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1 <?xml version="1.0"?>
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2 <tool id="CAPS_Marker_Design_2" name="CAPS Detection">
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3 <description>identify SNPs that condition restriction polymorphisms</description>
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4 <command interpreter="python">find_CAPS.py $inputFasta $inputSNPGff3File > $outputfile</command>
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5 <inputs>
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6 <param format="gff3" name="inputSNPGff3File" type="data" label="GFF3 file containing SNP data"/>
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7 <param format="fasta" name="inputFasta" type="data" label="fasta source file" />
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8 </inputs>
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9 <outputs>
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10 <data format="interval" name="outputfile" />
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11 </outputs>
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5
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12 <tests>
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13 <test>
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14 <param name="inputSNPGff3File" value="targets.gff" ftype="gff3"/>
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15 <param name="inputFasta" value="targets.fasta" ftype="fasta"/>
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16 <output name="outputfile" file="find_caps_output.txt"/>
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17 </test>
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18 </tests>
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19 <help>
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20 .. class:: infomark
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21
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22 **TIP**
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23
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24 This tool identifies SNPs that condition restriction polymorphisms.
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25
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26 Currently it utilizes a fixed list of robust enzymes known to work well in PCR buffers
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27
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28 AluI,ApaI,BamHI,BbrPI,BfrI,ClaI,DpnI,DraI,EcoRI,HaeIII,HindII,HinfI,HpaI,PvuII,RsaI,SacI,Sau3AI,SmaI,TaqI
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29
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30 It produces a tabular output in interval format
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31
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32 record ID, start, stop, feature ID,enzyme, phase (ie whether it cuts reference or variant sequence)
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33
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34
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35
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36
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37
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38 **Example**
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39
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40
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41
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42 *input GFF3*
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43
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44 ::
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45
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46 JR843866 gsmapper SNP 63 63 . . . ID=JR843866:gsmapperSNP:63;Reference_seq=T;Variant_seq=C;Total_reads=22;Variant_reads=20
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47 JR843866 gsmapper SNP 146 146 . . . ID=JR843866:gsmapperSNP:146;Reference_seq=T;Variant_seq=C;Total_reads=26;Variant_reads=10
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48 JR843866 gsmapper SNP 258 258 . . . ID=JR843866:gsmapperSNP:258;Reference_seq=T;Variant_seq=G;Total_reads=4;Variant_reads=3
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49 JR848320 gsmapper SNP 157 157 . . . ID=JR848320:gsmapperSNP:157;Reference_seq=C;Variant_seq=T;Total_reads=10;Variant_reads=10
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50 JR848554 gsmapper SNP 54 54 . . . ID=JR848554:gsmapperSNP:54;Reference_seq=T;Variant_seq=G;Total_reads=5;Variant_reads=5
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51 JR848554 gsmapper SNP 74 74 . . . ID=JR848554:gsmapperSNP:74;Reference_seq=C;Variant_seq=T;Total_reads=7;Variant_reads=7
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52 JR848554 gsmapper SNP 123 123 . . . ID=JR848554:gsmapperSNP:123;Reference_seq=T;Variant_seq=A;Total_reads=11;Variant_reads=11
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53 JR848554 gsmapper SNP 147 147 . . . ID=JR848554:gsmapperSNP:147;Reference_seq=T;Variant_seq=C;Total_reads=13;Variant_reads=13
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54 JR848554 gsmapper SNP 161 161 . . . ID=JR848554:gsmapperSNP:161;Reference_seq=C;Variant_seq=T;Total_reads=13;Variant_reads=13
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55
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56
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57
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58 *output columnar data*
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59
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60 ::
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61
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62 JR843866 63 64 JR843866:gsmapperSNP:63 HaeIII variant
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63 JR848320 157 158 JR848320:gsmapperSNP:157 TaqI variant
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64 JR848320 157 158 JR848320:gsmapperSNP:157 HinfI variant
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65 JR848554 162 163 JR848554:gsmapperSNP:162 TaqI variant
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66 JR848554 162 163 JR848554:gsmapperSNP:162 ClaI variant
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67 JR848554 306 307 JR848554:gsmapperSNP:306 TaqI variant
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68 JR848554 652 653 JR848554:gsmapperSNP:652 TaqI variant
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69
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70
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71 -------------------------------------------------------------------------------
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72
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73
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74 *If you use this tool please cite:*
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75
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76 A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data:
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77 Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
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78 (2012)
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79
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80 Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright,
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81 Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
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82
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83
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84
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85
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86
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87 </help>
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88 </tool>
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