Mercurial > repos > iuc > bcftools_convert_from_vcf

annotate bcftools_convert_from_vcf.xml @ 25:61d4b20f3b11 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 07:43:16 +0000
parents 0155f20adc71
children
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1 <tool name="bcftools @EXECUTABLE@ from vcf" id="bcftools_@EXECUTABLE@_from_vcf" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Converts VCF/BCF to IMPUTE2/SHAPEIT formats</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">convert</token>
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5 <import>macros.xml</import>
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6 <xml name="macro_vcf_ids">
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7 <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" checked="false" label="Output VCF IDs instead of CHROM:POS_REF_ALT" help="(\-\-vcf_ids)"/>
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8 </xml>
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9 <xml name="macro_haploid2diploid">
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10 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" checked="false" label="convert haploid genotypes to diploid homozygotes" help="(\-\-haploid2diploid)"/>
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11 </xml>
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12 <xml name="macro_sexinfo">
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13 <conditional name="sex_info">
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14 <param name="sex_info_src" type="select" label="sex column">
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15 <help><![CDATA[
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16 SampleName SexDesignation:
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17 <br>MaleSample M
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18 <br>FemaleSample F
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19 ]]></help>
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20 <option value="none">None</option>
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21 <option value="history">designations from history dataset</option>
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22 <option value="entry">designations from text input</option>
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23 </param>
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24 <when value="none"/>
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25 <when value="history">
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26 <param name="sex_info_file" type="data" format="tabular" label="per sample sex designation file"/>
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27 </when>
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28 <when value="entry">
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29 <param name="sex_info_lines" type="text" area="True" label="per sample sex designation">
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30 <validator type="regex" message="sample M or F separated by TAB">^(\S+[ \t][MF](\n\S+[ \t][MF])*)$</validator>
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31 <sanitizer sanitize="False"/>
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32 </param>
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33 </when>
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34 </conditional>
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35 </xml>
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36 <token name="@SAMPLE_SEX@">
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37 #if $convert.sex_info.sex_info_src == 'entry':
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38 --sex "$entered_sex_file"
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39 #elif $convert.sex_info.sex_info_src == 'history':
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40 --sex "$convert.sex_info.sex_info_file"
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41 #end if
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42 </token>
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43 </macros>
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44 <expand macro="bio_tools"/>
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45 <expand macro="requirements"/>
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46 <expand macro="version_command"/>
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47 <command detect_errors="aggressive"><![CDATA[
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48 @PREPARE_INPUT_FILE@
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49 #set $section = $sec_restrict
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50 @PREPARE_TARGETS_FILE@
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51 @PREPARE_REGIONS_FILE@
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52
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53 bcftools @EXECUTABLE@
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54
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55 #if $convert.convert_to == 'gen_sample':
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56 --tag $convert.tag $convert.convert_3N6 $convert.vcf_ids ## chrom option has been deprecated
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57 --gensample "$output_gen,$output_samples"
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58 #elif $convert.convert_to == 'hap_sample':
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59 $convert.vcf_ids $convert.haploid2diploid
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60 --hapsample "$output_hap,$output_samples"
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61 #elif $convert.convert_to == 'hap_legend_sample':
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62 $convert.vcf_ids $convert.haploid2diploid
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63 --haplegendsample "$output_hap,$output_legend,$output_samples"
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64 #end if
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65 @SAMPLE_SEX@
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66
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67 #if $keep_duplicates
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68 --keep-duplicates $keep_duplicates
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69 #end if
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70
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71 ## VCF input section
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72 #set $section = $sec_restrict
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73 @INCLUDE@
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74 @EXCLUDE@
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75 @REGIONS@
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76 @TARGETS@
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77 @SAMPLES@
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78
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79
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80 ## Primary Input/Outputs
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81 @INPUT_FILE@ .
