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1 <tool id="bcftools_view" name="BCFtools view" version="1.0.0">
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2 <description>Convert, view, subset, and filter VCF/BCF files</description>
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21
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3 <requirements>
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4 <requirement type="package" version="1.3">bcftools</requirement>
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5 </requirements>
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6 <command>
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7 #if str( $input_file_index ) != "None":
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8 ln -s -f $input input_file.${input.ext} &&
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9 ln -s -f $input_file_index input_file.${input.ext}.tbi &&
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10 #end if
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11 bcftools view
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12 ${drop_genotypes}
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13 ${header_only}
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14 ${no_header}
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15 --output-file "${output_file}"
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16 --output-type "${output_type}"
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17 #if str( $regions ) != "":
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18 --regions "${regions}"
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19 #end if
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20 #if str( $targets ) != "":
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21 --targets "${targets}"
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22 #end if
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23 #if str( $samples ) != "":
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24 --samples "${samples}"
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25 #end if
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26 #if str( $regions_file ) != "None":
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27 --regions-file "${regions_file}"
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28 #end if
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29 #if str( $targets_file ) != "None":
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30 --targets-file "${targets_file}"
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31 #end if
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32 #if str( $samples_file ) != "None":
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33 --samples-file "${samples_file}"
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34 #end if
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35 #if str( $apply_filters ) != "":
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36 --apply-filters "${apply_filters}"
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37 #end if
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38 #if str( $min_ac_cond.set_min_ac ) == "True":
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39 --min-ac $min_ac_cond.min_ac:$min_ac_cond.min_ac_type
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40 #end if
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41 #if str( $max_ac_cond.set_max_ac ) == "True":
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42 --max-ac $max_ac_cond.max_ac:$max_ac_cond.max_ac_type
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43 #end if
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44 #if str( $min_af_cond.set_min_af ) == "True":
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45 --min-af $min_af_cond.min_af:$min_af_cond.min_af_type
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46 #end if
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47 #if str( $max_af_cond.set_max_af ) == "True":
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48 --max-af $max_af_cond.max_af:$max_af_cond.max_af_type
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49 #end if
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50 #if str( $expr_cond.set_expr ) == "True":
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51 #if str( $expr_cond.include_or_exclude ) == "include":
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52 --include "${expr_cond.expr}"
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53 #else
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54 --exclude "${expr_cond.expr}"
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55 #end if
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56 #end if
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57 #if str( $genotype_cond.set_genotype ) == "True":
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58 #if str( $genotype_cond.include_or_exclude ) == "include":
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59 --genotype $genotype_cond.genotype
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60 #else
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61 --genotype ^$genotype_cond.genotype
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62 #end if
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63 #end if
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64 #if str( $var_type_cond.set_var_type ) == "True":
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65 #if str( $var_type_cond.include_or_exclude ) == "include":
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66 --types $var_type_cond.var_types
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67 #else
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68 --exclude-types $var_type_cond.var_types
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69 #end if
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70 #end if
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71 ${uncalled}
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72 ${exclude_uncalled}
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73 ${private}
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74 ${exclude_private}
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75
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76 #if str( $input_file_index ) != "None":
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77 input_file.${input.ext}
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78 #else
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79 $input
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80 #end if
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81 </command>
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82
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83 <inputs>
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84 <param name="input" type="data" format="vcf,bcf,bgzip" label="VCF or BCF input file" help="Input file can optionally be compressed and indexed using Bgzip and Tabix Galaxy tools. In this case, select bgzipped file here and index below."/>
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85 <param name="input_file_index" type="data" optional="true" label="Input file index" help="Tabix-generated index for input file. Run Tabix Galaxy tool on bgzipped input file to create index."/>
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86 <param name="output_type" type="select" label="Output data type" help="-O">
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87 <option value="v" selected="true">VCF</option>
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88 <option value="b">BCF</option>
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89 </param>
