Mercurial > repos > iuc > bcftools_view

annotate bcftools_view.xml @ 27:c6c23f9ef8d6 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 07:51:20 +0000
parents 9dac1d55dbfe
children
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rev   line source
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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>VCF/BCF conversion, view, subset and filter VCF/BCF files</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">view</token>
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5 <import>macros.xml</import>
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6 <xml name="macro_types_options">
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7 <option value="snps">snps</option>
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8 <option value="indels">indels</option>
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9 <option value="mnps">mnps</option>
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10 <option value="other">other</option>
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11 </xml>
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12 </macros>
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13 <expand macro="bio_tools" />
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14 <expand macro="requirements" />
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15 <expand macro="version_command" />
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16 <command detect_errors="aggressive"><![CDATA[
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17 @PREPARE_INPUT_FILE@
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18 #set $section = $sec_restrict
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19 @PREPARE_TARGETS_FILE@
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20 @PREPARE_REGIONS_FILE@
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21
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22 bcftools @EXECUTABLE@
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23
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24 ## Subset section
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25 #set $section = $sec_subset
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26 ${section.trim_alt_alleles}
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27 ${section.no_update}
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28 @SAMPLES@
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29 ${section.force_samples}
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30
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31
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32 ## Filter section
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33 #set $section = $sec_filter
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34 #if str($section.min_ac)
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35 --min-ac ${section.min_ac}
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36 #end if
4
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37 #if str($section.max_ac)
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38 --max-ac ${section.max_ac}
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39 #end if
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40 #if str($section.select_genotype) != "None":
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41 --genotype "${section.select_genotype}"
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42 #end if
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43 ## known or novel
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44 #if $section.known_or_novel:
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45 ${section.known_or_novel}
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46 #end if
4
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47 #if str($section.min_alleles)
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48 --min-alleles ${section.min_alleles}
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49 #end if
4
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50 #if str($section.max_alleles)
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51 --max-alleles ${section.max_alleles}
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52 #end if
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53 #if $section.phased:
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54 ${section.phased}
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55 #end if
4
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56 #if str($section.min_af)
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57 --min-af ${section.min_af}
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58 #end if
4
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59 #if str($section.max_af)
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60 --max-af ${section.max_af}
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61 #end if
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62 #if $section.uncalled:
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63 ${section.uncalled}
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64 #end if
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65 #if $section.types:
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66 --types "${section.types}"
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67 #end if
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68 #if $section.exclude_types:
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69 --exclude-types "${section.exclude_types}"
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70 #end if
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71 #if $section.private:
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72 ${section.private}
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73 #end if
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74
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75 ## Output section
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76 #set $section = $sec_output
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77 ${section.drop_genotypes}
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78 #if $section.header:
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79 ${section.header}
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80 #end if
4
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81 #if str($section.compression_level)
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82 --compression-level ${section.compression_level}
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83 #end if
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84
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85 #set $section = $sec_restrict
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86 @APPLY_FILTERS@
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87 @INCLUDE@
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88 @EXCLUDE@
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89 @REGIONS@
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90 @TARGETS@
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91
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92 @OUTPUT_TYPE@
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93 @THREADS@
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94
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95 ## Primary Input/Outputs
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96 @INPUT_FILE@
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97 > '$output_file'
0
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98 ]]>
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99 </command>
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100 <inputs>
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101 <expand macro="macro_input" />
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102 <section name="sec_restrict" expanded="false" title="Restrict to">
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103 <expand macro="macro_apply_filters" />
27
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104 <expand macro="macro_region_restrict" />
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105 <expand macro="macro_target_restrict" />
0
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106 <expand macro="macro_include" />
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107 <expand macro="macro_exclude" />
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108 </section>
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109 <section name="sec_subset" expanded="false" title="Subset Options">
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110 <expand macro="macro_samples" />
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111 <param name="force_samples" type="boolean" truevalue="--force-samples" falsevalue="" label="Force Samples"
0
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112 help="Only warn about unknown subset samples" />
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113 <param name="no_update" type="boolean" truevalue="--no-update" falsevalue="" label="No Update"
0
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114 help="Do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)" />
4
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115 <param name="trim_alt_alleles" type="boolean" truevalue="--trim-alt-alleles" falsevalue="" label="Trim Alt Alleles"
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116 help="Trim alternate alleles not seen in the subset" />
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117 </section>
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118 <section name="sec_filter" expanded="false" title="Filter Options">
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119 <param name="min_ac" type="integer" label="Min Ac" optional="True"
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120 help="(-c --min-ac) Minimum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
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121 <param name="max_ac" type="integer" label="Max Ac" optional="True"
0
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122 help="(-C --max-ac) Maximum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
14
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123 <param name="select_genotype" type="select" label="Select Genotype" optional="True">
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124 <help>
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125 Include only sites with one or more homozygous (hom), heterozygous (het) or missing (miss) genotypes.
