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1 <tool id="gd_average_fst" name="Average FST" version="1.0.0">
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2 <description>of two populations</description>
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3
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4 <command interpreter="python">
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5 average_fst.py "$input" "$p1_input" "$p2_input" "$data_source.ds_choice" "$data_source.min_value" "$discard_fixed" "$biased" "$output"
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6 #if $use_randomization.ur_choice == '1'
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7 "$use_randomization.shuffles" "$use_randomization.p0_input"
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8 #else
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9 "0" "/dev/null"
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10 #end if
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11 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
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12 #set $arg = '%s:%s' % ($individual_col, $individual)
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13 "$arg"
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14 #end for
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15 </command>
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16
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17 <inputs>
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18 <param name="input" type="data" format="wsf" label="SNP table" />
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19 <param name="p1_input" type="data" format="ind" label="Population 1 individuals" />
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20 <param name="p2_input" type="data" format="ind" label="Population 2 individuals" />
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21
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22 <conditional name="data_source">
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23 <param name="ds_choice" type="select" format="integer" label="Data source">
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24 <option value="0" selected="true">sequence coverage and ..</option>
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25 <option value="1">estimated genotype and ..</option>
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26 </param>
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27 <when value="0">
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28 <param name="min_value" type="integer" min="1" value="1" label="Minimum total read count for a population" />
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29 </when>
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30 <when value="1">
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31 <param name="min_value" type="integer" min="1" value="1" label="Minimum individual genotype quality" />
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32 </when>
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33 </conditional>
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34
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35 <param name="discard_fixed" type="select" label="Apparently fixed SNPs">
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36 <option value="0">Retain SNPs that appear fixed in the two populations</option>
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37 <option value="1" selected="true">Delete SNPs that appear fixed in the two populations</option>
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38 </param>
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39
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40 <param name="biased" type="select" label="FST estimator">
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41 <option value="0" selected="true">Wright's original definition</option>
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42 <option value="1">Weir's unbiased estimator</option>
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43 </param>
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44
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45 <conditional name="use_randomization">
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46 <param name="ur_choice" type="select" format="integer" label="Use randomization">
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47 <option value="0" selected="true">No</option>
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48 <option value="1">Yes</option>
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49 </param>
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50 <when value="0" />
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51 <when value="1">
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52 <param name="shuffles" type="integer" min="0" value="0" label="Shuffles" />
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53 <param name="p0_input" type="data" format="ind" label="Individuals for randomization" />
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54 </when>
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55 </conditional>
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56 </inputs>
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57
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58 <outputs>
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59 <data name="output" format="txt" />
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60 </outputs>
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61
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62 <tests>
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63 <test>
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64 <param name="input" value="genome_diversity/test_in/sample.wsf" ftype="wsf" />
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65 <param name="p1_input" value="genome_diversity/test_in/a.ind" ftype="ind" />
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66 <param name="p2_input" value="genome_diversity/test_in/b.ind" ftype="ind" />
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67 <param name="ds_choice" value="0" />
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68 <param name="min_value" value="3" />
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69 <param name="discard_fixed" value="1" />
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70 <param name="biased" value="0" />
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71 <param name="ur_choice" value="0" />
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72 <output name="output" file="genome_diversity/test_out/average_fst/average_fst.txt" />
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73 </test>
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74 </tests>
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75
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76 <help>
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77 **What it does**
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78
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79 The user specifies a SNP table and two "populations" of individuals,
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80 both previously defined using the Galaxy tool to select individuals from
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81 a SNP table. No individual can be in both populations. Other choices are
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82 as follows.
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83
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84 Data source. The allele frequencies of a SNP in the two populations can be
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85 estimated either by the total number of reads of each allele, or by adding
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86 the frequencies inferred from genotypes of individuals in the populations.
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87
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88 After specifying the data source, the user sets lower bounds on amount
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89 of data required at a SNP. For estimating the Fst using read counts,
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90 the bound is the minimum count of reads of the two alleles in a population.
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91 For estimations based on genotype, the bound is the minimum reported genotype
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92 quality per individual. SNPs not meeting these lower bounds are ignored.
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93
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94 The user specifies whether SNPs where both populations appear to be fixed
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95 for the same allele should be retained or discarded.
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96
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97 The user chooses which definition of Fst to use: Wright's original definition
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98 or Weir's unbiased estimator.
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99
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100 Finally, the user decides whether to use randomizations. If so, then the
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101 user specifies how many randomly generated population pairs (retaining
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102 the numbers of individuals of the originals) to generate, as well as the
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103 "population" of additional individuals (not in the first two populations)
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104 that can be used in the randomization process.
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105
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106 The program prints the average Fst for the original populations and the
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107 number of SNPs used to compute it. If randomizations were requested,
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108 it prints the average Fst for each randomly generated population pair,
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109 ending with a summary that includes the maximum and average value, and the
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110 highest-scoring population pair.
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111 </help>
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112 </tool>
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