annotate prepare_population_structure.xml @ 26:91e835060ad2

Updates to Admixture, Aggregate Individuals, and Restore Attributes to support gd_genotype
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 03 Jun 2013 12:29:29 -0400
parents 248b06e86022
children 8997f2ca8c7a
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1 <tool id="gd_prepare_population_structure" name="Prepare Input" version="1.1.0">
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2 <description>: Filter and convert to the format needed for these tools</description>
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3
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4 <command interpreter="python">
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5 prepare_population_structure.py "$input"
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6 #if $input_type.choice == '0'
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7 "gd_snp" "$input_type.min_reads" "$input_type.min_qual"
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8 #else if $input_type.choice == '1'
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9 "gd_genotype" "0" "0"
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10 #end if
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11 "$min_spacing" "$output" "$output.files_path"
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12 #if $individuals.choice == '0'
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13 "all_individuals"
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14 #else if $individuals.choice == '1'
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15 #for $population in $individuals.populations
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16 #set $pop_arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name))
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17 "$pop_arg"
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18 #end for
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19 #end if
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20 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
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21 #set $arg = 'individual:%s:%s' % ($individual_col, $individual)
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22 "$arg"
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23 #end for
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24 </command>
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25
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26 <inputs>
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27 <conditional name="input_type">
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28 <param name="choice" type="select" format="integer" label="Input format">
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29 <option value="0" selected="true">gd_snp</option>
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30 <option value="1">gd_genotype</option>
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31 </param>
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32 <when value="0">
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33 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
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34 <param name="min_reads" type="integer" min="0" value="0" label="Minimum SNP coverage" />
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35 <param name="min_qual" type="integer" min="0" value="0" label="Minimum SNP quality" />
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36 </when>
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37 <when value="1">
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38 <param name="input" type="data" format="gd_genotype" label="Genotype dataset" />
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39 </when>
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40 </conditional>
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41
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42 <conditional name="individuals">
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43 <param name="choice" type="select" label="Individuals">
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44 <option value="0" selected="true">All individuals</option>
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45 <option value="1">Specified populations</option>
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46 </param>
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47 <when value="0" />
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48 <when value="1">
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49 <repeat name="populations" title="Population" min="1">
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50 <param name="p_input" type="data" format="gd_indivs" label="Individuals" />
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51 </repeat>
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52 </when>
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53 </conditional>
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54
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55 <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs" />
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56 </inputs>
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57
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58 <outputs>
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59 <data name="output" format="gd_ped">
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60 <actions>
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61 <action type="metadata" name="base_name" default="admix" />
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62 </actions>
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63 </data>
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64 </outputs>
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65
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66 <tests>
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67 <test>
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68 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
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69 <param name="min_reads" value="3" />
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70 <param name="min_qual" value="30" />
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71 <param name="min_spacing" value="0" />
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72 <param name="choice" value="0" />
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73 <output name="output" file="test_out/prepare_population_structure/prepare_population_structure.html" ftype="html" compare="diff" lines_diff="2">
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74 <extra_files type="file" name="admix.map" value="test_out/prepare_population_structure/admix.map" />
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75 <extra_files type="file" name="admix.ped" value="test_out/prepare_population_structure/admix.ped" />
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76 </output>
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77 </test>
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78 </tests>
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79
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80 <help>
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81
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82 **Dataset formats**
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83
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84 The input datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats.
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85 The output dataset is in gd_ped_ format. (`Dataset missing?`_)
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86
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87 .. _gd_snp: ./static/formatHelp.html#gd_snp
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88 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
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89 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
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90 .. _gd_ped: ./static/formatHelp.html#gd_ped
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91 .. _Dataset missing?: ./static/formatHelp.html
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92
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93 -----
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94
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95 **What it does**
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96
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97 This tool converts a gd_snp dataset into the format needed for estimating
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98 the population structure. You can select the individuals to be included,
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99 by using "population" datasets created via the Specify Individuals tool.
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100 (It is important for these population datasets to have distinguishable names,
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101 since they will be stored in the output's metadata so that subsequent tools
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102 can use them as labels. If necessary, rename the datasets to give them
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103 distinct and meaningful names before running this tool.)
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104
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105 You can also filter the SNPs, based on criteria such as minimum coverage
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106 (a qualifying SNP must have at least this many reads for every included
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107 individual), minimum quality score (for every included individual), and/or
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108 minimum spacing (SNPs that are too close together on the same chromosome or
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109 scaffold are discarded). In addition to producing the filtered and formatted
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110 .map and .ped files for subsequent analysis, the tool reports the number of
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111 SNPs meeting these conditions, which can be seen by clicking on the eye icon
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112 in the history panel after the program runs.
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113
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114 -----
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115
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116 **Example**
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117
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118 - input::
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119
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120 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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121 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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122 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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123 etc.
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124
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125 - output cover page::
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126
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127 Prepare to look for population structure Galaxy Composite Dataset
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128 Output completed: 2012-10-01 04:09:36 PM
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129
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130 Outputs
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131 * admix.ped (link)
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132 * admix.map (link)
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133 * Using 222 of 400 SNPs
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134
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135 Inputs
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136 * Minimum reads covering a SNP, per individual: 6
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137 * Minimum quality value, per individual: 0
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138 * Minimum spacing between SNPs on the same scaffold: 0
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139
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140 Populations
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141 * Pop. A
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142 1. PB1
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143 2. PB2
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144 * Pop. B
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145 1. PB3
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146 2. PB4
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147 * Pop. C
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148 1. PB6
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149 2. PB8
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150
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151 </help>
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152 </tool>