Mercurial > repos > miller-lab > genome_diversity
annotate multiple_to_gd_genotype.xml @ 33:5064f618ec1c
remove munkres dependency
author | Richard Burhans <burhans@bx.psu.edu> |
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date | Fri, 20 Sep 2013 14:01:30 -0400 |
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1 <tool id="gd_multiple_to_gd_genotype" name="Convert" version="1.0.0"> |
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2 <description>: CSV, FSTAT, Genepop or VCF to either gd_snp or gd_genotype</description> |
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3 |
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4 <command interpreter="python"> |
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5 #import base64 |
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6 #set species_arg = base64.b64encode(str($species)) |
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7 multiple_to_gd_genotype.py --input '$input' --output '$output' --dbkey '$dbkey' --species '$species_arg' --format '$input_format' |
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8 </command> |
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9 |
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10 <inputs> |
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11 <param name="input" type="data" format="txt" label="Input dataset" /> |
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12 |
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13 <param name="input_format" type="select" label="Input format"> |
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14 <option value="csv" selected="true">CSV</option> |
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15 <option value="fstat">FSTAT</option> |
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16 <option value="genepop">Genepop</option> |
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17 <option value="vcf">VCF</option> |
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18 </param> |
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19 |
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20 <param name="species" type="text" label="Focus species"> |
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21 <sanitizer> |
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22 <valid initial="string.printable"/> |
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23 </sanitizer> |
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24 </param> |
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26 <param name="dbkey" type="genomebuild" label="Reference species" /> |
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27 </inputs> |
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28 |
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29 <outputs> |
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30 <data name="output" format="gd_genotype" /> |
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31 </outputs> |
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32 |
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33 <!-- |
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34 <tests> |
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35 <test> |
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36 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> |
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37 <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" /> |
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38 <param name="lo_coverage" value="0" /> |
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39 <param name="hi_coverage" value="1000" /> |
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40 <param name="low_ind_cov" value="3" /> |
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41 <param name="lo_quality" value="30" /> |
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42 <output name="output" file="test_out/modify_snp_table/modify.gd_snp" /> |
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43 </test> |
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44 </tests> |
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45 --> |
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46 |
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47 <help> |
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48 |
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49 **Dataset formats** |
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50 |
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51 The input dataset is formated as VCF, FSTAT, Genepop, or CSV, and is of |
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52 Galaxy datatype text_. Additionally, the name of the focus species (from |
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53 which the SNPs in the VCF file were obtained) and a reference species |
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54 are required. The output dataset is in gd_genotype_ or gd_snp_ format. |
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55 |
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56 For input datasets in Genepop, FSTAT, or CSV formats, the program ignores |
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57 population structures as well as alleles other than those encoded by 0, |
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58 1, and 2. For input datasets in FSTAT format the program accepts up to |
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59 9 digits and for Genepop files only 2 digits. Chromosome and position |
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60 for each SNPs must be separated by a space or a tab. Ancestral loci must |
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61 be encoded as 1, derived as 2 and missing as 0. In all cases ancestral |
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62 and derived SNPs are returned as N. Alternatively, a dataset in CSV |
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63 format can include nucleotides. In this case the ancestral nucleotide |
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64 is defined as the most common allele. |
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65 |
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66 .. _text: ./static/formatHelp.html#text |
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67 .. _gd_snp: ./static/formatHelp.html#gd_snp |
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68 .. _gd_genotype: ./static/formatHelp.html#gd_genotype |
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69 |
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70 ----- |
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71 |
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72 **What it does** |
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73 |
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74 This tool returns a gd_genotype dataset from VCF formatted files or three |
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75 other conventional population genetics formats (i.e. FSTAT, Genepop, |
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76 and CSV). For VCF files that include the fields allelic depth, genotype |
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77 quality and genotype ("AD", "GQ", and "GT" respectively in the "FORMAT" |
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78 field) the input dataset can be converted into a gd_snp file. |
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79 |
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80 ----- |
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81 |
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82 **Examples** |
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83 |
