Mercurial > repos > iuc > bcftools_view

annotate bcftools_view.xml @ 4:993ed534cc38 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
author iuc
date Sat, 11 Mar 2017 18:05:59 -0500
parents cc016cb332cd
children 741a08398a04
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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
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22 bcftools @EXECUTABLE@
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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 ${section.min_ac}
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36 #end if
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37 #if str($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 ${section.known_or_novel}
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46 #end if
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47 #if str($section.min_alleles)
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48 --min-alleles ${section.min_alleles}
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49 #end if
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50 #if str($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 ${section.phased}
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55 #end if
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56 #if str($section.min_af)
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57 --min-af ${section.min_af}
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58 #end if
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59 #if str($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 ${section.header}
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80 #end if
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81 #if str($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" />
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104 <expand macro="macro_regions" />
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105 <expand macro="macro_targets" />
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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"
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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"
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114 help="Do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)" />
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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"
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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" />
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123 <param name="select_genotype" type="select">
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124 <option value="__none__" selected="True">No selection</option>
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125 <option value="require one or more hom/het/missing genotype or" />
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126 <option value="if prefixed with &quot;^&quot;" />
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127 <option value="exclude sites with hom/het/missing genotypes" />
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128 </param>
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129
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130 <param name="types" type="select" label="Select Types" multiple="true" optional="True">
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131 <help>
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132 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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133 Types are determined by comparing the REF and ALT alleles in the VCF record.
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134 </help>
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135 <expand macro="macro_types_options" />
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136 </param>
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137
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138 <param name="exclude_types" type="select" label="Exclude Types" multiple="true" optional="True">
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139 <help>
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140 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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141 Types are determined by comparing the REF and ALT alleles in the VCF record.
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142 </help>
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143 <expand macro="macro_types_options" />
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144 </param>
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145
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146
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147 <param name="known_or_novel" type="select" label="filter known or novel ID" optional="true">
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148 <option value="--novel">(-k) print novel sites only (ID column is ".")</option>
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149 <option value="--known">(-n) print known sites only (ID column is not ".")</option>
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150 </param>
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151
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152 <param name="min_alleles" type="integer" label="Min Alleles" optional="True"
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153 help="(-m) Minimum number of alleles listed in REF and ALT (e.g. -m2)" />
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154 <param name="max_alleles" type="integer" label="Max Alleles" optional="True"
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155 help="(-M) Maximum number of alleles listed in REF and ALT (e.g. -M2 for biallelic sites)" />
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156
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157 <param name="phased" type="select" label="filter phased" optional="true">
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158 <help>
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159 Haploid genotypes are considered phased. Missing genotypes considered unphased unless the phased bit is set.
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160 </help>
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161 <option value="--phased">(-p) print sites where all samples are phased</option>
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162 <option value="--exclude-phased">(-P) exclude sites where all samples are phased</option>
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163 </param>
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164
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165 <!-- TODO optional select for type: nref,alt1,minor,major,sum -->
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166 <param name="min_af" type="float" label="Min Af" optional="True"
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167 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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168 <param name="max_af" type="float" label="Max Af" optional="True"
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169 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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170
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171 <param name="uncalled" type="select" label="filter on genotype uncalled" optional="true">
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172 <option value="--uncalled">uncalled - print sites without a called genotype</option>
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173 <option value="--exclude-uncalled">exclude-uncalled - exclude sites without a called genotype</option>
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174 </param>
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175
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176 <param name="private" type="select" label="filter on private" optional="true">
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177 <help><![CDATA[
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178 Private: Where only the subset samples carry an non-reference allele.
