Mercurial > repos > miller-lab > genome_diversity
annotate add_fst_column.xml @ 17:a3af29edcce2
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author | miller-lab |
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date | Fri, 28 Sep 2012 11:57:18 -0400 |
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1 <tool id="gd_add_fst_column" name="Per-SNP FSTs" version="1.0.0"> |
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2 <description>: Compute a fixation index score for each SNP</description> |
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3 |
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4 <command interpreter="python"> |
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5 add_fst_column.py "$input" "$p1_input" "$p2_input" "$data_source" "$min_reads" "$min_qual" "$retain" "$discard_fixed" "$biased" "$output" |
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6 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) |
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7 #set $arg = '%s:%s' % ($individual_col, $individual) |
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8 "$arg" |
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9 #end for |
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10 </command> |
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11 |
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12 <inputs> |
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13 <param name="input" type="data" format="gd_snp" label="SNP table" /> |
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14 <param name="p1_input" type="data" format="gd_indivs" label="Population 1 individuals" /> |
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15 <param name="p2_input" type="data" format="gd_indivs" label="Population 2 individuals" /> |
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16 |
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17 <param name="data_source" type="select" format="integer" label="Data source"> |
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18 <option value="0" selected="true">sequence coverage</option> |
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19 <option value="1">estimated genotype</option> |
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20 </param> |
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21 |
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22 <param name="min_reads" type="integer" min="0" value="0" label="Minimum total read count for a population" /> |
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23 <param name="min_qual" type="integer" min="0" value="0" label="Minimum individual genotype quality" /> |
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24 |
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25 <param name="retain" type="select" label="Special treatment"> |
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26 <option value="0" selected="true">Skip row</option> |
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27 <option value="1">Set FST = -1</option> |
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28 </param> |
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29 |
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30 <param name="discard_fixed" type="select" label="Apparently fixed SNPs"> |
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31 <option value="0">Retain SNPs that appear fixed in the two populations</option> |
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32 <option value="1" selected="true">Delete SNPs that appear fixed in the two populations</option> |
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33 </param> |
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34 |
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35 <param name="biased" type="select" label="FST estimator"> |
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36 <option value="0" selected="true">Wright's original definition</option> |
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37 <option value="1">Weir's unbiased estimator</option> |
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38 </param> |
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39 |
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40 </inputs> |
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41 |
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42 <outputs> |
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43 <data name="output" format="gd_snp" metadata_source="input" /> |
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44 </outputs> |
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45 |
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46 <tests> |
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47 <test> |
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48 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> |
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49 <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" /> |
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50 <param name="p2_input" value="test_in/b.gd_indivs" ftype="gd_indivs" /> |
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51 <param name="data_source" value="0" /> |
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52 <param name="min_reads" value="3" /> |
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53 <param name="min_qual" value="0" /> |
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54 <param name="retain" value="0" /> |
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55 <param name="discard_fixed" value="1" /> |
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56 <param name="biased" value="0" /> |
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57 <output name="output" file="test_out/add_fst_column/add_fst_column.gd_snp" /> |
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58 </test> |
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59 </tests> |
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60 |
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61 <help> |
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62 |
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63 **What it does** |
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64 |
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65 The user specifies a SNP table and two "populations" of individuals, |
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66 both previously defined using the Specify Individuals tool. |
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67 No individual can be in both populations. Other choices are as follows. |
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68 |
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69 Data source. The allele frequencies of a SNP in the two populations can be |
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70 estimated either by the total number of reads of each allele, or by adding |
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71 the frequencies inferred from genotypes of individuals in the populations. |
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72 |
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73 After specifying the data source, the user sets lower bounds on amount |
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74 of data required at a SNP. For estimating the Fst using read counts, |
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75 the bound is the minimum count of reads of the two alleles in a population. |
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76 For estimations based on genotype, the bound is the minimum reported genotype |
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77 quality per individual. |
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78 |
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79 The user specifies whether the SNPs that violate the lower bound should be |
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80 ignored or the Fst set to -1. |
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81 |
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82 The user specifies whether SNPs where both populations appear to be fixed |
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83 for the same allele should be retained or discarded. |
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84 |
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85 Finally, the user chooses which definition of Fst to use: Wright's original |
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86 definition or Weir's unbiased estimator. |
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87 |
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88 A column is appended to the SNP table giving the Fst for each retained SNP. |
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89 |
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90 </help> |
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91 </tool> |