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1 <tool id="gd_add_fst_column" name="Add an FST column" version="1.0.0">
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2 <description>to a table</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="wsf" label="SNP table" />
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14 <param name="p1_input" type="data" format="ind" label="Population 1 individuals" />
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15 <param name="p2_input" type="data" format="ind" 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="wsf" 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="genome_diversity/test_in/sample.wsf" ftype="wsf" />
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49 <param name="p1_input" value="genome_diversity/test_in/a.ind" ftype="ind" />
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50 <param name="p2_input" value="genome_diversity/test_in/b.ind" ftype="ind" />
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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="genome_diversity/test_out/add_fst_column/add_fst_column.wsf" />
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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 **What it does**
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63
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64 The user specifies a SNP table and two "populations" of individuals,
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65 both previously defined using the Galaxy tool to select individuals from
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66 a SNP table. No individual can be in both populations. Other choices are
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67 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 </help>
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90 </tool>
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