Mercurial > repos > miller-lab > genome_diversity
comparison add_fst_column.xml @ 17:a3af29edcce2
Uploaded Miller Lab Devshed version a51c894f5bed
| author | miller-lab |
|---|---|
| date | Fri, 28 Sep 2012 11:57:18 -0400 |
| parents | 8ae67e9fb6ff |
| children | f04f40a36cc8 |
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| 16:be0e2223c531 | 17:a3af29edcce2 |
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| 1 <tool id="gd_add_fst_column" name="Per-SNP FSTs" version="1.0.0"> | |
| 2 <description>: Compute a fixation index score for each SNP</description> | |
| 3 | |
| 4 <command interpreter="python"> | |
| 5 add_fst_column.py "$input" "$p1_input" "$p2_input" "$data_source" "$min_reads" "$min_qual" "$retain" "$discard_fixed" "$biased" "$output" | |
| 6 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) | |
| 7 #set $arg = '%s:%s' % ($individual_col, $individual) | |
| 8 "$arg" | |
| 9 #end for | |
| 10 </command> | |
| 11 | |
| 12 <inputs> | |
| 13 <param name="input" type="data" format="gd_snp" label="SNP table" /> | |
| 14 <param name="p1_input" type="data" format="gd_indivs" label="Population 1 individuals" /> | |
| 15 <param name="p2_input" type="data" format="gd_indivs" label="Population 2 individuals" /> | |
| 16 | |
| 17 <param name="data_source" type="select" format="integer" label="Data source"> | |
| 18 <option value="0" selected="true">sequence coverage</option> | |
| 19 <option value="1">estimated genotype</option> | |
| 20 </param> | |
| 21 | |
| 22 <param name="min_reads" type="integer" min="0" value="0" label="Minimum total read count for a population" /> | |
| 23 <param name="min_qual" type="integer" min="0" value="0" label="Minimum individual genotype quality" /> | |
| 24 | |
| 25 <param name="retain" type="select" label="Special treatment"> | |
| 26 <option value="0" selected="true">Skip row</option> | |
| 27 <option value="1">Set FST = -1</option> | |
| 28 </param> | |
| 29 | |
| 30 <param name="discard_fixed" type="select" label="Apparently fixed SNPs"> | |
| 31 <option value="0">Retain SNPs that appear fixed in the two populations</option> | |
| 32 <option value="1" selected="true">Delete SNPs that appear fixed in the two populations</option> | |
| 33 </param> | |
| 34 | |
| 35 <param name="biased" type="select" label="FST estimator"> | |
| 36 <option value="0" selected="true">Wright's original definition</option> | |
| 37 <option value="1">Weir's unbiased estimator</option> | |
| 38 </param> | |
| 39 | |
| 40 </inputs> | |
| 41 | |
| 42 <outputs> | |
| 43 <data name="output" format="gd_snp" metadata_source="input" /> | |
| 44 </outputs> | |
| 45 | |
| 46 <tests> | |
| 47 <test> | |
| 48 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> | |
| 49 <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" /> | |
| 50 <param name="p2_input" value="test_in/b.gd_indivs" ftype="gd_indivs" /> | |
| 51 <param name="data_source" value="0" /> | |
| 52 <param name="min_reads" value="3" /> | |
| 53 <param name="min_qual" value="0" /> | |
| 54 <param name="retain" value="0" /> | |
| 55 <param name="discard_fixed" value="1" /> | |
| 56 <param name="biased" value="0" /> | |
| 57 <output name="output" file="test_out/add_fst_column/add_fst_column.gd_snp" /> | |
| 58 </test> | |
| 59 </tests> | |
| 60 | |
| 61 <help> | |
| 62 | |
| 63 **What it does** | |
| 64 | |
| 65 The user specifies a SNP table and two "populations" of individuals, | |
| 66 both previously defined using the Specify Individuals tool. | |
| 67 No individual can be in both populations. Other choices are as follows. | |
| 68 | |
| 69 Data source. The allele frequencies of a SNP in the two populations can be | |
| 70 estimated either by the total number of reads of each allele, or by adding | |
| 71 the frequencies inferred from genotypes of individuals in the populations. | |
| 72 | |
| 73 After specifying the data source, the user sets lower bounds on amount | |
| 74 of data required at a SNP. For estimating the Fst using read counts, | |
| 75 the bound is the minimum count of reads of the two alleles in a population. | |
| 76 For estimations based on genotype, the bound is the minimum reported genotype | |
| 77 quality per individual. | |
| 78 | |
| 79 The user specifies whether the SNPs that violate the lower bound should be | |
| 80 ignored or the Fst set to -1. | |
| 81 | |
| 82 The user specifies whether SNPs where both populations appear to be fixed | |
| 83 for the same allele should be retained or discarded. | |
| 84 | |
| 85 Finally, the user chooses which definition of Fst to use: Wright's original | |
| 86 definition or Weir's unbiased estimator. | |
| 87 | |
| 88 A column is appended to the SNP table giving the Fst for each retained SNP. | |
| 89 | |
| 90 </help> | |
| 91 </tool> |