diff crt.xml @ 35:fa736576c7ed draft

planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty

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+<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>