Mercurial > repos > iuc > bcftools_view

annotate bcftools_view.xml @ 6:3a233c8eb814 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 880627162bdeb854582e9f58ddab451de35feba3
author iuc
date Tue, 12 Dec 2017 14:03:51 -0500
parents 741a08398a04
children d1f8f55f564d
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@">
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3 <description>VCF/BCF conversion, view, subset and filter VCF/BCF files</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">view</token>
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6 <import>macros.xml</import>
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7 <xml name="macro_types_options">
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8 <option value="snps">snps</option>
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9 <option value="indels">indels</option>
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10 <option value="mnps">mnps</option>
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11 <option value="other">mnps</option>
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12 </xml>
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13 </macros>
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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_ENV@
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18 @PREPARE_INPUT_FILE@
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19 #set $section = $sec_restrict
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20 @PREPARE_TARGETS_FILE@
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21 @PREPARE_REGIONS_FILE@
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23 bcftools @EXECUTABLE@
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25 ## Subset section
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26 #set $section = $sec_subset
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27 ${section.trim_alt_alleles}
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28 ${section.no_update}
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29 @SAMPLES@
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30 ${section.force_samples}
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31
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32
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33 ## Filter section
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34 #set $section = $sec_filter
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35 #if str($section.min_ac)
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36 --min-ac ${section.min_ac}
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37 #end if
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38 #if str($section.max_ac)
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39 --max-ac ${section.max_ac}
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40 #end if
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41 #if str($section.select_genotype) != "__none__":
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42 --genotype "${section.select_genotype}"
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43 #end if
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44 ## known or novel
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45 #if $section.known_or_novel:
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46 ${section.known_or_novel}
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47 #end if
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48 #if str($section.min_alleles)
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49 --min-alleles ${section.min_alleles}
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50 #end if
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51 #if str($section.max_alleles)
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52 --max-alleles ${section.max_alleles}
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53 #end if
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54 #if $section.phased:
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55 ${section.phased}
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56 #end if
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57 #if str($section.min_af)
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58 --min-af ${section.min_af}
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59 #end if
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60 #if str($section.max_af)
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61 --max-af ${section.max_af}
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62 #end if
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63 #if $section.uncalled:
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64 ${section.uncalled}
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65 #end if
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66 #if $section.types:
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67 --types "${section.types}"
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68 #end if
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69 #if $section.exclude_types:
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70 --exclude-types "${section.exclude_types}"
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71 #end if
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72 #if $section.private:
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73 ${section.private}
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74 #end if
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75
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76 ## Output section
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77 #set $section = $sec_output
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78 ${section.drop_genotypes}
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79 #if $section.header:
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80 ${section.header}
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81 #end if
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82 #if str($section.compression_level)
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83 --compression-level ${section.compression_level}
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84 #end if
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85
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86 #set $section = $sec_restrict
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87 @APPLY_FILTERS@
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88 @INCLUDE@
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89 @EXCLUDE@
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90 @REGIONS@
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91 @TARGETS@
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92
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93 @OUTPUT_TYPE@
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94 @THREADS@
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95
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96 ## Primary Input/Outputs
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97 @INPUT_FILE@
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98 > '$output_file'
0
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99 ]]>
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100 </command>
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101 <inputs>
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102 <expand macro="macro_input" />
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103 <section name="sec_restrict" expanded="false" title="Restrict to">
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104 <expand macro="macro_apply_filters" />
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105 <expand macro="macro_regions" />
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106 <expand macro="macro_targets" />
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107 <expand macro="macro_include" />
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108 <expand macro="macro_exclude" />
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109 </section>
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110 <section name="sec_subset" expanded="false" title="Subset Options">
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111 <expand macro="macro_samples" />
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112 <param name="force_samples" type="boolean" truevalue="--force-samples" falsevalue="" label="Force Samples"
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113 help="Only warn about unknown subset samples" />
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114 <param name="no_update" type="boolean" truevalue="--no-update" falsevalue="" label="No Update"
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115 help="Do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)" />
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116 <param name="trim_alt_alleles" type="boolean" truevalue="--trim-alt-alleles" falsevalue="" label="Trim Alt Alleles"
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117 help="Trim alternate alleles not seen in the subset" />
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118 </section>
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119 <section name="sec_filter" expanded="false" title="Filter Options">
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120 <param name="min_ac" type="integer" label="Min Ac" optional="True"
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121 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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122 <param name="max_ac" type="integer" label="Max Ac" optional="True"
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123 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" />
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124 <param name="select_genotype" type="select">
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125 <option value="__none__" selected="True">No selection</option>
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126 <option value="require one or more hom/het/missing genotype or" />
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127 <option value="if prefixed with &quot;^&quot;" />
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128 <option value="exclude sites with hom/het/missing genotypes" />
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129 </param>
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130
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131 <param name="types" type="select" label="Select Types" multiple="true" optional="True">
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132 <help>
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133 List of variant types to select. Site is selected if any of the ALT alleles is of the type requested.