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126 When prefixed with ^, the logic is reversed.
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127 Please notice that if the input file doesn't have any genotype columns,
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128 then this option is ignored altogether.
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129 </help>
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130 <option value="hom">hom</option>
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131 <option value="het">het</option>
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132 <option value="miss">miss</option>
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133 <option value="^hom">^hom</option>
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134 <option value="^het">^het</option>
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135 <option value="^miss">^miss</option>
0
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136 </param>
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137 <param name="types" type="select" label="Select Types" multiple="true" optional="True">
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138 <help>
4
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139 List of variant types to select. Site is selected if any of the ALT alleles is of the type requested.
0
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140 Types are determined by comparing the REF and ALT alleles in the VCF record.
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141 </help>
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142 <expand macro="macro_types_options" />
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143 </param>
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144
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145 <param name="exclude_types" type="select" label="Exclude Types" multiple="true" optional="True">
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146 <help>
4
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147 List of variant types to exclude. Site is excluded if any of the ALT alleles is of the type requested.
0
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148 Types are determined by comparing the REF and ALT alleles in the VCF record.
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149 </help>
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150 <expand macro="macro_types_options" />
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151 </param>
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152
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153
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154 <param name="known_or_novel" type="select" label="filter known or novel ID" optional="true">
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155 <option value="--novel">(-k) print novel sites only (ID column is ".")</option>
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156 <option value="--known">(-n) print known sites only (ID column is not ".")</option>
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157 </param>
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158
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159 <param name="min_alleles" type="integer" label="Min Alleles" optional="True"
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160 help="(-m) Minimum number of alleles listed in REF and ALT (e.g. -m2)" />
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161 <param name="max_alleles" type="integer" label="Max Alleles" optional="True"
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162 help="(-M) Maximum number of alleles listed in REF and ALT (e.g. -M2 for biallelic sites)" />
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163
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164 <param name="phased" type="select" label="filter phased" optional="true">
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165 <help>
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166 Haploid genotypes are considered phased. Missing genotypes considered unphased unless the phased bit is set.
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167 </help>
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168 <option value="--phased">(-p) print sites where all samples are phased</option>
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169 <option value="--exclude-phased">(-P) exclude sites where all samples are phased</option>
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170 </param>
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171
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172 <!-- TODO optional select for type: nref,alt1,minor,major,sum -->
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173 <param name="min_af" type="float" label="Min Af" optional="True"
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174 help="(-q) Minimum frequency for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
4
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175 <param name="max_af" type="float" label="Max Af" optional="True"
0
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176 help="(-Q) Maximum frequency for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
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177
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178 <param name="uncalled" type="select" label="filter on genotype uncalled" optional="true">
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179 <option value="--uncalled">uncalled - print sites without a called genotype</option>
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180 <option value="--exclude-uncalled">exclude-uncalled - exclude sites without a called genotype</option>
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181 </param>
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182
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183 <param name="private" type="select" label="filter on private" optional="true">
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184 <help><![CDATA[
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185 Private: Where only the subset samples carry an non-reference allele.
