Mercurial > repos > jjohnson > bcftools_convert_from_vcf

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sun, 26 Jun 2016 15:48:26 -0400
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d396503fdbdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool name="bcftools @EXECUTABLE@ from vcf" id="bcftools_@EXECUTABLE@_from_vcf" version="@VERSION@.0">
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3 <description>Converts VCF/BCF to IMPUTE2/SHAPEIT formats</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">convert</token>
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6 <import>macros.xml</import>
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7 <xml name="macro_vcf_ids">
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8 <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" checked="false"
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9 label="Output VCF IDs instead of CHROM:POS_REF_ALT" help="(\-\-vcf_ids)"/>
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10 </xml>
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11 <xml name="macro_haploid2diploid">
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12 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" checked="false"
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13 label="convert haploid genotypes to diploid homozygotes" help="(\-\-haploid2diploid)"/>
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14 </xml>
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15 </macros>
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16 <expand macro="requirements" />
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17 <expand macro="version_command" />
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18 <command detect_errors="aggressive"><![CDATA[
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19 @PREPARE_ENV@
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20 @PREPARE_INPUT_FILE@
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21 #set $section = $sec_restrict
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22 @PREPARE_TARGETS_FILE@
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23
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24 bcftools @EXECUTABLE@
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25
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26 #if $convert.convert_to == 'gen_sample':
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27 --tag $convert.tag $convert.chrom $convert.vcf_ids
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28 --gensample "$output_gen,$output_samples"
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29 #elif $convert.convert_to == 'hap_sample':
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30 $convert.vcf_ids $convert.haploid2diploid
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31 --hapsample "$output_hap,$output_samples"
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32 #elif $convert.convert_to == 'hap_legend_sample':
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33 $convert.vcf_ids $convert.haploid2diploid
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34 --haplegendsample "$output_hap,$output_legend,$output_samples"
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35 #end if
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36
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37 ## VCF input section
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38 #set $section = $sec_restrict
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39 @INCLUDE@
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40 @EXCLUDE@
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41 @REGIONS@
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42 @TARGETS@
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43 @SAMPLES@
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44
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45 ## Primary Input/Outputs
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46 "$input_file" .
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47 ]]>
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48 </command>
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49 <inputs>
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50 <expand macro="macro_input" />
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51 <section name="sec_restrict" expanded="false" title="Restrict to">
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52 <expand macro="macro_regions" />
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53 <expand macro="macro_targets" />
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54 <expand macro="macro_samples" />
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55 <expand macro="macro_include" />
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56 <expand macro="macro_exclude" />
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57 </section>
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58 <conditional name="convert">
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59 <param name="convert_to" type="select" label="convert to">
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60 <option value="gen_sample">gen sample - IMPUTE2 or SHAPEIT</option>
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61 <option value="hap_sample">hap sample - IMPUTE2 or SHAPEIT</option>
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62 <option value="hap_legend_sample">hap legend sample - IMPUTE2 or SHAPEIT</option>
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63 </param>
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64 <when value="gen_sample">
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65 <param name="tag" type="select" label="tag to take values for .gen file: GT,PL,GL,GP">
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66 <option value="GT">GT</option>
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67 <option value="PL">PL</option>
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68 <option value="GP">GP</option>
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69 <!--
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70 <option value="GL">GL</option>
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71 -->
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72 </param>
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73 <param name="chrom" type="boolean" truevalue="--chrom" falsevalue="" checked="false"
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74 label="Output chromosome in first column instead of CHROM:POS_REF_ALT" help="(\-\-chrom)"/>
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75 <expand macro="macro_vcf_ids"/>
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76 </when>
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77 <when value="hap_sample">
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78 <expand macro="macro_haploid2diploid"/>
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79 <expand macro="macro_vcf_ids"/>
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80 </when>
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81 <when value="hap_legend_sample">
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82 <expand macro="macro_haploid2diploid"/>
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83 <expand macro="macro_vcf_ids"/>
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84 </when>
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85 </conditional>
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86 </inputs>
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87 <outputs>
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88 <data name="output_gen" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.gen">
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89 <filter>convert['convert_to'] == 'gen_sample'</filter>
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90 </data>
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91 <data name="output_hap" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.haps">
