Mercurial > repos > jjohnson > bcftools_convert_to_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 15:34:05 -0400
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bca07db8f55c 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@ to vcf" id="bcftools_@EXECUTABLE@_to_vcf" version="@VERSION@.0">
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3 <description>Converts other formats to VCF/BCFk</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 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="version_command" />
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10 <command detect_errors="aggressive"><![CDATA[
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11 @PREPARE_ENV@
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12 #set $input_vcf = None
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13 #if $convert.convert_from == 'gvcf':
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14 #set $input_vcf = 'input.vcf.gz'
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15 #if $convert.input_file.datatype.file_ext == 'vcf'
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16 bgzip -c "$convert.input_file" > $input_vcf &&
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17 bcftools index $input_vcf &&
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18 #elif $convert.input_file.datatype.file_ext == 'vcf_bgzip'
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19 ln -s "$convert.input_file" $input_vcf
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20 #elif $convert.input_file.datatype.file_ext == 'bcf'
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21 #set $input_vcf = 'input.bcf'
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22 ln -s "$convert.input_file" $input_vcf &&
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23 bcftools index $input_vcf &&
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24 #elif $convert.input_file.datatype.file_ext == 'bcf_bgzip'
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25 ln -s "$convert.input_file" $input_vcf &&
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26 #end if
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27 #end if
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28 #set $section = $convert
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29 @PREPARE_FASTA_REF@
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30
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31 bcftools @EXECUTABLE@
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32
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33 @OUTPUT_TYPE@
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34
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35 #set $section = $convert
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36 #if $convert.convert_from == 'gen_sample':
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37 --gensample2vcf "$convert.input_file,$convert.input_sample"
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38 #elif $convert.convert_from == 'hap_sample':
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39 --hapsample2vcf "$convert.input_file,$convert.input_sample"
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40 #elif $convert.convert_from == 'hap_legend_sample':
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41 --haplegendsample2vcf "$convert.input_file,$convert.input_legend,$convert.input_sample"
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42 #elif $convert.convert_from == 'gvcf':
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43 @FASTA_REF@
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44 --gvcf2vcf $input_vcf
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45 #elif $convert.convert_from == 'tsv':
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46 @FASTA_REF@
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47 @SAMPLES@
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48 @COLUMNS@
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49 --tsv2vcf "$convert.input_file"
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50 #end if
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51 > "$output_file"
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52 ]]>
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53 </command>
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54 <inputs>
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55 <conditional name="convert">
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56 <param name="convert_from" type="select" label="convert from">
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57 <option value="tsv">tsv - TAB-Separated-Value (e.g. 23andMe)</option>
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58 <option value="gvcf">gVCF - GATK Variant Call Format</option>
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59 <option value="gen_sample">gen sample - IMPUTE2 or SHAPEIT</option>
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60 <option value="hap_sample">haps sample - IMPUTE2 or SHAPEIT</option>
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61 <option value="hap_legend_sample">haps legend sample - IMPUTE2 or SHAPEIT</option>
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62 </param>
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63 <when value="tsv">
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64 <param name="input_file" type="data" format="tabular" label="Tabular Variant Data"
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65 help="Reference sequence and samples are required"/>
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66 <expand macro="macro_fasta_ref" />
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67 <expand macro="macro_samples"/>
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68 <expand macro="macro_columns"/>
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69 </when>
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70 <when value="gvcf">
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71 <param name="input_file" type="data" format="gvcf" label="Genomic VCF (GATK HaplotypeCaller)" />
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72 <expand macro="macro_fasta_ref" />
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73 </when>
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74 <when value="gen_sample">
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75 <param name="input_file" type="data" format="tabular" label="The .gen file" />
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76 <param name="input_sample" type="data" format="tabular" label="The .samples file" />
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77 </when>
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78 <when value="hap_sample">
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79 <param name="input_file" type="data" format="tabular" label="The .hap file" />
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80 <param name="input_sample" type="data" format="tabular" label="The .samples file" />
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81 </when>
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82 <when value="hap_legend_sample">
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83 <param name="input_file" type="data" format="tabular" label="The .hap file" />
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84 <param name="input_legend" type="data" format="tabular" label="The .legend file" />
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85 <param name="input_sample" type="data" format="tabular" label="The .samples file" />
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86 </when>
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87
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88 </conditional>
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89 <expand macro="macro_select_output_type" />
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90 </inputs>