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90 <param name="regions_file" type="data" optional="true" label="Regions file" help="-R. Regions specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
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91 <param name="regions" type="text" size="80" optional="True" label="Regions list" help="-r. Comma-separated list of regions. Format: chr|chr:pos|chr:from-to|chr:from-[,...]">
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92 <sanitizer invalid_char="">
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93 <valid initial="string.digits"><add value="CHRchr-:,"/> </valid>
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94 </sanitizer>
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95 </param>
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96 <param name="targets_file" type="data" optional="true" label="Targets file" help="-T. Targets specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
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97 <param name="targets" type="text" size="80" optional="True" label="Targets list" help="-t. Comma-separated list of targets. Format: [^]chr|chr:pos|chr:from-to|chr:from-[,...]">
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98 <sanitizer invalid_char="">
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99 <valid initial="string.digits"><add value="CHRchr-:,^"/> </valid>
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100 </sanitizer>
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101 </param>
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102 <param name="samples_file" type="data" optional="true" label="Samples file" help="-S. File of sample names to include. One sample per line."/>
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103 <param name="samples" type="text" size="80" optional="True" label="Samples list" help="-s. Comma-separated list of samples to include or exclude. (Excludes if prefixed with ^)" />
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104 <param name="apply_filters" type="text" size="80" optional="True" label="Apply filters" help="-f. Comma-separated list of strings. Keeps only sites where FILTER column contains one of these strings." />
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105 <param name="drop_genotypes" type="boolean" checked="False" truevalue="--drop-genotypes" falsevalue="" label="Drop individual genotype information" help="-G" />
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106 <param name="no_header" type="boolean" checked="False" truevalue="--no-header" falsevalue="" label="Suppress the header in VCF output" help="-H" />
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107 <param name="header_only" type="boolean" checked="False" truevalue="--header-only" falsevalue="" label="Output the VCF header only" help="-h" />
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108 <conditional name="min_ac_cond">
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109 <param name="set_min_ac" type="boolean" checked="False" label="Set minimum allele count" help="-c" />
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110 <when value="true">
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111 <param name="min_ac" type="integer" optional="true" label="Minimum allele count" help="Minimum allele count of sites to be printed, for given allele type." />
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112 <param name="min_ac_type" type="select" label="Allele type">
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113 <option value="nref" selected="True">Non-reference</option>
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114 <option value="alt1">1st alternate</option>
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115 <option value="minor">Minor (least frequent)</option>
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116 <option value="major">Major (most frequent)</option>
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117 <option value="nonmajor">Nonmajor (Sum of all but most frequent)</option>
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118 </param>
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119 </when>
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120 </conditional>
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121 <conditional name="max_ac_cond">
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122 <param name="set_max_ac" type="boolean" checked="False" label="Set maximum allele count" help="-C" />
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123 <when value="true">
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124 <param name="max_ac" type="integer" optional="true" label="Maximum allele count" help="Maximum allele count of sites to be printed, for given allele type." />
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125 <param name="max_ac_type" type="select" label="Allele type">
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126 <option value="nref" selected="True">Non-reference</option>
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127 <option value="alt1">1st alternate</option>
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128 <option value="minor">Minor (least frequent)</option>
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129 <option value="major">Major (most frequent)</option>
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130 <option value="nonmajor">Nonmajor (Sum of all but most frequent)</option>
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131 </param>
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132 </when>
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133 </conditional>
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134
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135 <conditional name="min_af_cond">
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136 <param name="set_min_af" type="boolean" checked="False" label="Set minimum allele frequency" help="-q" />
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137 <when value="true">
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138 <param name="min_af" type="integer" optional="true" label="Minimum allele frequency" help="Minimum allele frequency of sites to be printed, for given allele type." />
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139 <param name="min_af_type" type="select" label="Allele type">
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140 <option value="nref" selected="True">Non-reference</option>
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141 <option value="alt1">1st alternate</option>
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142 <option value="minor">Minor (least frequent)</option>
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143 <option value="major">Major (most frequent)</option>
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144 <option value="nonmajor">Nonmajor (Sum of all but most frequent)</option>
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145 </param>
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146 </when>
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147 </conditional>
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148 <conditional name="max_af_cond">
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149 <param name="set_max_af" type="boolean" checked="False" label="Set maximum allele frequency" help="-Q" />
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150 <when value="true">
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151 <param name="max_af" type="integer" optional="true" label="Maximum allele frequency" help="Maximum allele frequency of sites to be printed, for given allele type." />
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152 <param name="max_af_type" type="select" label="Allele type">