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92 <filter>convert['convert_to'] in ('hap_sample','hap_legend_sample')</filter>
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93 </data>
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94 <data name="output_legend" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.legend">
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95 <filter>convert['convert_to'] == 'hap_legend_sample'</filter>
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96 </data>
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97 <data name="output_samples" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.samples"/>
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98 </outputs>
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99 <tests>
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100 <test>
d396503fdbdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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101 <param name="input_file" ftype="vcf" value="convert.vcf" />
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102 <param name="convert_to" value="gen_sample" />
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103 <output name="output_gen">
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104 <assert_contents>
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105 <has_text text="X:2698560_G_A X:2698560_G_A 2698560 G A 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0"/>
d396503fdbdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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106 </assert_contents>
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107 </output>
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108 <output name="output_samples">
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109 <assert_contents>
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110 <has_text text="NA00001 NA00001 0"/>
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111 </assert_contents>
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112 </output>
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113 </test>
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114 <test>
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115 <param name="input_file" ftype="vcf" value="convert.vcf" />
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116 <param name="convert_to" value="gen_sample" />
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117 <param name="tag" value="GP" />
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118 <param name="chrom" value="True" />
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119 <output name="output_gen">
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120 <assert_contents>
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121 <has_text text="X X:2698560_G_A 2698560 G A 1.00"/>
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122 </assert_contents>
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123 </output>
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124 </test>
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125 <test>
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126 <param name="input_file" ftype="vcf" value="check.vcf" />
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127 <param name="convert_to" value="gen_sample" />
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128 <param name="tag" value="GT" />
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129 <param name="chrom" value="True" />
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130 <param name="vcf_ids" value="True" />
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131 <output name="output_gen">
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132 <assert_contents>
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133 <has_text text="1 id3D 3062915 GTTT G 0 1 0 0 1 0"/>
d396503fdbdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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134 </assert_contents>
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135 </output>
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136 </test>
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137 <test>
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138 <param name="input_file" ftype="vcf" value="convert.vcf" />
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139 <param name="convert_to" value="hap_sample" />
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140 <output name="output_hap">
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141 <assert_contents>
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142 <has_text text="X X:2698769_AAG_A 2698769 AAG A 1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0"/>
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143 </assert_contents>
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144 </output>
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145 </test>
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146 <test>
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147 <param name="input_file" ftype="vcf" value="convert.vcf" />
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148 <param name="convert_to" value="hap_legend_sample" />
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149 <output name="output_hap">
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150 <assert_contents>
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151 <has_text text="1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0"/>
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152 </assert_contents>
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153 </output>
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154 <output name="output_legend">
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155 <assert_contents>
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156 <has_text text="X:2698769_AAG_A 2698769 AAG A"/>
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157 </assert_contents>
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158 </output>
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159 <output name="output_samples">
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160 <assert_contents>
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161 <has_text text="sample population group sex"/>
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162 <has_text text="NA00001 NA00001 NA00001 2"/>
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163 </assert_contents>
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164 </output>
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165 </test>
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166 </tests>
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167
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168 <help><![CDATA[
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169 =====================================
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170 bcftools @EXECUTABLE@ from vcf
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171 =====================================
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172
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173 Converts VCF/BCF to other formats. See man page for file formats details.
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174
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175 @REGIONS_HELP@
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176 @TARGETS_HELP@
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177 @EXPRESSIONS_HELP@
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178
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179 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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180
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181 @BCFTOOLS_WIKI@
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182 ]]>
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183 </help>
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184 <expand macro="citations" />
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185 </tool>