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134 Types are determined by comparing the REF and ALT alleles in the VCF record.
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135 </help>
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136 <expand macro="macro_types_options" />
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137 </param>
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138
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139 <param name="exclude_types" type="select" label="Exclude Types" multiple="true" optional="True">
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140 <help>
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141 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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142 Types are determined by comparing the REF and ALT alleles in the VCF record.
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143 </help>
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144 <expand macro="macro_types_options" />
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145 </param>
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146
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147
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148 <param name="known_or_novel" type="select" label="filter known or novel ID" optional="true">
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149 <option value="--novel">(-k) print novel sites only (ID column is ".")</option>
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150 <option value="--known">(-n) print known sites only (ID column is not ".")</option>
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151 </param>
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152
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153 <param name="min_alleles" type="integer" label="Min Alleles" optional="True"
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154 help="(-m) Minimum number of alleles listed in REF and ALT (e.g. -m2)" />
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155 <param name="max_alleles" type="integer" label="Max Alleles" optional="True"
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156 help="(-M) Maximum number of alleles listed in REF and ALT (e.g. -M2 for biallelic sites)" />
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157
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158 <param name="phased" type="select" label="filter phased" optional="true">
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159 <help>
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160 Haploid genotypes are considered phased. Missing genotypes considered unphased unless the phased bit is set.
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161 </help>
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162 <option value="--phased">(-p) print sites where all samples are phased</option>
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163 <option value="--exclude-phased">(-P) exclude sites where all samples are phased</option>
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164 </param>
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165
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166 <!-- TODO optional select for type: nref,alt1,minor,major,sum -->
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167 <param name="min_af" type="float" label="Min Af" optional="True"
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168 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" />
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169 <param name="max_af" type="float" label="Max Af" optional="True"
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170 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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171
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172 <param name="uncalled" type="select" label="filter on genotype uncalled" optional="true">
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173 <option value="--uncalled">uncalled - print sites without a called genotype</option>
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174 <option value="--exclude-uncalled">exclude-uncalled - exclude sites without a called genotype</option>
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175 </param>
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176
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177 <param name="private" type="select" label="filter on private" optional="true">
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178 <help><![CDATA[
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179 Private: Where only the subset samples carry an non-reference allele.
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180 ( Ignored if samples are not included )
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181 ]]></help>
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182 <option value="--private">(-x) private - print sites where only the subset samples carry an non-reference allele</option>
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183 <option value="--exclude-private">(-X) exclude-private - exclude sites where only the subset samples carry an non-reference allele</option>
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184 </param>
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185
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186 </section>
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187
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188 <section name="sec_output" expanded="false" title="Output Options">
4
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189 <param name="drop_genotypes" type="boolean" truevalue="--drop-genotypes" falsevalue="" label="Drop Genotypes"
0
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190 help="Drop individual genotype information (after subsetting if -s option set)" />
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191 <param name="header" type="select" label="output header" optional="true">
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192 <option value="--no-header">(-h) no-header</option>
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193 <option value="--header-only">(-H) header-only</option>
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194 </param>
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195 <param name="compression_level" type="integer" min="0" max="9" label="Compression Level" optional="True"
0
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196 help="Compression level: 0 uncompressed, 1 best speed, 9 best compression" />
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197 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets File"
0
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198 help="Inverts the query/filtering applied by Targets File" />
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199 </section>
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200 <expand macro="macro_select_output_type" />
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201 </inputs>
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202 <outputs>
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203 <expand macro="macro_vcf_output" />
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204 </outputs>
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205 <tests>
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206 <test>
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207 <param name="input_file" ftype="vcf" value="view.vcf" />
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208 <param name="min_ac" value="1" />
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209 <param name="max_ac" value="1" />
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210 <param name="samples" value="NA00002" />
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211 <param name="types" value="snps" />
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212 <param name="output_type" value="v" />
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213 <output name="output_file">
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214 <assert_contents>
4
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215 <has_text text="rs2298108" />
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216 <not_has_text text="rs6111385" />
0
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217 </assert_contents>
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218 </output>
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219 </test>
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220 <test>
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221 <param name="input_file" ftype="vcf" value="view.vcf" />
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222 <param name="known_or_novel" value="--novel" />
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223 <param name="private" value="--exclude-private" />
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224 <param name="samples" value="NA00003" />
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225 <param name="regions" value="20,Y" />
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226 <param name="output_type" value="v" />
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227 <output name="output_file">
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228 <assert_contents>
4
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229 <has_text text="8657215" />
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230 <not_has_text text="rs6111385" />
0
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231 </assert_contents>
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232 </output>
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233 </test>
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234 <test>
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235 <param name="input_file" ftype="vcf" value="view.vcf" />
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236 <param name="known_or_novel" value="--known" />
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237 <param name="private" value="--exclude-private" />
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238 <param name="apply_filters" value="PASS" />
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239 <param name="samples" value="NA00003" />
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240 <param name="regions" value="20,Y" />
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241 <param name="output_type" value="v" />
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242 <output name="output_file">
