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Update to Miller Lab devshed revision 4ede22dd5500
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 17 Jul 2013 12:46:46 -0400
parents 8997f2ca8c7a
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1 <tool id="gd_sum_gd_snp" name="Aggregate Individuals" version="1.1.0">
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2 <description>: Append summary columns for a population</description>
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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'
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21 </command>
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23 <inputs>
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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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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
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39 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" />
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40 </inputs>
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41
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42 <outputs>
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43 <data name="output" format="input" format_source="input" metadata_source="input" />
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44 </outputs>
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45
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46 <tests>
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47 <test>
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48 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
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49 <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" />
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50 <output name="output" file="test_out/modify_snp_table/modify.gd_snp" />
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51 </test>
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52 </tests>
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53
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54 <help>
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55
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56 **Dataset formats**
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57
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58 The input datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats.
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59 The output dataset is in gd_snp_ or gd_genotype_ format. (`Dataset missing?`_)
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60
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61 .. _gd_snp: ./static/formatHelp.html#gd_snp
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62 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
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63 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
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64 .. _Dataset missing?: ./static/formatHelp.html
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65
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66 -----
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67
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68 **What it does**
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69
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70 The user specifies that some of the individuals in a gd_snp or gd_genotype
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71 dataset form a "population", by supplying a list that has been previously
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72 created using the Specify Individuals tool. The program appends a new
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73 "entity" (set of four columns for a gd_snp table, or one column for a
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74 gd_genotype table), analogous to the column(s) for an individual but
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75 containing summary data for the population as a group. For a gd_snp
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76 table, these four columns give the total counts for the two alleles,
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77 the "genotype" for the population, and the maximum quality value, taken
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78 over all individuals in the population. If all defined genotypes in
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79 the population are 2 (agree with the reference), then the population's
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80 genotype is 2, and similarly for 0; otherwise the genotype is 1 (unless
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81 all individuals have undefined genotype, in which case it is -1).
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82 For a gd_genotype file, only the aggregate genotype is appended.
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83
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84 -----
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85
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86 **Example**
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87
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88 - input gd_snp::
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89
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90 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
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91 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
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92 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
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93 etc.
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94
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95 - input individuals::
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96
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97 9 PB1
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98 13 PB2
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99 17 PB3
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100
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101 - output::
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102
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103 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
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104 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
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105 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
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106 etc.
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107
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108 </help>
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109 </tool>