comparison prepare_population_structure.xml @ 12:4b6590dd7250

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author miller-lab
date Wed, 12 Sep 2012 17:10:26 -0400
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11:d4ec09e8079f 12:4b6590dd7250
1 <tool id="gd_prepare_population_structure" name="Prepare" version="1.0.0">
2 <description>to look for population structure</description>
3
4 <command interpreter="python">
5 prepare_population_structure.py "$input" "$min_reads" "$min_qual" "$min_spacing" "$output" "$output.files_path"
6 #if $individuals.choice == '0'
7 "all_individuals"
8 #else if $individuals.choice == '1'
9 #for $population in $individuals.populations
10 #set $pop_arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name))
11 "$pop_arg"
12 #end for
13 #end if
14 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
15 #set $arg = 'individual:%s:%s' % ($individual_col, $individual)
16 "$arg"
17 #end for
18 </command>
19
20 <inputs>
21 <param name="input" type="data" format="gd_snp" label="SNP table" />
22 <param name="min_reads" type="integer" min="0" value="0" label="Minimum reads covering a SNP, per individual" />
23 <param name="min_qual" type="integer" min="0" value="0" label="Minimum quality value, per individual" />
24 <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs on the same scaffold" />
25 <conditional name="individuals">
26 <param name="choice" type="select" label="Individuals">
27 <option value="0" selected="true">All</option>
28 <option value="1">Choose</option>
29 </param>
30 <when value="0" />
31 <when value="1">
32 <repeat name="populations" title="Population" min="1">
33 <param name="p_input" type="data" format="gd_indivs" label="Individuals" />
34 </repeat>
35 </when>
36 </conditional>
37 </inputs>
38
39 <outputs>
40 <data name="output" format="gd_ped">
41 <actions>
42 <action type="metadata" name="base_name" default="admix" />
43 </actions>
44 </data>
45 </outputs>
46
47 <tests>
48 <test>
49 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
50 <param name="min_reads" value="3" />
51 <param name="min_qual" value="30" />
52 <param name="min_spacing" value="0" />
53 <param name="choice" value="0" />
54 <output name="output" file="test_out/prepare_population_structure/prepare_population_structure.html" ftype="html" compare="diff" lines_diff="2">
55 <extra_files type="file" name="admix.map" value="test_out/prepare_population_structure/admix.map" />
56 <extra_files type="file" name="admix.ped" value="test_out/prepare_population_structure/admix.ped" />
57 </output>
58 </test>
59 </tests>
60
61 <help>
62 **What it does**
63
64 The tool converts a SNP table into two tables, called "admix.map" and
65 "admix.ped", needed for estimating the population structure. The user
66 can read or download those files, or simply pass this tool's output on to
67 other programs. The user imposes conditions on which SNPs to consider,
68 such as the minimum coverage and/or quality value for every individual,
69 or the distance to the closest SNP in the same contig (as named in the
70 first column of the SNP table). A useful piece of information produced
71 by the tool is the number of SNPs meeting those conditions, which can
72 be found by clicking on the "eye" after the program runs.
73 </help>
74 </tool>