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Updates to Admixture, Aggregate Individuals, and Restore Attributes to support gd_genotype
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 03 Jun 2013 12:29:29 -0400
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1 <tool id="gd_extract_primers" name="Pick Primers" version="1.0.0">
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2 <description>: Find suitable PCR primers for 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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13 <inputs>
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14 <param format="tabular" name="input" type="data" label="SNP dataset"/>
14
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15 <conditional name="override_metadata">
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16 <param name="choice" type="select" format="integer" label="Choose columns" help="Datasets in gd_snp format have the columns in the metadata, all others need the columns chosen." >
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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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46
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47 <help>
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48
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49 **Dataset formats**
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50
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51 The input dataset is in tabular_ format and must contain a scaffold or
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52 chromosome column and a position column. The output dataset is in text_
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53 format as described below.
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54 (`Dataset missing?`_)
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55
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56 .. _tabular: ./static/formatHelp.html#tab
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57 .. _text: ./static/formatHelp.html#text
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58 .. _Dataset missing?: ./static/formatHelp.html
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59
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60 -----
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61
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62 **What it does**
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63
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64 This tool extracts primers for SNPs in the dataset using the Primer3 program
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65 (Steve Rozen and Helen J. Skaletsky, 2000).
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66 The first line of output for a given SNP reports the name of the assembled
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67 contig, the SNP's position in the contig, the two variant nucleotides, and
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68 Primer3's "pair penalty". The next line, if not blank, names restriction
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69 enzymes (from the user-adjustable list) that differentially cut at that
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70 site, but do not cut at any other position between and including the
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71 primer positions. The next lines show the SNP's flanking regions, with
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72 the SNP position indicated by "n", including the primer positions and an
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73 additional 3 nucleotides.
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74 <!-- is this precomputed?? how, where is the user-adjustable list? -->
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76 -----
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77
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78 **Example**
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79
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80 - input (gd_snp format)::
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81
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82 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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83 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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84 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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85 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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86 etc.
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87
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88 - output::
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89
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90 chr5_30800874_30802049 734 G A 0.352964
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91 BglII,MboI,Sau3AI,Tru9I,XhoII
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92 1 CTGAAGGTGAGCAGGATTCAGGAGACAGAAAACAAAGCCCAGGCCTGCCCAAGGTGGAAA
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93 >>>>>>>>>>>>>>>>>>>>
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94
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95 61 AGTCTAACAACTCGCCCTCTGCTTAnATCTGAGACTCACAGGGATAATAACACACTTGGT
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97
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98 21 CAAGGAATAAACTAGATATTATTCACTCCTCTAGAAGGCTGCCAGGAAAATTGCCTGACT
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99 &lt;&lt;&lt;&lt;&lt;&lt;&lt;
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100
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101 181 TGAACCTTGGCTCTGA
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102 &lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;
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103 etc.
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104
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105 </help>
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106 </tool>