Mercurial > repos > miller-lab > genome_diversity
annotate aggregate_gd_indivs.xml @ 26:91e835060ad2
Updates to Admixture, Aggregate Individuals, and Restore Attributes to support gd_genotype
| author | Richard Burhans <burhans@bx.psu.edu> |
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| date | Mon, 03 Jun 2013 12:29:29 -0400 |
| parents | 95a05c1ef5d5 |
| children | 8997f2ca8c7a |
| rev | line source |
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1 <tool id="gd_sum_gd_snp" name="Aggregate Individuals" version="1.1.0"> |
| 13 | 2 <description>: Append summary columns for a population</description> |
| 3 | |
| 4 <command interpreter="python"> | |
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5 aggregate_gd_indivs.py "$input" "$p1_input" "$output" |
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6 #if $input_type.choice == '0' |
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7 "gd_snp" |
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8 #else if $input_type.choice == '1' |
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9 "gd_genotype" |
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10 #end if |
| 13 | 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> | |
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18 |
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19 <conditional name="input_type"> |
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20 <param name="choice" type="select" format="integer" label="Input format"> |
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21 <option value="0" selected="true">gd_snp</option> |
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22 <option value="1">gd_genotype</option> |
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23 </param> |
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24 |
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25 <when value="0"> |
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26 <param name="input" type="data" format="gd_snp" label="SNP dataset" /> |
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27 </when> |
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28 <when value="1"> |
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29 <param name="input" type="data" format="gd_genotype" label="Genotype dataset" /> |
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30 </when> |
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31 </conditional> |
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32 |
| 13 | 33 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" /> |
| 34 </inputs> | |
| 35 | |
| 36 <outputs> | |
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37 <data name="output" format="input" format_source="input" metadata_source="input" /> |
| 13 | 38 </outputs> |
| 39 | |
| 40 <tests> | |
| 41 <test> | |
| 42 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> | |
| 43 <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" /> | |
| 44 <output name="output" file="test_out/modify_snp_table/modify.gd_snp" /> | |
| 45 </test> | |
| 46 </tests> | |
| 47 | |
| 48 <help> | |
| 49 | |
| 50 **Dataset formats** | |
| 51 | |
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52 The input datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats. |
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53 The output dataset is in gd_snp_ or gd_genotype_ format. (`Dataset missing?`_) |
| 13 | 54 |
| 55 .. _gd_snp: ./static/formatHelp.html#gd_snp | |
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56 .. _gd_genotype: ./static/formatHelp.html#gd_genotype |
| 13 | 57 .. _gd_indivs: ./static/formatHelp.html#gd_indivs |
| 58 .. _Dataset missing?: ./static/formatHelp.html | |
| 59 | |
| 60 ----- | |
| 61 | |
| 62 **What it does** | |
| 63 | |
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64 The user specifies that some of the individuals in a gd_snp or gd_genotype |
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65 dataset form a "population", by supplying a list that has been previously |
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66 created using the Specify Individuals tool. The program appends a new |
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67 "entity" (set of four columns for a gd_snp table, or one column for a |
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68 gd_genotype table), analogous to the column(s) for an individual but |
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parents:
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69 containing summary data for the population as a group. For a gd_snp |
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70 table, these four columns give the total counts for the two alleles, |
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71 the "genotype" for the population, and the maximum quality value, taken |
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72 over all individuals in the population. If all defined genotypes in |
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73 the population are 2 (agree with the reference), then the population's |
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74 genotype is 2, and similarly for 0; otherwise the genotype is 1 (unless |
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75 all individuals have undefined genotype, in which case it is -1). |
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76 For a gd_genotype file, only the aggregate genotype is appended. |
| 13 | 77 |
| 78 ----- | |
| 79 | |
| 80 **Example** | |
| 81 | |
| 82 - input gd_snp:: | |
| 83 | |
| 84 Contig161_chr1_4641264_4641879 115 C T 73.5 chr1 4641382 C 6 0 2 45 8 0 2 51 15 0 2 72 5 0 2 42 6 0 2 45 10 0 2 57 Y 54 0.323 0 | |
| 85 Contig48_chr1_10150253_10151311 11 A G 94.3 chr1 10150264 A 1 0 2 30 1 0 2 30 1 0 2 30 3 0 2 36 1 0 2 30 1 0 2 30 Y 22 +99. 0 | |
| 86 Contig20_chr1_21313469_21313570 66 C T 54.0 chr1 21313534 C 4 0 2 39 4 0 2 39 5 0 2 42 4 0 2 39 4 0 2 39 5 0 2 42 N 1 +99. 0 | |
| 87 etc. | |
| 88 | |
| 89 - input individuals:: | |
| 90 | |
| 91 9 PB1 | |
| 92 13 PB2 | |
| 93 17 PB3 | |
| 94 | |
| 95 - output:: | |
| 96 | |
| 97 Contig161_chr1_4641264_4641879 115 C T 73.5 chr1 4641382 C 6 0 2 45 8 0 2 51 15 0 2 72 5 0 2 42 6 0 2 45 10 0 2 57 Y 54 0.323 0 29 0 2 72 | |
| 98 Contig48_chr1_10150253_10151311 11 A G 94.3 chr1 10150264 A 1 0 2 30 1 0 2 30 1 0 2 30 3 0 2 36 1 0 2 30 1 0 2 30 Y 22 +99. 0 3 0 2 30 | |
| 99 Contig20_chr1_21313469_21313570 66 C T 54.0 chr1 21313534 C 4 0 2 39 4 0 2 39 5 0 2 42 4 0 2 39 4 0 2 39 5 0 2 42 N 1 +99. 0 13 0 2 42 | |
| 100 etc. | |
| 101 | |
| 102 </help> | |
| 103 </tool> |