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84 - If the input format is VCF and includes the fields allelic depth, genotype quality and genotype ("AD", "GQ", and "GT" respectively in the "FORMAT" field). Focus species name is "aye-aye" and reference species is "Human Feb. 2009 (GRCh37/hg19) (hg19)":: |
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85 |
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86 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 19_F 19.1_F 19.2_F |
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87 Chr21 382242 rs134033430 T C 3296.97 . . GT:GQ:DP:PL:AD 1/1:75:26:943,75,0:0,26 1/1:3:1:30,3,0:0,1 ./. |
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88 Chr21 383680 rs137652597 T C 2236.62 . . GT:GQ:DP:PL:AD 1/1:36:12:436,36,0:0,12 ./. 1/1:3:1:31,3,0:0,1 |
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89 Chr21 387251 . G T 2407.88 . . GT:GQ:DP:PL:AD 1/1:30:12:394,30,0:0,10 ./. ./. |
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90 etc. |
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91 |
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92 - output (gd_snp):: |
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93 |
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94 #{"column_names":["chr","pos","A","B","Q","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q"],"dbkey":"aye-aye","individuals":[["19_F",6],["19.1_F",10],["19.2_F",14]],"pos":2,"rPos":2,"ref":1, |
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95 #"scaffold":1,"species":"hg19"} |
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96 Chr21 382242 T C 3296.97 0 26 0 75 0 1 0 3 0 0 -1 -1 |
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97 Chr21 383680 T C 2236.62 0 12 0 36 0 0 -1 -1 0 1 0 3 |
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98 Chr21 387251 G T 2407.88 0 10 0 30 0 0 -1 -1 0 0 -1 -1 |
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99 etc. |
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100 |
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101 - If the input format is VCF, focus species is "aye-aye" and reference species is "Human Feb. 2009 (GRCh37/hg19) (hg19)":: |
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102 |
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103 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 19_F 19.1_F 19.2_F |
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104 Chr21 382242 rs134033430 T C 3296.97 . . GT:GQ:DP:PL 1/1:75:26:943,75,0 1/1:3:1:30,3,0:0,1 ./. |
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105 Chr21 383680 rs137652597 T C 2236.62 . . GT:GQ:DP:PL 1/1:36:12:436,36,0 ./. 1/1:3:1:31,3,0:0,1 |
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106 Chr21 387251 . G T 2407.88 . . GT:GQ:DP:PL 1/1:30:12:394,30,0 ./. ./. |
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107 etc. |
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108 |
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109 - output (gd_genotype):: |
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110 |
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111 #{"column_names":["chr","pos","A","B","1G","2G","3G"],"dbkey":"aye-aye","individuals":[["19_F",5],["19.1_F",6],["19.2_F",7]],"pos":2,"rPos":2,"ref":1,"scaffold":1,"species":"hg19"} |
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112 Chr21 382242 T C 0 0 -1 |
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113 Chr21 383680 T C 0 -1 0 |
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114 Chr21 387251 G T 0 -1 -1 |
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115 etc. |
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116 |
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117 - If the input format is Genepop:: |
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118 |
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119 Microsat on aye-aye from different locations |
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120 Chr21 382242, Chr21 383680, Chr21 387251 |
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121 POP |
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122 19_F, 0202 0202 0202 |
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123 Pop |
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124 19.1_F, 0202 0000 0000 |
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125 19.2_F, 0000 0202 0000 |
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126 etc. |
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127 |
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128 - or the input format is FSTAT:: |
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129 |
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130 300 3 2 1 |
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131 Chr21 382242 |
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132 Chr21 383680 |
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133 Chr21 387251 |
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134 19_F 22 22 22 |
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135 19.1_F 22 00 00 |
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136 19.2_F 00 22 00 |
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137 etc. |
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138 |
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139 - or the input format is CSV:: |
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140 |
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141 ,19_F,19.1_F,19.2_F,... |
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142 Chr21 382242,22,22,00 |
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143 Chr21 383680,22,00,22 |
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144 Chr21 387251,22,00,00 |
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145 etc. |
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146 |
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147 - output (gd_genotype):: |
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148 |
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149 #{"column_names":["chr","pos","A","B","1G","2G","3G"],"dbkey":"aye-aye","individuals":[["19_F",5],["19.1_F",6],["19.2_F",7]],"pos":2,"rPos":2,"ref":1,"scaffold":1,"species":"hg19"} |
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150 Chr21 382242 N N 0 0 -1 |
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151 Chr21 383680 N N 0 -1 0 |
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152 Chr21 387251 N N 0 -1 -1 |
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153 etc. |
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154 |
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155 - if the input format is CSV:: |
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156 |
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157 ,19_F,19.1_F,19.2_F,... |
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158 Chr21 382242,C,C,N |
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159 Chr21 383680,C,N,C |
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160 Chr21 387251,T,N,N |
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161 etc. |
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162 |
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163 - output (gd_genotype):: |
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164 |
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165 #{"column_names":["chr","pos","A","B","1G","2G","3G","4G"],"dbkey":"aye-aye","individuals":[["19_F",5],["19.1_F",6],["19.2_F",7],["...",8]],"pos":2,"rPos":2,"ref":1,"scaffold":1,"species":"hg19"} |
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166 Chr21 382242 C N 2 2 -1 |
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167 Chr21 383680 T N 2 -1 2 |
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168 Chr21 387251 T N 2 -1 -1 |
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169 etc. |
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170 </help> |
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171 </tool> |