Mercurial > repos > alperkucukural > crisprseek

comparison compare2sequences.xml @ 7:ca68df041d0d draft default tip

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planemo upload
author alperkucukural
date Wed, 04 Nov 2015 16:46:58 -0500
parents 10db17004ffa
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6:10db17004ffa 7:ca68df041d0d
10 <configfiles> 10 <configfiles>
11 <configfile name="compare2sequences"><![CDATA[ 11 <configfile name="compare2sequences"><![CDATA[
12 ## code chunk: Load all required libraries quietly 12 ## code chunk: Load all required libraries quietly
13 library(CRISPRseek, quietly=TRUE, warn.conflicts=FALSE,verbose = FALSE) 13 library(CRISPRseek, quietly=TRUE, warn.conflicts=FALSE,verbose = FALSE)
14 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}" ) 15 compare2Sequences("${inputfile1}", "${inputfile2}", inputNames=c("Seq1", "Seq2"), REpatternFile = system.file('extdata', 'NEBenzymes.fa', package = 'CRISPRseek'), max.mismatch="${maxmismatch}", searchDirection="both", findPairedgRNAOnly=${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 16
17 ]]></configfile> 17 ]]></configfile>
18 </configfiles> 18 </configfiles>
19 <inputs> 19 <inputs>
20 <conditional name="s1"> 20 <param format="fastq,fa,fasta" name="inputfile1" type="data" label="Input File Path" />
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"> 21 <param format="fastq,fa,fasta" name="inputfile2" type="data" label="Input File Path" />
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"/> 22 <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"> 23 <conditional name="a">
55 <param name="advanced" type="select" label="Advanced Options"> 24 <param name="advanced" type="select" label="Advanced Options">
56 <option value="No" selected="True">No</option> 25 <option value="No" selected="True">No</option>
57 <option value="Yes">Yes</option> 26 <option value="Yes">Yes</option>
58 </param> 27 </param>