Mercurial > repos > miller-lab > genome_diversity
annotate aggregate_gd_indivs.xml @ 36:51cd0307fb70
Phylip's extra ouputs are now stored in the job working directory
| author | Richard Burhans <burhans@bx.psu.edu> |
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| date | Wed, 20 Nov 2013 16:32:01 -0500 |
| parents | a631c2f6d913 |
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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 #import json |
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6 #import base64 |
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7 #import zlib |
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8 #set $ind_names = $input.dataset.metadata.individual_names |
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9 #set $ind_colms = $input.dataset.metadata.individual_columns |
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10 #set $ind_dict = dict(zip($ind_names, $ind_colms)) |
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11 #set $ind_json = json.dumps($ind_dict, separators=(',',':')) |
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12 #set $ind_comp = zlib.compress($ind_json, 9) |
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13 #set $ind_arg = base64.b64encode($ind_comp) |
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14 aggregate_gd_indivs.py '$input' '$p1_input' '$output' |
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15 #if $input_type.choice == '0' |
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16 'gd_snp' |
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17 #else if $input_type.choice == '1' |
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18 'gd_genotype' |
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19 #end if |
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20 '$ind_arg' |
| 13 | 21 </command> |
| 22 | |
| 23 <inputs> | |
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24 |
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25 <conditional name="input_type"> |
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26 <param name="choice" type="select" format="integer" label="Input format"> |
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27 <option value="0" selected="true">gd_snp</option> |
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28 <option value="1">gd_genotype</option> |
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29 </param> |
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30 |
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31 <when value="0"> |
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32 <param name="input" type="data" format="gd_snp" label="SNP dataset" /> |
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33 </when> |
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34 <when value="1"> |
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35 <param name="input" type="data" format="gd_genotype" label="Genotype dataset" /> |
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36 </when> |
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37 </conditional> |
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38 |
| 13 | 39 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" /> |
| 40 </inputs> | |
| 41 | |
| 42 <outputs> | |
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43 <data name="output" format="input" format_source="input" metadata_source="input" /> |
| 13 | 44 </outputs> |
| 45 | |
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46 <requirements> |
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47 <requirement type="package" version="0.1">gd_c_tools</requirement> |
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48 </requirements> |
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49 |
| 13 | 50 <tests> |
| 51 <test> | |
| 52 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> | |
| 53 <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" /> | |
| 54 <output name="output" file="test_out/modify_snp_table/modify.gd_snp" /> | |
| 55 </test> | |
| 56 </tests> | |
| 57 | |
| 58 <help> | |
| 59 | |
| 60 **Dataset formats** | |
| 61 | |
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62 The input datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats. |
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63 The output dataset is in gd_snp_ or gd_genotype_ format. (`Dataset missing?`_) |
| 13 | 64 |
| 65 .. _gd_snp: ./static/formatHelp.html#gd_snp | |
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66 .. _gd_genotype: ./static/formatHelp.html#gd_genotype |
| 13 | 67 .. _gd_indivs: ./static/formatHelp.html#gd_indivs |
| 68 .. _Dataset missing?: ./static/formatHelp.html | |
| 69 | |
| 70 ----- | |
| 71 | |
| 72 **What it does** | |
| 73 | |
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74 The user specifies that some of the individuals in a gd_snp or gd_genotype |
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75 dataset form a "population", by supplying a list that has been previously |
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76 created using the Specify Individuals tool. The program appends a new |
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77 "entity" (set of four columns for a gd_snp table, or one column for a |
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78 gd_genotype table), analogous to the column(s) for an individual but |
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79 containing summary data for the population as a group. For a gd_snp |
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80 table, these four columns give the total counts for the two alleles, |
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81 the "genotype" for the population, and the maximum quality value, taken |
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82 over all individuals in the population. If all defined genotypes in |
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83 the population are 2 (agree with the reference), then the population's |
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84 genotype is 2, and similarly for 0; otherwise the genotype is 1 (unless |
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85 all individuals have undefined genotype, in which case it is -1). |
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86 For a gd_genotype file, only the aggregate genotype is appended. |
| 13 | 87 |
| 88 ----- | |
| 89 | |
| 90 **Example** | |
| 91 | |
| 92 - input gd_snp:: | |
| 93 | |
| 94 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 | |
| 95 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 | |
| 96 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 | |
| 97 etc. | |
| 98 | |
| 99 - input individuals:: | |
| 100 | |
| 101 9 PB1 | |
| 102 13 PB2 | |
| 103 17 PB3 | |
| 104 | |
| 105 - output:: | |
| 106 | |
| 107 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 | |
| 108 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 | |
| 109 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 | |
| 110 etc. | |
| 111 | |
| 112 </help> | |
| 113 </tool> |