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186 ( Ignored if samples are not included )
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187 ]]></help>
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188 <option value="--private">(-x) private - print sites where only the subset samples carry an non-reference allele</option>
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189 <option value="--exclude-private">(-X) exclude-private - exclude sites where only the subset samples carry an non-reference allele</option>
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190 </param>
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191
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192 </section>
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193
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194 <section name="sec_output" expanded="false" title="Output Options">
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195 <param name="drop_genotypes" type="boolean" truevalue="--drop-genotypes" falsevalue="" label="Drop Genotypes"
0
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196 help="Drop individual genotype information (after subsetting if -s option set)" />
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197 <param name="header" type="select" label="output header" optional="true">
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198 <option value="--no-header">(-h) no-header</option>
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199 <option value="--header-only">(-H) header-only</option>
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200 </param>
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201 <param name="compression_level" type="integer" min="0" max="9" label="Compression Level" optional="True"
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202 help="Compression level: 0 uncompressed, 1 best speed, 9 best compression" />
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203 </section>
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204 <expand macro="macro_select_output_type" />
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205 </inputs>
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206 <outputs>
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207 <expand macro="macro_vcf_output" />
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208 </outputs>
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209 <tests>
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210 <test>
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211 <param name="input_file" ftype="vcf" value="view.vcf" />
27
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212 <section name="sec_filter">
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213 <param name="min_ac" value="1" />
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214 <param name="max_ac" value="1" />
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215 <param name="types" value="snps" />
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216 </section>
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217 <section name="sec_subset">
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218 <param name="samples" value="NA00002" />
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219 </section>
0
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220 <param name="output_type" value="v" />
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221 <output name="output_file">
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222 <assert_contents>
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223 <has_text text="rs2298108" />
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224 <not_has_text text="rs6111385" />
0
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225 </assert_contents>
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226 </output>
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227 </test>
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228 <test>
8
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229 <param name="input_file" ftype="bcf" value="view.bcf" />
27
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230 <section name="sec_filter">
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231 <param name="min_ac" value="1" />
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232 <param name="max_ac" value="1" />
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233 <param name="types" value="snps" />
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234 </section>
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235 <section name="sec_subset">
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236 <param name="samples" value="NA00002" />
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237 </section>
8
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238 <param name="output_type" value="v" />
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239 <output name="output_file">
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240 <assert_contents>
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241 <has_text text="rs2298108" />
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242 <not_has_text text="rs6111385" />
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243 </assert_contents>
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244 </output>
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245 </test>
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246 <test>
0
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247 <param name="input_file" ftype="vcf" value="view.vcf" />
27
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248 <section name="sec_filter">
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249 <param name="known_or_novel" value="--novel" />
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250 <param name="private" value="--exclude-private" />
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251 </section>
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252 <section name="sec_subset">
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253 <param name="samples" value="NA00003" />
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254 </section>
23
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255 <section name="sec_restrict">
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256 <conditional name="regions">
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257 <param name="regions_src" value="regions"/>
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258 <repeat name="region_specs">
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259 <param name="chrom" value="Y" />
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260 <param name="start" value="20" />
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261 </repeat>
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262 </conditional>
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263 </section>
0
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264 <param name="output_type" value="v" />
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265 <output name="output_file">
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266 <assert_contents>
4
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267 <has_text text="8657215" />
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268 <not_has_text text="rs6111385" />
0
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269 </assert_contents>
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270 </output>
19
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271 <assert_command>
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272 <has_text text="--regions 'Y:20-'"/>
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273 </assert_command>
0
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274 </test>
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275 <test>
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276 <param name="input_file" ftype="vcf" value="view.vcf" />
27
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277 <section name="sec_filter">
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278 <param name="known_or_novel" value="--known" />
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279 <param name="private" value="--exclude-private" />
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280 </section>
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281 <section name="sec_subset">
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282 <param name="samples" value="NA00003" />
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283 </section>
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284 <section name="sec_restrict">
27
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285 <param name="apply_filters" value="PASS" />
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286 <conditional name="regions">
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287 <param name="regions_src" value="regions"/>