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82 ]]>
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83 </command>
5
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84 <configfiles>
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85 <configfile name="entered_sex_file"><![CDATA[#slurp
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86 #if $convert.sex_info.sex_info_src == 'entry':
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87 $convert.sex_info.sex_info_lines.__str__.strip().replace(' ','\t')#slurp
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88 #end if]]></configfile>
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89 </configfiles>
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90 <inputs>
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91 <expand macro="macro_input"/>
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92 <section name="sec_restrict" expanded="false" title="Restrict to">
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93 <expand macro="macro_region_restrict"/>
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94 <expand macro="macro_target_restrict"/>
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95 <expand macro="macro_samples"/>
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96 <expand macro="macro_include"/>
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97 <expand macro="macro_exclude"/>
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98 </section>
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99 <param argument="--keep-duplicates" type="boolean" truevalue="--keep-duplicates" falsevalue="" checked="false" label="Keep duplicates" help="Keep all multiallelic variants"/>
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100 <conditional name="convert">
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101 <param name="convert_to" type="select" label="convert to">
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102 <option value="gen_sample">gen sample - IMPUTE2 or SHAPEIT</option>
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103 <option value="hap_sample">hap sample - IMPUTE2 or SHAPEIT</option>
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104 <option value="hap_legend_sample">hap legend sample - IMPUTE2 or SHAPEIT</option>
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105 </param>
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106 <when value="gen_sample">
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107 <param name="tag" type="select" label="tag to take values for .gen file: GT,PL,GL,GP">
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108 <option value="GT">GT</option>
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109 <option value="PL">PL</option>
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110 <option value="GP">GP</option>
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111 <!--
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112 <option value="GL">GL</option>
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113 -->
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114 </param>
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115 <param name="convert_3N6" argument="--3N6" type="boolean" truevalue="--3N6" falsevalue="" checked="false" label="3N6 format" help="Use 3N+6 column format instead of the old 3N+5 column format"/>
0
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116 <expand macro="macro_vcf_ids"/>
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117 <expand macro="macro_sexinfo"/>
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118 </when>
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119 <when value="hap_sample">
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120 <expand macro="macro_haploid2diploid"/>
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121 <expand macro="macro_vcf_ids"/>
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122 <expand macro="macro_sexinfo"/>
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123 </when>
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124 <when value="hap_legend_sample">
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125 <expand macro="macro_haploid2diploid"/>
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126 <expand macro="macro_vcf_ids"/>
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127 <expand macro="macro_sexinfo"/>
0
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128 </when>
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129 </conditional>
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130 </inputs>
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131 <outputs>
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132 <data name="output_gen" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.gen">
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133 <filter>convert['convert_to'] == 'gen_sample'</filter>
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134 </data>
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135 <data name="output_hap" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.haps">
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136 <filter>convert['convert_to'] in ('hap_sample','hap_legend_sample')</filter>
0
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137 </data>
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138 <data name="output_legend" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.legend">
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139 <filter>convert['convert_to'] == 'hap_legend_sample'</filter>
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140 </data>
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141 <data name="output_samples" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.samples"/>
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142 </outputs>
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143 <tests>
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144 <test expect_num_outputs="2">
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145 <param name="input_file" ftype="vcf" value="convert.vcf"/>
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146 <conditional name="convert">
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147 <param name="convert_to" value="gen_sample"/>
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148 </conditional>
0
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149 <output name="output_gen">
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150 <assert_contents>
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151 <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"/>
6004a3019af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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152 </assert_contents>
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153 </output>
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154 <output name="output_samples">
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155 <assert_contents>
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156 <has_text text="NA00001 NA00001 0"/>
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157 </assert_contents>
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158 </output>
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159 </test>
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160 <test expect_num_outputs="2">
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161 <param name="input_file" ftype="vcf" value="convert.vcf"/>
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162 <conditional name="convert">
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163 <param name="convert_to" value="gen_sample"/>
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164 <param name="tag" value="GP"/>
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165 <param name="convert_3N6" value="True"/>
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166 </conditional>
0
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167 <output name="output_gen">
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168 <assert_contents>
18
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169 <has_text text="X:2698630_A_G X:2698630_A_G 2698630 A G 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000"/>
0
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170 </assert_contents>
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171 </output>
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172 </test>
22
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173 <test expect_num_outputs="2">
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174 <param name="input_file" ftype="vcf" value="check.vcf"/>
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175 <conditional name="convert">
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176 <param name="convert_to" value="gen_sample"/>
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177 <param name="tag" value="GT"/>
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178 <param name="convert_3N6" value="True"/>
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179 <param name="vcf_ids" value="True"/>
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180 </conditional>
0
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181 <output name="output_gen">
