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comparison compare2sequences.xml @ 6:10db17004ffa draft

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author alperkucukural
date Wed, 04 Nov 2015 15:30:22 -0500
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1 <tool id="compare2sequences" name="compare2sequences" version="1.0.0">
2 <description>CRISPRSeek compare2sequences</description>
3 <macros>
4 <import>crisprseek_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code">
8 Rscript "${compare2sequences}"
9 </command>
10 <configfiles>
11 <configfile name="compare2sequences"><![CDATA[
12 ## code chunk: Load all required libraries quietly
13 library(CRISPRseek, quietly=TRUE, warn.conflicts=FALSE,verbose = FALSE)
14
15 compare2Sequences("${s1.inputfile}", "${s2.inputfile}", inputNames=c("Seq1", "Seq2"), REpatternFile = system.file('extdata', 'NEBenzymes.fa', package = 'CRISPRseek'), max.mismatch="${maxmismatch}", searchDirection="${a.searchDirection}", findPairedgRNAOnly=${a.fg.fpg_only}, min.gap = "${a.fg.mingap}", max.gap = "${a.fg.maxgap}", gRNA.name.prefix = "gRNA", PAM.size = "${a.PAMsize}", gRNA.size = "${a.gRNAsize}", PAM = "${a.PAM}", PAM.pattern = "${a.PAMPattern}", outputDir, weights="${a.weights}" )
16
17 ]]></configfile>
18 </configfiles>
19 <inputs>
20 <conditional name="s1">
21 <param name="input_source" type="select" label="Select Input File Path" help="Sequence input file path that contains sequences to be searched for potential gRNAs">
22 <option value="history">History</option>
23 <option value="FullPath">Free Text</option>
24 <option value="Fasta">Fasta</option>
25 </param>
26 <when value="FullPath">
27 <param name="inputfile" type="text" area="true" size="2x60" label="Input File Path" help="Full path in the cluster"/>
28 </when>
29 <when value="Fasta">
30 <param name="inputfile" type="text" area="true" size="2x60" label="Input Fasta Sequence/s" help="Free text fasta sequences"/>
31 </when>
32 <when value="history">
33 <param format="fastq,fa,fasta" name="inputfile" type="data" label="Input File Path" />
34 </when>
35 </conditional>
36 <conditional name="s2">
37 <param name="input_source" type="select" label="Select Input File Path" help="Sequence input file path that contains sequences to be searched for potential gRNAs">
38 <option value="history">History</option>
39 <option value="FullPath">Free Text</option>
40 <option value="Fasta">Fasta</option>
41 </param>
42 <when value="FullPath">
43 <param name="inputfile" type="text" area="true" size="2x60" label="Input File Path" help="Full path in the cluster"/>
44 </when>
45 <when value="Fasta">
46 <param name="inputfile" type="text" area="true" size="2x60" label="Input Fasta Sequence/s" help="Free text fasta sequences"/>
47 </when>
48 <when value="history">
49 <param format="fastq,fa,fasta" name="inputfile" type="data" label="Input File Path" />
50 </when>
51 </conditional>
52 <param name="maxmismatch" type="text" label="Max Mismatch" value="3" help="Maximum mismatch allowed in off target search, default 3. Warning: will be considerably slower if set > 3"/>
53 <param name="outputdir" type="text" area="true" size="2x60" label="Output Directory" help="Output directory in the cluster"/>
54 <conditional name="a">
55 <param name="advanced" type="select" label="Advanced Options">
56 <option value="No" selected="True">No</option>
57 <option value="Yes">Yes</option>
58 </param>
59 <when value="Yes">
60 <param name="searchDirection" type="select" label="Search Direction">
61 <option value="both" selected="True">both</option>
62 <option value="1to2">1to2</option>
63 <option value="2to1">2to1</option>
64 </param>
65 <conditional name="fg">
66 <param name="fpg_only" type="select" label="Find Paired gRNA Only" help="Choose whether to only search for paired gRNAs in such an orientation that the first one is on minus strand called reverse gRNA and the second one is on plus strand called forward gRNA. TRUE or FALSE, default FALSE">
67 <option value="FALSE" selected="True">No</option>
68 <option value="TRUE">Yes</option>
69 </param>
70 <when value="True">
71 <param name="mingap" type="text" label="Min Gap" value="0" />
72 <param name="maxgap" type="text" label="Max Gap" value="20" />
73 </when>