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153 <option value="nref" selected="True">Non-reference</option>
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154 <option value="alt1">1st alternate</option>
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155 <option value="minor">Minor (least frequent)</option>
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156 <option value="major">Major (most frequent)</option>
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157 <option value="nonmajor">Nonmajor (Sum of all but most frequent)</option>
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158 </param>
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159 </when>
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160 </conditional>
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161
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162 <conditional name="genotype_cond">
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163 <param name="set_genotype" type="boolean" checked="False" label="Filter by genotype" help="-g. Include only, or exclude, sites with one or more of given genotype."/>
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164 <when value="true">
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165 <param name="include_or_exclude" type="select" label="Include or exclude by genotype">
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166 <option value="include">Include</option>
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167 <option value="exclude">Exclude</option>
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168 </param>
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169 <param name="genotype" type="select" label="Genotype">
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170 <option value="hom">Homozygous</option>
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171 <option value="het">Heterozygous</option>
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172 <option value="miss">Missing</option>
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173 </param>
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174 </when>
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175 </conditional>
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176
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177 <conditional name="expr_cond">
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178 <param name="set_expr" type="boolean" checked="False" label="Filter by expression" help="-i, -e. Include/ exclude sites for which expression is true. Must use valid expression."/>
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179 <when value="true">
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180 <param name="include_or_exclude" type="select" label="Include or exclude by expression">
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181 <option value="include">Include</option>
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182 <option value="exclude">Exclude</option>
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183 </param>
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184 <param name="expr" type="text" size="80" label="Expression">
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185 <sanitizer invalid_char="">
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186 <valid initial="string.letters,string.digits"><add value="~`!@#$%^&*()-_=+[{]}\|;:'",<.>?/ " /> </valid>
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187 </sanitizer>
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188 </param>
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189 </when>
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190 </conditional>
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191
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192 <conditional name="var_type_cond">
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193 <param name="set_var_type" type="boolean" checked="False" label="Filter by variant type" help="-v, -V. Include/ exclude sites where any ALT allele is one of the given variant types."/>
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194 <when value="true">
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195 <param name="include_or_exclude" type="select" label="Include or exclude by variant type">
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196 <option value="include">Include</option>
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197 <option value="exclude">Exclude</option>
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198 </param>
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199 <param name="var_types" type="select" multiple="true" display="checkboxes" label="Variant type">
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200 <option value="snps">SNPs</option>
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201 <option value="indels">Indels</option>
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202 <option value="mnps">MNPs</option>
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203 <option value="other">Other</option>
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204 </param>
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205 </when>
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206 </conditional>
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207
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208 <param name="uncalled" type="boolean" checked="False" truevalue="--uncalled" falsevalue="" label="Print sites without a called genotype" help="-u" />
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209 <param name="exclude_uncalled" type="boolean" checked="False" truevalue="--exclude-uncalled" falsevalue="" label="Exclude sites without a called genotype" help="-U" />
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210 <param name="private" type="boolean" checked="False" truevalue="--private" falsevalue="" label="Print sites where only the subset samples carry a non-reference allele" help="-x. Requires samples file or samples list."/>
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211 <param name="exclude_private" type="boolean" checked="False" truevalue="--exclude-private" falsevalue="" label="Exclude sites where only the subset samples carry a non-reference allele" help="-X. Requires samples file or samples list."/>
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212 </inputs>
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213 <outputs>
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214 <data name="output_file" format="vcf" label="${tool.name} on ${on_string}">
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215 <change_format>
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216 <when input="output_type" value="b" format="bcf" />
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217 </change_format>
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218 </data>
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219 </outputs>
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220 <help>
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221 **About this tool**
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222
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223 **BCFtools view**: View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF. Former bcftools subset.
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224
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225 Please see https://samtools.github.io/bcftools/bcftools.html for more info on options.
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226 </help>
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227 </tool>
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