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182 <assert_contents>
18
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183 <has_text text="1:3062915_GTTT_G id3D 3062915 GTTT G 0 1 0 0 1 0"/>
0
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184 </assert_contents>
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185 </output>
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186 </test>
22
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187 <test expect_num_outputs="2">
25
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188 <param name="input_file" ftype="vcf" value="convert.vcf"/>
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189 <conditional name="convert">
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190 <param name="convert_to" value="hap_sample"/>
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191 </conditional>
0
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192 <output name="output_hap">
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193 <assert_contents>
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194 <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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195 </assert_contents>
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196 </output>
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197 </test>
22
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198 <test expect_num_outputs="3">
25
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199 <param name="input_file" ftype="vcf" value="convert.vcf"/>
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200 <conditional name="convert">
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201 <param name="convert_to" value="hap_legend_sample"/>
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202 </conditional>
0
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203 <output name="output_hap">
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204 <assert_contents>
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205 <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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206 </assert_contents>
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207 </output>
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208 <output name="output_legend">
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209 <assert_contents>
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210 <has_text text="X:2698769_AAG_A 2698769 AAG A"/>
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211 </assert_contents>
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212 </output>
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213 <output name="output_samples">
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214 <assert_contents>
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215 <has_text text="sample population group sex"/>
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216 <has_text text="NA00001 NA00001 NA00001 2"/>
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217 </assert_contents>
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218 </output>
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219 </test>
18
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220 <!-- Test keep-duplicates option -->
22
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221 <test expect_num_outputs="3">
25
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222 <param name="input_file" ftype="vcf" value="convert.vcf"/>
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223 <conditional name="convert">
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224 <param name="convert_to" value="hap_legend_sample"/>
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225 </conditional>
18
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226 <param name="keep_duplicates" value="true"/>
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227 <output name="output_hap">
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228 <assert_contents>
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229 <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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230 </assert_contents>
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231 </output>
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232 <output name="output_legend">
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233 <assert_contents>
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234 <has_text text="X:2698769_AAG_A 2698769 AAG A"/>
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235 </assert_contents>
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236 </output>
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237 <output name="output_samples">
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238 <assert_contents>
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239 <has_text text="sample population group sex"/>
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240 <has_text text="NA00001 NA00001 NA00001 2"/>
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241 </assert_contents>
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242 </output>
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243 <assert_command>
25
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244 <has_text text="--keep-duplicates"/>
18
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245 </assert_command>
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246 </test>
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247 <!-- Test region overlap -->
22
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248 <test expect_num_outputs="2">
25
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249 <param name="input_file" ftype="vcf" value="convert.vcf"/>
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250 <conditional name="convert">
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251 <param name="convert_to" value="gen_sample"/>
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252 </conditional>
18
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253 <section name="sec_restrict">
25
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254 <conditional name="regions">
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255 <param name="regions_src" value="regions" />
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256 <repeat name="region_specs">
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257 <param name="chrom" value="X" />
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258 </repeat>
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259 </conditional>
18
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260 </section>
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261 <output name="output_gen">
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262 <assert_contents>
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263 <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"/>
10e2db4ba5f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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264 </assert_contents>
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265 </output>
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266 <output name="output_samples">
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267 <assert_contents>
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268 <has_text text="NA00001 NA00001 0"/>
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269 </assert_contents>
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270 </output>
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271 <assert_command>
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272 <has_text text="--regions-overlap"/>
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273 </assert_command>
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274 </test>
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275 </tests>
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276 <help><![CDATA[
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277 =====================================
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278 bcftools @EXECUTABLE@ from vcf
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279 =====================================
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280
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281 Converts VCF/BCF to other formats. See man page for file formats details.
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282
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283 @REGIONS_HELP@
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284 @TARGETS_HELP@
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285 @EXPRESSIONS_HELP@
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286
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287 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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288
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289 @BCFTOOLS_HOWTOS@
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290 ]]>
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291 </help>
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292 <expand macro="citations"/>
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293 </tool>