74 </conditional>
75 <param name="PAMsize" type="text" label="PAM Size" value="3" help="PAM length, default 3"/>
76 <param name="PAM" type="text" label="PAM" value="NGG" help="PAM sequence after the gRNA, default NGG"/>
77 <param name="PAMPattern" type="text" label="PAM Pattern" value="N[A_p_G]G_d_" help="Regular expression of protospacer-adjacent motif (PAM), default N[A|G]G$. Please use _p_ for | and _d_ for $ symbols"/>
78 <param name="gRNAsize" type="text" label="gRNA Size" value="20" help="The size of the gRNA, default 20"/>
79 <param name="weights" type="text" area="true" size="5x60" value="0, 0, 0.014, 0, 0, 0.395, 0.317, 0, 0.389, 0.079, 0.445, 0.508, 0.613, 0.851, 0.732, 0.828, 0.615, 0.804, 0.685, 0.583" label="Off Target Weights" help="a numeric vector size of gRNA length, default 0, 0, 0.014, 0, 0, 0.395, 0.317, 0, 0.389, 0.079, 0.445, 0.508, 0.613, 0.851, 0.732, 0.828, 0.615, 0.804, 0.685, 0.583 which is used in Hsu et al., 2013 cited in the reference section"/>
80 </when>
81 </conditional>
82 </inputs>
83 <outputs>
84 <data format="gz" name="output"/>
85 </outputs>
86 <help>
87
88 **What it does**
89
90 The package includes functions to find potential guide RNAs for input target se-
91 quences, optionally filter guide RNAs without restriction enzyme cut site, or with-
92 out paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank se-
93 quence and indicate whether the target and off-targets are located in exon region or not. Poten-
94 tial guide RNAs are annotated with total score of the top5 and topN off-targets, de-
95 tailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs.
96
97 **Description**
98
99 Generate all possible guide RNAs (gRNAs) for two input sequences, or two sets of sequences and generate scores for potential off-targets in the other sequence.
100
101 **Usage**
102
103 compare2Sequences(inputFile1Path, inputFile2Path, inputNames=c("Seq1", "Seq2"), format = "fasta", findgRNAsWithREcutOnly = FALSE, searchDirection=c("both","1to2", "2to1"), REpatternFile=system.file("extdata", "NEBenzymes.fa", package = "CRISPRseek"), minREpatternSize = 6, overlap.gRNA.positions = c(17, 18), findPairedgRNAOnly = FALSE, min.gap = 0, max.gap = 20, gRNA.name.prefix = "gRNA", PAM.size = 3, gRNA.size = 20, PAM = "NGG", PAM.pattern = "N[A|G]G$", max.mismatch = 3, outputDir, weights = c(0, 0, 0.014, 0, 0, 0.395, 0.317, 0, 0.389, 0.079, 0.445, 0.508, 0.613, 0.851, 0.732, 0.828, 0.615, 0.804, 0.685, 0.583), overwrite = FALSE)
104
105 **Author(s)**
106
107 Lihua Julie Zhu and Michael Brodsky Maintainer: julie.zhu@umassmed.edu
108
109 Alper Kucukural, Galaxy Maintainer: alper.kucukural@umassmed.edu
110
111 **Citation**
112
113 (from within R, enter citation("CRISPRseek")):
114
115 Zhu LJ, Holmes BR, Aronin N and Brodsky MH (2014). “CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems.” PLoS one, 9(9). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172692/.
116
117 **References**
118
119 Patrick D Hsu, David A Scott, Joshua A Weinstein, F Ann Ran, Silvana Konermann, Vineeta Agar-
120 wala, Yinqing Li, Eli J Fine, Xuebing Wu, Ophir Shalem, Thomas J Cradick, Luciano A Marraffini,
121 Gang Bao, Feng Zhang (2013) DNA targeting specificity of rNA-guided Cas9 nucleases. Nature
122 Biotechnology 31:827-83
123
124 Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM.CAS9
125 transcriptional activators for target specificity screening and paired nickases for cooperative genome
126 engineering. Nat Biotechnol. 2013. 31(9):833-8 Patrick D Hsu, David A Scott, Joshua A Wein-
127 stein, F Ann Ran, Silvana Konermann, Vineeta Agarwala, Yinqing Li, Eli J Fine, Xuebing Wu,
128 Ophir Shalem, Thomas J Cradick, Luciano A Marraffini, Gang Bao, Feng Zhang. DNA targeting
129 specificity of rNA-guided Cas9 nucleases. Nat Biotechnol. 2013. 31:827-834
130
131 **Reference Manual and Materials**
132
133 http://www.bioconductor.org/packages/release/bioc/vignettes/CRISPRseek/inst/doc/CRISPRseek.pdf
134
135 http://www.bioconductor.org/packages/release/bioc/manuals/CRISPRseek/man/CRISPRseek.pdf
136
137 http://www.bioconductor.org/packages/release/bioc/vignettes/CRISPRseek/inst/doc/CRISPRseek.R
138
139
140
141
142
143 </help>
144 <expand macro="citations" />
145
146 </tool>
147