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288 <repeat name="region_specs">
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289 <param name="chrom" value="Y" />
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290 <param name="start" value="20" />
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291 </repeat>
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292 </conditional>
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293 </section>
0
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294 <param name="output_type" value="v" />
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295 <output name="output_file">
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296 <assert_contents>
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297 <has_text text="Minimum number of alternate bases" />
4
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298 <not_has_text text="8657215" />
0
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299 </assert_contents>
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300 </output>
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301 </test>
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302 <test>
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303 <param name="input_file" ftype="vcf" value="view.vcf" />
27
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304 <section name="sec_filter">
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305 <param name="private" value="--private" />
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306 </section>
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307 <section name="sec_subset">
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308 <param name="samples" value="NA00003" />
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309 </section>
0
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310 <param name="output_type" value="v" />
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311 <output name="output_file">
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312 <assert_contents>
4
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313 <has_text text="rs62584840" />
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314 <not_has_text text="8657215" />
0
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315 </assert_contents>
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316 </output>
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317 </test>
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318 <test>
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319 <param name="input_file" ftype="vcf" value="view.vcf" />
27
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320 <section name="sec_restrict">
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321 <param name="include" value="QUAL==999 &amp;&amp; (FS&lt;20 || FS&gt;=41.02) &amp;&amp; ICF&gt;-0.1 &amp;&amp; HWE*2&gt;1.2" />
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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322 </section>
0
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323 <param name="output_type" value="v" />
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324 <output name="output_file">
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325 <assert_contents>
4
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326 <has_text text="rs5939407" />
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327 <not_has_text text="8657215" />
0
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328 </assert_contents>
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329 </output>
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330 </test>
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331 <test>
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332 <param name="input_file" ftype="vcf" value="view.vcf" />
27
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333 <section name="sec_filter">
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334 <param name="phased" value="--phased" />
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335 </section>
0
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336 <param name="output_type" value="v" />
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337 <output name="output_file">
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338 <assert_contents>
4
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339 <has_text text="rs78249411" />
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340 <not_has_text text="rs6111385" />
0
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341 </assert_contents>
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342 </output>
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343 </test>
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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344 <test>
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345 <param name="input_file" ftype="vcf" value="view.vcf" />
27
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346 <section name="sec_filter">
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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347 <param name="phased" value="--exclude-phased" />
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348 </section>
0
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349 <param name="output_type" value="v" />
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350 <output name="output_file">
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351 <assert_contents>
4
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352 <has_text text="rs6111385" />
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parents: 2
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353 <not_has_text text="rs78249411" />
0
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354 </assert_contents>
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355 </output>
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356 </test>
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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357 <test>
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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358 <param name="input_file" ftype="vcf" value="view.vcf" />
27
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diff changeset
359 <section name="sec_filter">
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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360 <param name="min_alleles" value="2" />
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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361 <param name="max_alleles" value="2" />
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diff changeset
362 <param name="min_af" value="0.3" />
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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diff changeset
363 <param name="max_af" value="0.7" />
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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diff changeset
364 </section>
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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diff changeset
365 <section name="sec_output">
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
366 <param name="header" value="--header-only" />
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
367 </section>
0
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
368 <param name="output_type" value="v" />
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
369 <output name="output_file">
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
370 <assert_contents>
4
b8f8fdd611ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 2
diff changeset
371 <has_text text="##bcftools_viewCommand" />
b8f8fdd611ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 2
diff changeset
372 <not_has_text text="rs78249411" />
0
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
373 </assert_contents>
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
374 </output>
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
375 </test>
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
376 <test>
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
377 <param name="input_file" ftype="vcf" value="view.vcf" />
27
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
378 <section name="sec_filter">
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
379 <param name="uncalled" value="--uncalled" />
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
380 </section>
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
381 <section name="sec_output">
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
382 <param name="header" value="--no-header" />
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
383 </section>
0
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
384 <param name="output_type" value="v" />
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
385 <output name="output_file">
