|
2
|
1 <tool id="gd_coverage_distributions" name="Coverage" version="1.0.0">
|
|
|
2 <description>distributions</description>
|
|
|
3
|
|
|
4 <command interpreter="python">
|
|
|
5 coverage_distributions.py "$input" "0" "$output" "$output.extra_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="wsf" label="SNP table" />
|
|
|
25
|
|
|
26 <conditional name="individuals">
|
|
|
27 <param name="choice" type="select" label="Individuals">
|
|
|
28 <option value="0" selected="true">All</option>
|
|
|
29 <option value="1">Individuals in a population</option>
|
|
|
30 <option value="2">Population totals</option>
|
|
|
31 </param>
|
|
|
32 <when value="0" />
|
|
|
33 <when value="1">
|
|
|
34 <param name="p1_input" type="data" format="ind" 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="ind" 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="genome_diversity/test_in/sample.wsf" ftype="wsf" />
|
|
|
58 <param name="choice" value="0" />
|
|
|
59 <output name="output" file="genome_diversity/test_out/coverage_distributions/coverage.html" ftype="html" compare="diff" lines_diff="2">
|
|
|
60 <extra_files type="file" name='coverage.pdf' value="genome_diversity/test_out/coverage_distributions/coverage.pdf" compare="sim_size" delta = "1000"/>
|
|
|
61 <extra_files type="file" name='coverage.txt' value="genome_diversity/test_out/coverage_distributions/coverage.txt" />
|
|
|
62 </output>
|
|
|
63 </test>
|
|
|
64 </tests>
|
|
|
65
|
|
|
66 <help>
|
|
|
67 **What it does**
|
|
|
68
|
|
|
69 This tool reports distributions of SNP reliability indicators for
|
|
|
70 individuals or populations. The reliability is measured by the sequence
|
|
|
71 coverage. Textual and graphical reports are generated, where the text
|
|
|
72 output gives the cumulative distributions.
|
|
|
73 </help>
|
|
|
74 </tool>
|
|
|
75
|
