly without any major
			conversion or preprocessing of the input. This leads to a program
			that is easy to describe and understand; yet it is very accurate,
			fast and memory efficient, being O(n) in space and O(nm/l) in time.},
			author = {Bland, Charles and Ramsey, Teresa L and Sabree, Fareedah
			and Lowe, Micheal and Brown, Kyndall and Kyrpides, Nikos C and
			Hugenholtz, Philip},
			doi = {10.1186/1471-2105-8-209},
			file =
			{:Users/koeho006/Library/Application Support/Mendeley
			Desktop/Downloaded/Bland et al. - 2007 - CRISPR recognition tool
			(CRT) a tool for automatic detection of clustered regularly
			interspaced palindromic repeat.pdf:pdf},
			isbn = {1471-2105
			(Electronic)$\backslash$n1471-2105 (Linking)},
			issn = {14712105},
			journal = {BMC bioinformatics},
			mendeley-groups = {VAPP Application
			note},
			pages = {209},
			pmid = {17577412},
			title = {{CRISPR recognition
			tool (CRT): a tool for automatic detection of
			clustered regularly
			interspaced palindromic repeats.}},
			volume = {8},
			year = {2007}
			}
		</citation>
	</citations>
</tool>