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
386 <assert_contents>
4
b8f8fdd611ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 2
diff changeset
387 <not_has_text text="##bcftools_viewCommand" />
b8f8fdd611ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 2
diff changeset
388 <has_text text="5464562" />
0
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
389 </assert_contents>
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
390 </output>
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
391 </test>
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
392 <test>
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
393 <param name="input_file" ftype="vcf" value="view.vcf" />
27
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
394 <section name="sec_filter">
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
395 <param name="exclude_types" value="snps" />
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
396 </section>
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
397 <section name="sec_output">
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
398 <param name="drop_genotypes" value="true" />
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
399 </section>
0
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
400 <param name="output_type" value="v" />
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
401 <output name="output_file">
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
402 <assert_contents>
4
b8f8fdd611ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 2
diff changeset
403 <not_has_text text="##FORMAT=&lt;ID=GT" />
b8f8fdd611ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 2
diff changeset
404 <not_has_text text="rs62584840" />
b8f8fdd611ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 2
diff changeset
405 <has_text text="2343543" />
0
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
406 </assert_contents>
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
407 </output>
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
408 </test>
14
11f6245358e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
iuc
parents: 12
diff changeset
409 <test>
11f6245358e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
iuc
parents: 12
diff changeset
410 <param name="input_file" ftype="vcf" value="view.vcf" />
27
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
411 <section name="sec_filter">
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
412 <param name="phased" value="--phased" />
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
413 <param name="select_genotype" value="^het" />
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
414 </section>
14
11f6245358e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
iuc
parents: 12
diff changeset
415 <param name="output_type" value="v" />
11f6245358e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
iuc
parents: 12
diff changeset
416 <output name="output_file">
11f6245358e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
iuc
parents: 12
diff changeset
417 <assert_contents>
11f6245358e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
iuc
parents: 12
diff changeset
418 <has_text text="--genotype ^het" />
11f6245358e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
iuc
parents: 12
diff changeset
419 <has_text text="rs78249411" />
11f6245358e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
iuc
parents: 12
diff changeset
420 <not_has_text text="3048719" />
11f6245358e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
iuc
parents: 12
diff changeset
421 </assert_contents>
11f6245358e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
iuc
parents: 12
diff changeset
422 </output>
11f6245358e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
iuc
parents: 12
diff changeset
423 </test>
20
a950754650d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 19
diff changeset
424 <!-- Test region overlap option -->
a950754650d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 19
diff changeset
425 <test>
a950754650d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 19
diff changeset
426 <param name="input_file" ftype="vcf" value="view.vcf" />
27
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
427 <section name="sec_filter">
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
428 <param name="min_ac" value="1" />
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
429 <param name="max_ac" value="1" />
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
430 <param name="types" value="snps" />
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
431 </section>
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
432 <section name="sec_subset">
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
433 <param name="samples" value="NA00002" />
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
434 </section>
20
a950754650d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 19
diff changeset
435 <param name="output_type" value="v" />
a950754650d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 19
diff changeset
436 <section name="sec_restrict">
27
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
437 <conditional name="regions">
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
438 <param name="regions_src" value="regions" />
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
439 <repeat name="region_specs">
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
440 <param name="chrom" value="20" />
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
441 </repeat>
c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 26
diff changeset
442 </conditional>
20
a950754650d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 19
diff changeset
443 </section>
a950754650d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 19
diff changeset
444 <output name="output_file">
a950754650d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 19
diff changeset
445 <assert_contents>
a950754650d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 19
diff changeset
446 <has_text text="rs2298108" />
a950754650d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 19
diff changeset
447 <not_has_text text="rs6111385" />
a950754650d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 19
diff changeset
448 </assert_contents>
a950754650d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 19
diff changeset
449 </output>
a950754650d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 19
diff changeset
450 <assert_command>
a950754650d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 19
diff changeset
451 <has_text text="--regions-overlap" />
a950754650d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 19
diff changeset
452 </assert_command>
a950754650d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 19
diff changeset
453 </test>
0
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
454 </tests>
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
455 <help><![CDATA[
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
456 =====================================
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
457 bcftools @EXECUTABLE@
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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458 =====================================
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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459
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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460 VCF/BCF conversion, view, subset and filter VCF/BCF files.
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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461
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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462 @REGIONS_HELP@
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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463 @TARGETS_HELP@
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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464 @EXPRESSIONS_HELP@
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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465
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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466 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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467
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c6c23f9ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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468 @BCFTOOLS_HOWTOS@
0
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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469 ]]>
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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470 </help>
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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471 <expand macro="citations" />
89dff8355de4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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472 </tool>