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annotate prepare_population_structure.xml @ 30:4188853b940b

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Update to Miller Lab devshed revision eb4e61d024db
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 26 Jul 2013 12:51:13 -0400
parents 8997f2ca8c7a
children a631c2f6d913
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1 <tool id="gd_prepare_population_structure" name="Prepare Input" version="1.2.0">
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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 #import json
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6 #import base64
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7 #import zlib
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8 #set $ind_names = $input.dataset.metadata.individual_names
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9 #set $ind_colms = $input.dataset.metadata.individual_columns
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10 #set $ind_dict = dict(zip($ind_names, $ind_colms))
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11 #set $ind_json = json.dumps($ind_dict, separators=(',',':'))
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12 #set $ind_comp = zlib.compress($ind_json, 9)
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13 #set $ind_arg = base64.b64encode($ind_comp)
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14 prepare_population_structure.py '$input'
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15 #if $input_type.choice == '0'
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16 'gd_snp' '$input_type.min_reads' '$input_type.min_qual'
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17 #else if $input_type.choice == '1'
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18 'gd_genotype' '0' '0'
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19 #end if
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20 '0' '$output' '$output.files_path' '$ind_arg'
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21 #if $individuals.choice == '0'
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22 'all_individuals'
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23 #else if $individuals.choice == '1'
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24 #for $population in $individuals.populations
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25 #set $pop_arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name))
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26 '$pop_arg'
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27 #end for
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28 #end if
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29 </command>
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30
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31 <inputs>
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32 <conditional name="input_type">
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33 <param name="choice" type="select" format="integer" label="Input format">
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34 <option value="0" selected="true">gd_snp</option>
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35 <option value="1">gd_genotype</option>
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36 </param>
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37 <when value="0">
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38 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
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39 <param name="min_reads" type="integer" min="0" value="0" label="Minimum SNP coverage" />
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40 <param name="min_qual" type="integer" min="0" value="0" label="Minimum SNP quality" />
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41 </when>
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42 <when value="1">
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43 <param name="input" type="data" format="gd_genotype" label="Genotype dataset" />
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44 </when>
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45 </conditional>
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46
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47 <conditional name="individuals">
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48 <param name="choice" type="select" label="Individuals">
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49 <option value="0" selected="true">All individuals</option>
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50 <option value="1">Specified populations</option>
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51 </param>
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52 <when value="0" />
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53 <when value="1">
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54 <repeat name="populations" title="Population" min="1">
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55 <param name="p_input" type="data" format="gd_indivs" label="Individuals" />
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56 </repeat>
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57 </when>
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58 </conditional>
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59
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60 <!--
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61 <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs" />
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62 "$min_spacing" "$output" "$output.files_path"
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63 -->
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64 </inputs>
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65
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66 <outputs>
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67 <data name="output" format="gd_ped">
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68 <actions>
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69 <action type="metadata" name="base_name" default="admix" />
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70 </actions>
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71 </data>
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72 </outputs>
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73
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74 <tests>
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75 <test>
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76 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
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77 <param name="min_reads" value="3" />
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78 <param name="min_qual" value="30" />
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79 <param name="min_spacing" value="0" />
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80 <param name="choice" value="0" />
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81 <output name="output" file="test_out/prepare_population_structure/prepare_population_structure.html" ftype="html" compare="diff" lines_diff="2">
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82 <extra_files type="file" name="admix.map" value="test_out/prepare_population_structure/admix.map" />
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83 <extra_files type="file" name="admix.ped" value="test_out/prepare_population_structure/admix.ped" />
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84 </output>
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85 </test>
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86 </tests>
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87
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88 <help>
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89
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90 **Dataset formats**
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91
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92 The input datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats.
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93 The output dataset is in gd_ped_ format. (`Dataset missing?`_)
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94
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95 .. _gd_snp: ./static/formatHelp.html#gd_snp
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96 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
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97 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
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98 .. _gd_ped: ./static/formatHelp.html#gd_ped
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99 .. _Dataset missing?: ./static/formatHelp.html
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100
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101 -----
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102
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103 **What it does**
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104
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105 This tool converts a gd_snp dataset into the format needed for estimating
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106 the population structure. You can select the individuals to be included,
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107 by using "population" datasets created via the Specify Individuals tool.
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108 (It is important for these population datasets to have distinguishable names,
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109 since they will be stored in the output's metadata so that subsequent tools
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110 can use them as labels. If necessary, rename the datasets to give them
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111 distinct and meaningful names before running this tool.)
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112
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113 You can also filter the SNPs, based on criteria such as minimum coverage
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114 (a qualifying SNP must have at least this many reads for every included
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115 individual), minimum quality score (for every included individual), and/or
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116 minimum spacing (SNPs that are too close together on the same chromosome or
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117 scaffold are discarded). In addition to producing the filtered and formatted
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118 .map and .ped files for subsequent analysis, the tool reports the number of
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119 SNPs meeting these conditions, which can be seen by clicking on the eye icon
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120 in the history panel after the program runs.
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121
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122 -----
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123
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124 **Example**
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125
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126 - input::
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127
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128 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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129 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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130 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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131 etc.
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132
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133 - output cover page::
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134
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135 Prepare to look for population structure Galaxy Composite Dataset
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136 Output completed: 2012-10-01 04:09:36 PM
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137
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138 Outputs
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139 * admix.ped (link)
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140 * admix.map (link)
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141 * Using 222 of 400 SNPs
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142
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143 Inputs
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144 * Minimum reads covering a SNP, per individual: 6
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145 * Minimum quality value, per individual: 0
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146 * Minimum spacing between SNPs on the same scaffold: 0
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147
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148 Populations
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149 * Pop. A
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150 1. PB1
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151 2. PB2
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152 * Pop. B
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153 1. PB3
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154 2. PB4
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155 * Pop. C
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156 1. PB6
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157 2. PB8
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158
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159 </help>
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160 </tool>