Mercurial > repos > iuc > bcftools_query

annotate bcftools_query.xml @ 25:eea8a0f18b24 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 07:42:36 +0000
parents 7106fdae4823
children
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1 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Extracts fields from VCF/BCF file and prints them in user-defined format</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">query</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="bio_tools" />
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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_INPUT_FILES@
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12 #set $section = $sec_restrict
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13 @PREPARE_TARGETS_FILE@
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14 @PREPARE_REGIONS_FILE@
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16 bcftools @EXECUTABLE@
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18 ## Query section
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19 #set $section = $sec_query
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20 --format '${section.format}'
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22 ${section.allow_undef_tags}
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24 ${section.print_header}
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26 ## Default section
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27 #set $section = $sec_restrict
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28 @INCLUDE@
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29 @EXCLUDE@
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30 @COLLAPSE@
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31 @REGIONS@
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32 @SAMPLES@
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33 @TARGETS@
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34
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35 ## Primary Input/Outputs
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36 --vcf-list @INPUT_LIST_FILE@
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37 > $output_file
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38 ]]>
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39 </command>
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40 <inputs>
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41 <expand macro="macro_inputs" />
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42 <section name="sec_restrict" expanded="false" title="Restrict to">
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43 <expand macro="macro_collapse" />
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44 <expand macro="macro_samples" />
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45 <expand macro="macro_region_restrict" />
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46 <expand macro="macro_target_restrict" />
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47 <expand macro="macro_include" />
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48 <expand macro="macro_exclude" />
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49 </section>
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50 <section name="sec_query" expanded="true" title="Query Options">
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51 <param name="format" type="text" value="" label="Format for Output">
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52 <help>
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53 <![CDATA[
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54 Example: %CHROM\t%POS\t%REF\t%ALT{0}\n
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55 ( NOTE TAB: '\t' and new line character: '\n' )
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56 ]]>
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57 </help>
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58 <sanitizer sanitize="False"/>
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59 <validator type="empty_field" />
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60 </param>
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61 <param name="tsv" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Output is tab-delimited"
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62 help="Fields in your Format are separated by a TAB character: \t"/>
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63 <param name="allow_undef_tags" type="boolean" truevalue="--allow-undef-tags" falsevalue="" label="Allow Undefined Tags"
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64 help="Print &quot;.&quot; for undefined tags" />
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65 <param name="print_header" type="boolean" truevalue="--print-header" falsevalue="" label="Print Header Line" />
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66 </section>
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67
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68 </inputs>
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69 <outputs>
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70 <data name="output_file" format="txt">
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71 <change_format>
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72 <when input="tsv" value="True" format="tabular" />
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73 </change_format>
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74 </data>
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75 </outputs>
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76 <tests>
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77 <test>
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78 <param name="input_files" ftype="vcf" value="query.vcf" />
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79 <section name="sec_query">
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80 <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" />
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81 <param name="tsv" value="True" />
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82 </section>
0
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83 <output name="output_file" file="query.out" />
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84 </test>
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85 <!-- Test region overlap option-->
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86 <test>
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87 <param name="input_files" ftype="vcf" value="query.vcf" />
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88 <section name="sec_query">
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89 <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" />
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90 <param name="tsv" value="True" />
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91 </section>
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92 <section name="sec_restrict">
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93 <conditional name="regions">
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94 <param name="regions_src" value="regions" />
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95 <repeat name="region_specs">
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96 <param name="chrom" value="1" />
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97 </repeat>
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98 </conditional>
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99 </section>
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100 <output name="output_file" file="query.out" compare="contains" lines_diff="4"/>
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101 <assert_command>
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102 <has_text text="--regions-overlap" />
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103 </assert_command>
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104 </test>
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105 </tests>
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106 <help><![CDATA[
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107 =====================================
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108 bcftools @EXECUTABLE@
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109 =====================================
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110
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111 Extracts fields from VCF/BCF file and prints them in user-defined format
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112
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113 Format:
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114
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115 ::
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116
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117 ``%CHROM`` The CHROM column (similarly also other columns: POS, ID, REF, ALT, QUAL, FILTER)
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118 ``%INFO/TAG`` Any tag in the INFO column
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119 ``%TYPE`` Variant type (REF, SNP, MNP, INDEL, OTHER)
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120 ``%MASK`` Indicates presence of the site in other files (with multiple files)
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121 ``%TAG{INT}`` Curly brackets to subscript vectors (0-based)
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122 ``%FIRST_ALT`` Alias for %ALT{0}
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123 ``[]`` The brackets loop over all samples
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124 ``%GT`` Genotype (e.g. 0/1)
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125 ``%TBCSQ`` Translated FORMAT/BCSQ. See the csq command above for explanation and examples.
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126 ``%TGT`` Translated genotype (e.g. C/A)
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127 ``%IUPACGT`` Genotype translated to IUPAC ambiguity codes (e.g. M instead of C/A)
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128 ``%LINE`` Prints the whole line
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129 ``%SAMPLE`` Sample name
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130 ``%POS0`` POS in 0-based coordinates
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131 ``%END`` End position of the REF allele
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132 ``%END0`` End position of the REF allele in 0-based cordinates
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133 ``\n`` new line
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134 ``\t`` tab character
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135
0
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136
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137 Examples:
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138
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139 ::
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140
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141 # Print chromosome, position, ref allele and the first alternate allele
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142 bcftools query -f '%CHROM %POS %REF %ALT{0}\n' file.vcf.gz
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143
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144 # Similar to above, but use tabs instead of spaces, add sample name and genotype
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145 bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz
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146
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147 # Print FORMAT/GT fields followed by FORMAT/GT fields
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148 bcftools query -f 'GQ:[ %GQ] \t GT:[ %GT]\n' file.vcf
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149
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150 # Make a BED file: chr, pos (0-based), end pos (1-based), id
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151 bcftools query -f'%CHROM\t%POS0\t%END\t%ID\n' file.bcf
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152
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153
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154 @COLLAPSE_HELP@
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155 @REGIONS_HELP@
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156 @TARGETS_HELP@
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157 @EXPRESSIONS_HELP@
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158
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159 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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160
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161 @BCFTOOLS_HOWTOS@
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162 ]]>
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163 </help>
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164 <expand macro="citations" />
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165 </tool>