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comparison find_CAPS.xml @ 0:21053f7f9ed1 draft

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First upload of PCR Marker tools
author john-mccallum
date Thu, 14 Jun 2012 19:29:26 -0400
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children b321e0517be3
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-1:000000000000 0:21053f7f9ed1
1 <?xml version="1.0"?>
2 <tool id="CAPS_Marker_Design_2" name="CAPS Detection">
3 <description>identify SNPs that condition restriction polymorphisms</description>
4 <command interpreter="python">find_CAPS.py $inputFasta $inputSNPGff3File > $outputfile</command>
5 <inputs>
6 <param format="gff3" name="inputSNPGff3File" type="data" label="GFF3 file containing SNP data"/>
7 <param format="fasta" name="inputFasta" type="data" label="fasta source file" />
8 </inputs>
9 <outputs>
10 <data format="interval" name="outputfile" />
11 </outputs>
12 <help>
13 .. class:: infomark
14
15 **TIP**
16
17 This tool identifies SNPs that condition restriction polymorphisms.
18
19 Currently it utilizes a fixed list of robust enzymes known to work well in PCR buffers
20
21 AluI,ApaI,BamHI,BbrPI,BfrI,ClaI,DpnI,DraI,EcoRI,HaeIII,HindII,HinfI,HpaI,PvuII,RsaI,SacI,Sau3AI,SmaI,TaqI
22
23 It produces a tabular output in interval format
24
25 record ID, start, stop, feature ID,enzyme, phase (ie whether it cuts reference or variant sequence)
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27
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29
30
31 **Example**
32
33
34
35 *input GFF*
36
37 ::
38
39 JR843866 gsmapper SNP 63 63 . . . ID=JR843866:gsmapperSNP:63;Reference_seq=T;Variant_seq=C;Total_reads=22;Variant_reads=20
40 JR843866 gsmapper SNP 146 146 . . . ID=JR843866:gsmapperSNP:146;Reference_seq=T;Variant_seq=C;Total_reads=26;Variant_reads=10
41 JR843866 gsmapper SNP 258 258 . . . ID=JR843866:gsmapperSNP:258;Reference_seq=T;Variant_seq=G;Total_reads=4;Variant_reads=3
42 JR848320 gsmapper SNP 157 157 . . . ID=JR848320:gsmapperSNP:157;Reference_seq=C;Variant_seq=T;Total_reads=10;Variant_reads=10
43 JR848554 gsmapper SNP 54 54 . . . ID=JR848554:gsmapperSNP:54;Reference_seq=T;Variant_seq=G;Total_reads=5;Variant_reads=5
44 JR848554 gsmapper SNP 74 74 . . . ID=JR848554:gsmapperSNP:74;Reference_seq=C;Variant_seq=T;Total_reads=7;Variant_reads=7
45 JR848554 gsmapper SNP 123 123 . . . ID=JR848554:gsmapperSNP:123;Reference_seq=T;Variant_seq=A;Total_reads=11;Variant_reads=11
46 JR848554 gsmapper SNP 147 147 . . . ID=JR848554:gsmapperSNP:147;Reference_seq=T;Variant_seq=C;Total_reads=13;Variant_reads=13
47 JR848554 gsmapper SNP 161 161 . . . ID=JR848554:gsmapperSNP:161;Reference_seq=C;Variant_seq=T;Total_reads=13;Variant_reads=13
48
49
50
51 *output columnar data*
52
53 ::
54
55 JR843866 63 64 JR843866:gsmapperSNP:63 HaeIII variant
56 JR848320 157 158 JR848320:gsmapperSNP:157 TaqI variant
57 JR848320 157 158 JR848320:gsmapperSNP:157 HinfI variant
58 JR848554 162 163 JR848554:gsmapperSNP:162 TaqI variant
59 JR848554 162 163 JR848554:gsmapperSNP:162 ClaI variant
60 JR848554 306 307 JR848554:gsmapperSNP:306 TaqI variant
61 JR848554 652 653 JR848554:gsmapperSNP:652 TaqI variant
62
63
64 -------------------------------------------------------------------------------
65
66
67 *If you use this tool please cite:*
68
69 A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data:
70 Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
71 (2012)
72
73 Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright,
74 Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
75
76
77
78
79
80 </help>
81 </tool>