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91 <outputs>
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92 <expand macro="macro_vcf_output"/>
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93 </outputs>
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94 <tests>
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95 <test>
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96 <param name="convert_from" value="gen_sample" />
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97 <param name="input_file" ftype="tabular" value="convert.gs.gt.gen" />
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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98 <param name="input_sample" ftype="tabular" value="convert.gs.gt.samples" />
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99 <param name="output_type" value="v" />
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100 <output name="output_file">
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101 <assert_contents>
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102 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" />
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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103 <has_text_matching expression="X\t2698560\t.\tG\tA\t.\t.\t.\tGT:GP" />
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104 </assert_contents>
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105 </output>
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106 </test>
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107 <test>
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108 <param name="convert_from" value="hap_sample" />
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109 <param name="input_file" ftype="tabular" value="convert.hs.gt.hap" />
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110 <param name="input_sample" ftype="tabular" value="convert.hs.gt.samples" />
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111 <param name="output_type" value="v" />
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112 <output name="output_file">
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113 <assert_contents>
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114 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" />
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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115 <has_text_matching expression="X\t2698769\t.\tAAG\tA\t.\t.\t.\tGT\t1|0\t1|1\t0|1\t1|0\t1|0\t0|0\t0|0\t0|0\t0|0\t0|0" />
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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116 </assert_contents>
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117 </output>
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118 </test>
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119 <test>
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120 <param name="convert_from" value="hap_legend_sample" />
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121 <param name="input_file" ftype="tabular" value="convert.hls.gt.hap" />
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122 <param name="input_legend" ftype="tabular" value="convert.hls.gt.legend" />
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123 <param name="input_sample" ftype="tabular" value="convert.hls.gt.samples" />
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124 <param name="output_type" value="v" />
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125 <output name="output_file">
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126 <assert_contents>
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127 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" />
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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128 <has_text_matching expression="X\t2698769\t.\tAAG\tA\t.\t.\t.\tGT\t1|0\t1|1\t0|1\t1|0\t1|0\t0|0\t0|0\t0|0\t0|0\t0|0" />
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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129 </assert_contents>
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130 </output>
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131 </test>
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132 <test>
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133 <param name="convert_from" value="gvcf" />
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134 <param name="input_file" ftype="vcf" value="convert.gvcf.vcf" />
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135 <param name="fasta_ref" ftype="fasta" value="gvcf.fa" />
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136 <param name="output_type" value="v" />
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137 <output name="output_file">
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138 <assert_contents>
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139 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE99" />
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140 <has_text_matching expression="22\t10\t.\tC\t.\t0\tLowGQX\tEND=20;BLOCKAVG_min30p3a\tGT:GQX:DP:DPF\t0/0:5:2:0" />
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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141 </assert_contents>
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142 </output>
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143 </test>
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144 <test>
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145 <param name="convert_from" value="tsv" />
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146 <param name="input_file" ftype="tabular" value="convert.23andme" />
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147 <param name="fasta_ref" ftype="fasta" value="23andme.fa" />
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148 <param name="samples" value="SAMPLE1" />
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149 <param name="columns" value="ID,CHROM,POS,AA" />
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150 <param name="output_type" value="v" />
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151 <output name="output_file">
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152 <assert_contents>
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153 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE1" />
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154 <has_text_matching expression="1\t10\trs002\tG\tA\t.\t.\t.\tGT\t1/0" />
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155 </assert_contents>
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156 </output>
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157 </test>
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158 </tests>
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159
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160 <help><![CDATA[
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161 =====================================
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162 bcftools @EXECUTABLE@ plugin
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163 =====================================
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164
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165 Converts other variant formats to vcf. See man page for file formats details.
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166
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167 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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168
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169 @BCFTOOLS_WIKI@
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170 ]]>
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171 </help>
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172 <expand macro="citations" />
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173 </tool>