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1 <?xml version="1.0"?>
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2 <tool id="Genetic_Marker_Design_2" name="Design primers to features">
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3 <description>Design PCR Primers to Features</description>
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5
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4 <command interpreter="python -W ignore">
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5 #if 'Yes' in $uMelt.value
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6 design_primers.py -i $inputfastaFile -g $inputSNPfile -T $inputTargetfile -p $min_size -P $max_size -u > $primer_outputfile
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7 #else
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8 design_primers.py -i $inputfastaFile -g $inputSNPfile -T $inputTargetfile -p $min_size -P $max_size > $primer_outputfile
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9 #end if
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10 </command>
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11
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12 <inputs>
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13 <param format="fasta" name="inputfastaFile" type="data" label="Multifasta Source file" />
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14 <param format="gff3" name="inputSNPfile" type="data" label="annotation file(Gff3)" />
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15 <param format="txt" name="inputTargetfile" type="data" optional="false" label="Target file" help="IN FORMAT Sequence id:source:type:start e.g. 1174806:gsMapper:SNP:292" ></param>
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16 <param name="min_size" size="20" type="text" value="75" label="Minimum Product Size Range" />
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17 <param name="max_size" size="20" type="text" value="100" label="Maximum Product Size Range" />
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18 <param name="uMelt" type="select" label="uMelt prediction for HRM">
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19 <option value="No" selected= "true">No</option>
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20 <option value="Yes">Yes</option>
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21 </param>
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22 </inputs>
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23 <outputs>
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24 <data format="tabular" name="primer_outputfile" />
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25 </outputs>
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26 <stdio>
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27 <exit_code range="1:" level="fatal" description="Fatal Error" />
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28 </stdio>
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29 <help>
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30 .. class:: infomark
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31
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32 **TIP**
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33
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34 This tool designs primer pairs to flank features
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35 Optionally it can predict reference and variant Tm using the uMelt web service provided by University of Utah
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36
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37 It takes
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38
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39 * an input reference sequence file
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40 * a gff3 file containing feature information
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41 * a single column file containing list of features
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42
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43 ----
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44
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45 **Example**
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46
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47 --input GFF
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48
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49 ::
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50
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51 PGSC0003DMB000000001 samtools SNP 6345 6346 4.84 . . ID=PGSC0003DMB000000001:SAMTOOLS:SNP:6345;Variant_seq=C;Reference_seq=T;Total_reads=2
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52 PGSC0003DMB000000001 samtools SNP 6453 6454 18 . . ID=PGSC0003DMB000000001:SAMTOOLS:SNP:6453;Variant_seq=T;Reference_seq=G;Total_reads=8
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53 PGSC0003DMB000000001 samtools SNP 7255 7256 149 . . ID=PGSC0003DMB000000001:SAMTOOLS:SNP:7255;Variant_seq=G;Reference_seq=T;Total_reads=14
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54 PGSC0003DMB000000001 samtools SNP 7371 7372 86.8 . . ID=PGSC0003DMB000000001:SAMTOOLS:SNP:7371;Variant_seq=C;Reference_seq=T;Total_reads=9
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55 PGSC0003DMB000000001 samtools SNP 8288 8289 10.7 . . ID=PGSC0003DMB000000001:SAMTOOLS:SNP:8288;Variant_seq=A;Reference_seq=G;Total_reads=5
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56
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57
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58 --input features
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59
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60 ::
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61
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62 PGSC0003DMB000000001:SAMTOOLS:SNP:1012901
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63 PGSC0003DMB000000001:SAMTOOLS:SNP:1021771
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64 PGSC0003DMB000000001:SAMTOOLS:SNP:1025761
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65 PGSC0003DMB000000001:SAMTOOLS:SNP:1026717
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66 PGSC0003DMB000000001:SAMTOOLS:SNP:1026834
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67 PGSC0003DMB000000001:SAMTOOLS:SNP:1029542
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68
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69
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70 --output columnar data
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71
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72 ::
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73
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74 PGSC0003DMB000000001:SAMTOOLS:SNP:1012901 AGAGGTCGGCTCTCTAGTAGCA GGGGATCCACTAACTATGTCACTT 86
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75 PGSC0003DMB000000001:SAMTOOLS:SNP:1021771 CCTATGCGAGAAAGGGACAC GCCCTTCCATGTTGTACGAG 100
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76 PGSC0003DMB000000001:SAMTOOLS:SNP:1025761 TGTGAGTAACTTAGTGTCCTACGTCAA CACTCAATGAGCCAAAGCAA 92
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77 PGSC0003DMB000000001:SAMTOOLS:SNP:1026717 TTCCTAAGTCATGGGAAAGCA AGTTCATCCAAGGCAAGCAT 76
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78 PGSC0003DMB000000001:SAMTOOLS:SNP:1026834 AATGAAGTGACTGGGGAGGA TGCTGGTCGAAGCTTTCTTT 98
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79 PGSC0003DMB000000001:SAMTOOLS:SNP:1029542 TAACCAGAAAGTCCGGATGG TTCTGAAGTCAAGTGGGGAGA 75
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80
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81 -----------------------
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82
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83 *If you use this tool please cite:*
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84
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85 A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data:
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86 Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
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87 (2012)
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88
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89 Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright,
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90 Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
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91
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92 </help>
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93
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94 </tool>
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