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comparison prepare_population_structure.xml @ 24:248b06e86022

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Added gd_genotype datatype. Modified tools to support new datatype.
author Richard Burhans <burhans@bx.psu.edu>
date Tue, 28 May 2013 16:24:19 -0400
parents f04f40a36cc8
children 8997f2ca8c7a
comparison
equal deleted inserted replaced
23:66a183c44dd5 24:248b06e86022
1 <tool id="gd_prepare_population_structure" name="Prepare Input" version="1.0.0"> 1 <tool id="gd_prepare_population_structure" name="Prepare Input" version="1.1.0">
2 <description>: Filter and convert to the format needed for these tools</description> 2 <description>: Filter and convert to the format needed for these tools</description>
3 3
4 <command interpreter="python"> 4 <command interpreter="python">
5 prepare_population_structure.py "$input" "$min_reads" "$min_qual" "$min_spacing" "$output" "$output.files_path" 5 prepare_population_structure.py "$input"
6 #if $input_type.choice == '0'
7 "gd_snp" "$input_type.min_reads" "$input_type.min_qual"
8 #else if $input_type.choice == '1'
9 "gd_genotype" "0" "0"
10 #end if
11 "$min_spacing" "$output" "$output.files_path"
6 #if $individuals.choice == '0' 12 #if $individuals.choice == '0'
7 "all_individuals" 13 "all_individuals"
8 #else if $individuals.choice == '1' 14 #else if $individuals.choice == '1'
9 #for $population in $individuals.populations 15 #for $population in $individuals.populations
10 #set $pop_arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name)) 16 #set $pop_arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name))
16 "$arg" 22 "$arg"
17 #end for 23 #end for
18 </command> 24 </command>
19 25
20 <inputs> 26 <inputs>
21 <param name="input" type="data" format="gd_snp" label="SNP dataset" /> 27 <conditional name="input_type">
28 <param name="choice" type="select" format="integer" label="Input format">
29 <option value="0" selected="true">gd_snp</option>
30 <option value="1">gd_genotype</option>
31 </param>
32 <when value="0">
33 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
34 <param name="min_reads" type="integer" min="0" value="0" label="Minimum SNP coverage" />
35 <param name="min_qual" type="integer" min="0" value="0" label="Minimum SNP quality" />
36 </when>
37 <when value="1">
38 <param name="input" type="data" format="gd_genotype" label="Genotype dataset" />
39 </when>
40 </conditional>
41
22 <conditional name="individuals"> 42 <conditional name="individuals">
23 <param name="choice" type="select" label="Individuals"> 43 <param name="choice" type="select" label="Individuals">
24 <option value="0" selected="true">All individuals</option> 44 <option value="0" selected="true">All individuals</option>
25 <option value="1">Specified populations</option> 45 <option value="1">Specified populations</option>
26 </param> 46 </param>
29 <repeat name="populations" title="Population" min="1"> 49 <repeat name="populations" title="Population" min="1">
30 <param name="p_input" type="data" format="gd_indivs" label="Individuals" /> 50 <param name="p_input" type="data" format="gd_indivs" label="Individuals" />
31 </repeat> 51 </repeat>
32 </when> 52 </when>
33 </conditional> 53 </conditional>
34 <param name="min_reads" type="integer" min="0" value="0" label="Minimum SNP coverage" /> 54
35 <param name="min_qual" type="integer" min="0" value="0" label="Minimum SNP quality" />
36 <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs" /> 55 <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs" />
37 </inputs> 56 </inputs>
38 57
39 <outputs> 58 <outputs>
40 <data name="output" format="gd_ped"> 59 <data name="output" format="gd_ped">
60 79
61 <help> 80 <help>
62 81
63 **Dataset formats** 82 **Dataset formats**
64 83
65 The input datasets are in gd_snp_ and gd_indivs_ formats. 84 The input datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats.
66 The output dataset is in gd_ped_ format. (`Dataset missing?`_) 85 The output dataset is in gd_ped_ format. (`Dataset missing?`_)
67 86
68 .. _gd_snp: ./static/formatHelp.html#gd_snp 87 .. _gd_snp: ./static/formatHelp.html#gd_snp
88 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
69 .. _gd_indivs: ./static/formatHelp.html#gd_indivs 89 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
70 .. _gd_ped: ./static/formatHelp.html#gd_ped 90 .. _gd_ped: ./static/formatHelp.html#gd_ped
71 .. _Dataset missing?: ./static/formatHelp.html 91 .. _Dataset missing?: ./static/formatHelp.html
72 92
73 ----- 93 -----