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comparison coverage_distributions.xml @ 14:8ae67e9fb6ff

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Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
author miller-lab
date Fri, 28 Sep 2012 11:35:56 -0400
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children f04f40a36cc8
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13:fdb4240fb565 14:8ae67e9fb6ff
1 <tool id="gd_coverage_distributions" name="Coverage Distributions" version="1.0.0">
2 <description>: Examine sequence coverage for SNPs</description>
3
4 <command interpreter="python">
5 coverage_distributions.py "$input" "0" "$output" "$output.files_path"
6 #if $individuals.choice == '0'
7 "all_individuals"
8 #else if $individuals.choice == '1'
9 #set $arg = 'individuals:%s' % str($individuals.p1_input)
10 "$arg"
11 #else if $individuals.choice == '2'
12 #for $population in $individuals.populations
13 #set $arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name))
14 "$arg"
15 #end for
16 #end if
17 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
18 #set $individual_arg = 'individual:%s:%s' % ($individual_col, $individual)
19 "$individual_arg"
20 #end for
21 </command>
22
23 <inputs>
24 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
25
26 <conditional name="individuals">
27 <param name="choice" type="select" label="Compute for">
28 <option value="0" selected="true">All individuals</option>
29 <option value="1">Individuals in a population</option>
30 <option value="2">Totals of populations</option>
31 </param>
32 <when value="0" />
33 <when value="1">
34 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" />
35 </when>
36 <when value="2">
37 <repeat name="populations" title="Population" min="1">
38 <param name="p_input" type="data" format="gd_indivs" label="individuals" />
39 </repeat>
40 </when>
41 </conditional>
42
43 <!--
44 <param name="data_source" type="select" label="Data source">
45 <option value="0" selected="true">Sequence coverage</option>
46 <option value="1">Genotype quality</option>
47 </param>
48 -->
49 </inputs>
50
51 <outputs>
52 <data name="output" format="html" />
53 </outputs>
54
55 <tests>
56 <test>
57 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
58 <param name="choice" value="0" />
59 <output name="output" file="test_out/coverage_distributions/coverage.html" ftype="html" compare="diff" lines_diff="2">
60 <extra_files type="file" name="coverage.pdf" value="test_out/coverage_distributions/coverage.pdf" compare="sim_size" delta = "1000"/>
61 <extra_files type="file" name="coverage.txt" value="test_out/coverage_distributions/coverage.txt" />
62 </output>
63 </test>
64 </tests>
65
66 <help>
67
68 **Dataset formats**
69
70 The input dataset is in gd_snp_ format.
71 The output is a composite dataset, containing both a text table and a PDF plot.
72 (`Dataset missing?`_)
73
74 .. _gd_snp: ./static/formatHelp.html#gd_snp
75 .. _Dataset missing?: ./static/formatHelp.html
76
77 -----
78
79 **What it does**
80
81 This tool reports distributions of a SNP reliability indicator, in this case
82 sequence coverage, for individuals or populations.
83 The coverage can be computed for all individuals, a subset of individuals,
84 or totals for populations defined by the Specify Individuals tool.
85 The results are reported as a text table giving the cumulative distributions,
86 and as a plot.
87
88 -----
89
90 **Examples**
91
92 - input::
93
94 chr1 14929 A G 999 21 30 1 127 7 11 1 28 7 29 0 5 2 5 1 17 10 14 1 81 17 74 1 42 15 22 1 125 29 84 1 88 6 10 1 11 30 23 1 79 19 1 2 71 24 0 2 99 41 10 2 2
95 chr1 17451 C T 6.88 119 1 2 255 12 0 2 63 35 0 2 59 14 0 2 72 19 1 2 57 101 1 2 255 38 8 1 20 125 0 2 255 13 0 2 62 42 0 2 51 44 0 2 64 26 0 2 108 59 0 2 194
96 chr1 30922 G T 999 0 23 0 66 0 0 -1 0 0 0 -1 0 0 0 -1 0 0 2 0 3 0 14 0 39 14 16 1 153 0 45 0 132 6 0 2 48 19 0 2 87 3 0 2 32 0 0 -1 0 0 0 -1 0
97 etc.
98
99 - text output::
100
101 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
102 John West 0 0 0 0 0 0 0 0 1 1 1 1 2 2 3 3 4 4 5 6
103 NA12892 0 2 5 11 20 31 43 55 67 77 84 90 93 96 97 98 99 99 99 99
104 NA12891 0 0 0 0 0 1 1 2 3 5 6 9 11 15 19 23 29 35 41 47
105 NA12249 1 4 11 23 38 54 68 79 88 93 96 98 99 99 99 99 99 99 99 99
106 NA12342 0 0 1 1 2 4 6 9 13 18 23 29 36 43 50 58 65 71 77 82
107 KB1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 2 2
108 ABT 0 0 0 0 0 0 1 1 1 2 3 4 5 6 8 10 12 14 18 21
109 NA18507 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1
110 NA19238 0 0 0 1 2 4 6 10 14 19 25 32 39 47 55 62 69 76 81 86
111 NA19239 0 0 0 0 1 1 2 4 5 8 11 15 19 24 31 37 44 51 58 65
112 YH 2 4 6 7 8 8 9 10 11 12 14 17 19 22 25 29 32 36 40 45
113 KOREAN 0 0 1 1 3 4 5 7 10 12 15 19 22 27 31 37 42 48 54 60
114 JPT 0 0 0 0 0 0 0 0 1 1 1 2 2 3 4 5 7 8 10 12
115 etc.
116
117 graphical output:
118
119 .. image:: ${static_path}/images/gd_coverage.png
120
121 </help>
122 </tool>