Mercurial > repos > miller-lab > genome_diversity
annotate average_fst.xml @ 10:9b92372de9f6
rename snp to gsSnp, sap to gdSap
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Tue, 04 Sep 2012 12:49:53 -0400 |
| parents | e29f4d801bb0 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="gd_average_fst" name="Average FST" version="1.0.0"> |
| 2 <description>of two populations</description> | |
| 3 | |
| 4 <command interpreter="python"> | |
| 5 average_fst.py "$input" "$p1_input" "$p2_input" "$data_source.ds_choice" "$data_source.min_value" "$discard_fixed" "$biased" "$output" | |
| 6 #if $use_randomization.ur_choice == '1' | |
| 7 "$use_randomization.shuffles" "$use_randomization.p0_input" | |
| 8 #else | |
| 9 "0" "/dev/null" | |
| 10 #end if | |
| 11 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) | |
| 12 #set $arg = '%s:%s' % ($individual_col, $individual) | |
| 13 "$arg" | |
| 14 #end for | |
| 15 </command> | |
| 16 | |
| 17 <inputs> | |
|
10
9b92372de9f6
rename snp to gsSnp, sap to gdSap
Richard Burhans <burhans@bx.psu.edu>
parents:
7
diff
changeset
|
18 <param name="input" type="data" format="gdSnp" label="SNP table" /> |
| 0 | 19 <param name="p1_input" type="data" format="ind" label="Population 1 individuals" /> |
| 20 <param name="p2_input" type="data" format="ind" label="Population 2 individuals" /> | |
| 21 | |
| 22 <conditional name="data_source"> | |
| 23 <param name="ds_choice" type="select" format="integer" label="Data source"> | |
| 24 <option value="0" selected="true">sequence coverage and ..</option> | |
| 25 <option value="1">estimated genotype and ..</option> | |
| 26 </param> | |
| 27 <when value="0"> | |
| 28 <param name="min_value" type="integer" min="1" value="1" label="Minimum total read count for a population" /> | |
| 29 </when> | |
| 30 <when value="1"> | |
| 31 <param name="min_value" type="integer" min="1" value="1" label="Minimum individual genotype quality" /> | |
| 32 </when> | |
| 33 </conditional> | |
| 34 | |
| 35 <param name="discard_fixed" type="select" label="Apparently fixed SNPs"> | |
| 36 <option value="0">Retain SNPs that appear fixed in the two populations</option> | |
| 37 <option value="1" selected="true">Delete SNPs that appear fixed in the two populations</option> | |
| 38 </param> | |
| 39 | |
| 40 <param name="biased" type="select" label="FST estimator"> | |
| 41 <option value="0" selected="true">Wright's original definition</option> | |
| 42 <option value="1">Weir's unbiased estimator</option> | |
| 43 </param> | |
| 44 | |
| 45 <conditional name="use_randomization"> | |
| 46 <param name="ur_choice" type="select" format="integer" label="Use randomization"> | |
| 47 <option value="0" selected="true">No</option> | |
| 48 <option value="1">Yes</option> | |
| 49 </param> | |
| 50 <when value="0" /> | |
| 51 <when value="1"> | |
| 52 <param name="shuffles" type="integer" min="0" value="0" label="Shuffles" /> | |
| 53 <param name="p0_input" type="data" format="ind" label="Individuals for randomization" /> | |
| 54 </when> | |
| 55 </conditional> | |
| 56 </inputs> | |
| 57 | |
| 58 <outputs> | |
| 59 <data name="output" format="txt" /> | |
| 60 </outputs> | |
| 61 | |
| 62 <tests> | |
| 63 <test> | |
|
10
9b92372de9f6
rename snp to gsSnp, sap to gdSap
Richard Burhans <burhans@bx.psu.edu>
parents:
7
diff
changeset
|
64 <param name="input" value="test_in/sample.gdSnp" ftype="gdSnp" /> |
| 0 | 65 <param name="p1_input" value="test_in/a.ind" ftype="ind" /> |
| 66 <param name="p2_input" value="test_in/b.ind" ftype="ind" /> | |
| 67 <param name="ds_choice" value="0" /> | |
| 68 <param name="min_value" value="3" /> | |
| 69 <param name="discard_fixed" value="1" /> | |
| 70 <param name="biased" value="0" /> | |
| 71 <param name="ur_choice" value="0" /> | |
| 72 <output name="output" file="test_out/average_fst/average_fst.txt" /> | |
| 73 </test> | |
| 74 </tests> | |
| 75 | |
| 76 <help> | |
| 77 **What it does** | |
| 78 | |
| 79 The user specifies a SNP table and two "populations" of individuals, | |
| 80 both previously defined using the Galaxy tool to select individuals from | |
| 81 a SNP table. No individual can be in both populations. Other choices are | |
| 82 as follows. | |
| 83 | |
| 84 Data source. The allele frequencies of a SNP in the two populations can be | |
| 85 estimated either by the total number of reads of each allele, or by adding | |
| 86 the frequencies inferred from genotypes of individuals in the populations. | |
| 87 | |
| 88 After specifying the data source, the user sets lower bounds on amount | |
| 89 of data required at a SNP. For estimating the Fst using read counts, | |
| 90 the bound is the minimum count of reads of the two alleles in a population. | |
| 91 For estimations based on genotype, the bound is the minimum reported genotype | |
| 92 quality per individual. SNPs not meeting these lower bounds are ignored. | |
| 93 | |
| 94 The user specifies whether SNPs where both populations appear to be fixed | |
| 95 for the same allele should be retained or discarded. | |
| 96 | |
| 97 The user chooses which definition of Fst to use: Wright's original definition | |
| 98 or Weir's unbiased estimator. | |
| 99 | |
| 100 Finally, the user decides whether to use randomizations. If so, then the | |
| 101 user specifies how many randomly generated population pairs (retaining | |
| 102 the numbers of individuals of the originals) to generate, as well as the | |
| 103 "population" of additional individuals (not in the first two populations) | |
| 104 that can be used in the randomization process. | |
| 105 | |
| 106 The program prints the average Fst for the original populations and the | |
| 107 number of SNPs used to compute it. If randomizations were requested, | |
| 108 it prints the average Fst for each randomly generated population pair, | |
| 109 ending with a summary that includes the maximum and average value, and the | |
| 110 highest-scoring population pair. | |
| 111 </help> | |
| 112 </tool> |