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243 <assert_contents>
4
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diff changeset
244 <has_text text="rs6111385" />
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245 <not_has_text text="8657215" />
0
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246 </assert_contents>
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247 </output>
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248 </test>
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249 <test>
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250 <param name="input_file" ftype="vcf" value="view.vcf" />
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251 <param name="private" value="--private" />
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252 <param name="samples" value="NA00003" />
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253 <param name="output_type" value="v" />
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254 <output name="output_file">
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255 <assert_contents>
4
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diff changeset
256 <has_text text="rs62584840" />
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257 <not_has_text text="8657215" />
0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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258 </assert_contents>
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259 </output>
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260 </test>
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261 <test>
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262 <param name="input_file" ftype="vcf" value="view.vcf" />
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263 <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" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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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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parents: 2
diff changeset
267 <has_text text="rs5939407" />
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
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diff changeset
268 <not_has_text text="8657215" />
0
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269 </assert_contents>
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270 </output>
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271 </test>
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272 <test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
273 <param name="input_file" ftype="vcf" value="view.vcf" />
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274 <param name="phased" value="--phased" />
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275 <param name="output_type" value="v" />
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276 <output name="output_file">
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277 <assert_contents>
4
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
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diff changeset
278 <has_text text="rs78249411" />
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279 <not_has_text text="rs6111385" />
0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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280 </assert_contents>
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281 </output>
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282 </test>
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283 <test>
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284 <param name="input_file" ftype="vcf" value="view.vcf" />
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285 <param name="phased" value="--exclude-phased" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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286 <param name="output_type" value="v" />
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287 <output name="output_file">
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288 <assert_contents>
4
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
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289 <has_text text="rs6111385" />
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
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290 <not_has_text text="rs78249411" />
0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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291 </assert_contents>
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292 </output>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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293 </test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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294 <test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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295 <param name="input_file" ftype="vcf" value="view.vcf" />
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296 <param name="min_alleles" value="2" />
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297 <param name="max_alleles" value="2" />
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298 <param name="min_af" value="0.3" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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299 <param name="max_af" value="0.7" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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300 <param name="header" value="--header-only" />
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301 <param name="output_type" value="v" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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302 <output name="output_file">
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303 <assert_contents>
4
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
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304 <has_text text="##bcftools_viewCommand" />
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
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305 <not_has_text text="rs78249411" />
0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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306 </assert_contents>
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307 </output>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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308 </test>
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309 <test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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310 <param name="input_file" ftype="vcf" value="view.vcf" />
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311 <param name="uncalled" value="--uncalled" />
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312 <param name="header" value="--no-header" />
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313 <param name="output_type" value="v" />
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314 <output name="output_file">
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315 <assert_contents>
4
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
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316 <not_has_text text="##bcftools_viewCommand" />
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
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317 <has_text text="5464562" />
0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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318 </assert_contents>
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319 </output>
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320 </test>
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321 <test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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322 <param name="input_file" ftype="vcf" value="view.vcf" />
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323 <param name="exclude_types" value="snps" />
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324 <param name="drop_genotypes" value="true" />
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325 <param name="output_type" value="v" />
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326 <output name="output_file">
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327 <assert_contents>
4
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
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328 <not_has_text text="##FORMAT=&lt;ID=GT" />
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329 <not_has_text text="rs62584840" />
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
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330 <has_text text="2343543" />
0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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331 </assert_contents>
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332 </output>
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333 </test>
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334 </tests>
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335 <help><![CDATA[
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336 =====================================
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337 bcftools @EXECUTABLE@
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338 =====================================
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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339
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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340 VCF/BCF conversion, view, subset and filter VCF/BCF files.
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341
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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342 @REGIONS_HELP@
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343 @TARGETS_HELP@
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344 @EXPRESSIONS_HELP@
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345
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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346 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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347
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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348 @BCFTOOLS_WIKI@
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349 ]]>
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350 </help>
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351 <expand macro="citations" />
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352 </tool>