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1 <tool id="gd_extract_primers" name="Extract primers" version="1.0.0">
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2 <description>for selected SNPs</description>
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3
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4 <command interpreter="python">
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5 extract_primers.py "--input=$input" "--output=$output" "--primers_loc=${GALAXY_DATA_INDEX_DIR}/gd.primers.loc"
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6 #if $override_metadata.choice == "0":
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7 "--scaffold_col=${input.metadata.scaffold}" "--pos_col=${input.metadata.pos}" "--species=${input.metadata.species}"
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8 #else
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9 "--scaffold_col=$scaf_col" "--pos_col=$pos_col" "--species=$species"
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10 #end if
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11 </command>
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12
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13 <inputs>
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14 <param format="tabular" name="input" type="data" label="Selected SNPS dataset"/>
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15 <conditional name="override_metadata">
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16 <param name="choice" type="select" format="integer" label="choose columns">
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17 <option value="0" selected="true">No, get columns from metadata</option>
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18 <option value="1" >Yes, choose columns</option>
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19 </param>
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20 <when value="0" />
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21 <when value="1">
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22 <param name="scaf_col" type="data_column" data_ref="input" numerical="false" label="Column with scaffold"/>
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23 <param name="pos_col" type="data_column" data_ref="input" numerical="true" label="Column with position"/>
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24 <param name="species" type="select" label="Choose species">
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25 <options from_file="gd.species.txt">
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26 <column name="name" index="1"/>
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27 <column name="value" index="0"/>
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28 </options>
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29 </param>
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30 </when>
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31 </conditional>
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32 </inputs>
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33
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34 <outputs>
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35 <data format="txt" name="output"/>
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36 </outputs>
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37
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38 <tests>
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39 <test>
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40 <param name="input" value="test_out/select_snps/select_snps.gd_snp" ftype="gd_snp" />
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41 <param name="choice" value="0"/>
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42 <output name="output" file="test_out/extract_primers/extract_primers.txt" />
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43 </test>
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44 </tests>
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45
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46
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47 <help>
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48 **What it does**
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49
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50 This tool extracts primers for SNPs in the dataset using the Primer3 program.
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51 The first line of output for a given SNP reports the name of the assembled
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52 contig, the SNP's position in the contig, the two variant nucleotides, and
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53 Primer3's "pair penalty". The next line, if not blank, names restriction
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54 enzymes (from the user-adjustable list) that differentially cut at that
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55 site, but do not cut at any other position between and including the
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56 primer positions. The next lines show the SNP's flanking regions, with
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57 the SNP position indicated by "n", including the primer positions and an
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58 additional 3 nucleotides.
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59
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60 -----
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61
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62 **Example**
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63
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64 - input file::
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65
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66 chr5_30800874_30802049 734 G A chr5 30801606 A 24 0 99 4 11 97 Y 496 0.502 0.033 0.215 6
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67 chr8_55117827_55119487 994 A G chr8 55118815 G 25 0 102 4 11 96 Y 22 0.502 0.025 2.365 1
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68 chr9_100484836_100485311 355 C T chr9 100485200 T 27 0 108 6 17 100 Y 190 0.512 0.880 2.733 4
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69 chr12_3635530_3637738 2101 T C chr12 3637630 T 25 0 102 4 13 93 Y 169 0.554 0.024 0.366 4
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70
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71 - output file::
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72
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73 chr5_30800874_30802049 734 G A 0.352964
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74 BglII,MboI,Sau3AI,Tru9I,XhoII
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75 1 CTGAAGGTGAGCAGGATTCAGGAGACAGAAAACAAAGCCCAGGCCTGCCCAAGGTGGAAA
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76 >>>>>>>>>>>>>>>>>>>>
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77
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78 61 AGTCTAACAACTCGCCCTCTGCTTAnATCTGAGACTCACAGGGATAATAACACACTTGGT
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79
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80
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81 21 CAAGGAATAAACTAGATATTATTCACTCCTCTAGAAGGCTGCCAGGAAAATTGCCTGACT
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82 <<<<<<<
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83
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84 181 TGAACCTTGGCTCTGA
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85 <<<<<<<<<<<<<
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86 etc.
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87 </help>
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88 </tool>
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