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1 <tool id="gd_sum_gd_snp" name="Aggregate Individuals" version="1.0.0">
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2 <description>: Append summary columns for a population</description>
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3
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4 <command interpreter="python">
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5 modify_snp_table.py "$input" "$p1_input" "$output" "-1" "-1" "-1" "-1"
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6 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
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7 #set $arg = '%s:%s' % ($individual_col, $individual)
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8 "$arg"
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9 #end for
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10 </command>
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11
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12 <inputs>
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13 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
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14 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" />
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15 </inputs>
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16
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17 <outputs>
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18 <data name="output" format="gd_snp" metadata_source="input" />
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19 </outputs>
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20
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21 <tests>
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22 <test>
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23 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
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24 <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" />
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25 <param name="choice" value="1" />
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26 <param name="lo_coverage" value="0" />
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27 <param name="hi_coverage" value="1000" />
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28 <param name="low_ind_cov" value="3" />
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29 <param name="lo_quality" value="30" />
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30 <output name="output" file="test_out/modify_snp_table/modify.gd_snp" />
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31 </test>
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32 </tests>
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33
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34 <help>
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35
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36 **Dataset formats**
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37
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38 The input datasets are in gd_snp_ and gd_indivs_ formats.
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39 The output dataset is in gd_snp_ format. (`Dataset missing?`_)
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40
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41 .. _gd_snp: ./static/formatHelp.html#gd_snp
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42 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
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43 .. _Dataset missing?: ./static/formatHelp.html
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44
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45 -----
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46
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47 **What it does**
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48
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49 The user specifies that some of the individuals in a gd_snp dataset form a
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50 "population", by supplying a list that has been previously created using the
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51 Specify Individuals tool. The program appends a
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52 new "entity" (set of four columns) to the gd_snp table, analogous to the columns
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53 for an individual but containing summary data for the population as a group.
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54 These four columns give the total counts for the two alleles, the "genotype" for
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55 the population, and the maximum quality value, taken over all individuals in the
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56 population. If all defined genotypes in the population are 2 (agree with the
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57 reference), then the population's genotype is 2, and similarly for 0; otherwise
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58 the genotype is 1 (unless all individuals have undefined genotype, in which case
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59 it is -1).
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60
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61 -----
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62
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63 **Example**
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64
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65 - input gd_snp::
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66
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67 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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68 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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69 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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70 etc.
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71
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72 - input individuals::
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73
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74 9 PB1
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75 13 PB2
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76 17 PB3
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77
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78 - output::
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79
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80 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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81 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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82 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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83 etc.
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84
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85 </help>
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86 </tool>
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