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179 ( Ignored if samples are not included )
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180 ]]></help>
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181 <option value="--private">(-x) private - print sites where only the subset samples carry an non-reference allele</option>
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182 <option value="--exclude-private">(-X) exclude-private - exclude sites where only the subset samples carry an non-reference allele</option>
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183 </param>
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184
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185 </section>
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186
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187 <section name="sec_output" expanded="false" title="Output Options">
4
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188 <param name="drop_genotypes" type="boolean" truevalue="--drop-genotypes" falsevalue="" label="Drop Genotypes"
0
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189 help="Drop individual genotype information (after subsetting if -s option set)" />
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190 <param name="header" type="select" label="output header" optional="true">
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191 <option value="--no-header">(-h) no-header</option>
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192 <option value="--header-only">(-H) header-only</option>
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193 </param>
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194 <param name="compression_level" type="integer" min="0" max="9" label="Compression Level" optional="True"
0
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195 help="Compression level: 0 uncompressed, 1 best speed, 9 best compression" />
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196 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets File"
0
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197 help="Inverts the query/filtering applied by Targets File" />
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198 </section>
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199 <expand macro="macro_select_output_type" />
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200 </inputs>
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201 <outputs>
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202 <expand macro="macro_vcf_output" />
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203 </outputs>
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204 <tests>
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205 <test>
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206 <param name="input_file" ftype="vcf" value="view.vcf" />
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207 <param name="min_ac" value="1" />
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208 <param name="max_ac" value="1" />
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209 <param name="samples" value="NA00002" />
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210 <param name="types" value="snps" />
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211 <param name="output_type" value="v" />
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212 <output name="output_file">
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213 <assert_contents>
4
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214 <has_text text="rs2298108" />
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215 <not_has_text text="rs6111385" />
0
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216 </assert_contents>
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217 </output>
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218 </test>
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219 <test>
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220 <param name="input_file" ftype="vcf" value="view.vcf" />
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221 <param name="known_or_novel" value="--novel" />
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222 <param name="private" value="--exclude-private" />
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223 <param name="samples" value="NA00003" />
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224 <param name="regions" value="20,Y" />
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225 <param name="output_type" value="v" />
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226 <output name="output_file">
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227 <assert_contents>
4
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228 <has_text text="8657215" />
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229 <not_has_text text="rs6111385" />
0
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230 </assert_contents>
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231 </output>
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232 </test>
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233 <test>
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234 <param name="input_file" ftype="vcf" value="view.vcf" />
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235 <param name="known_or_novel" value="--known" />
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236 <param name="private" value="--exclude-private" />
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237 <param name="apply_filters" value="PASS" />
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238 <param name="samples" value="NA00003" />
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239 <param name="regions" value="20,Y" />
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240 <param name="output_type" value="v" />
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241 <output name="output_file">
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242 <assert_contents>
4
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diff changeset
243 <has_text text="rs6111385" />
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244 <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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245 </assert_contents>
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246 </output>
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247 </test>
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248 <test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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249 <param name="input_file" ftype="vcf" value="view.vcf" />
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250 <param name="private" value="--private" />
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251 <param name="samples" value="NA00003" />
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252 <param name="output_type" value="v" />
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253 <output name="output_file">
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254 <assert_contents>
4
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diff changeset
255 <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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256 <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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257 </assert_contents>
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258 </output>
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259 </test>
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260 <test>
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261 <param name="input_file" ftype="vcf" value="view.vcf" />
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262 <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
iuc
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263 <param name="output_type" value="v" />
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264 <output name="output_file">
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265 <assert_contents>
4
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parents: 2
diff changeset
266 <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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267 <not_has_text text="8657215" />
0
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268 </assert_contents>
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269 </output>
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270 </test>
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271 <test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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272 <param name="input_file" ftype="vcf" value="view.vcf" />
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273 <param name="phased" value="--phased" />
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274 <param name="output_type" value="v" />
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275 <output name="output_file">
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276 <assert_contents>
4
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 2
diff changeset
277 <has_text text="rs78249411" />
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
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diff changeset
278 <not_has_text text="rs6111385" />
0
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279 </assert_contents>
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280 </output>
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281 </test>
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282 <test>
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283 <param name="input_file" ftype="vcf" value="view.vcf" />
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284 <param name="phased" value="--exclude-phased" />
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285 <param name="output_type" value="v" />
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286 <output name="output_file">
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287 <assert_contents>
4
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288 <has_text text="rs6111385" />
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289 <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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290 </assert_contents>
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291 </output>
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292 </test>
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293 <test>
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294 <param name="input_file" ftype="vcf" value="view.vcf" />
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295 <param name="min_alleles" value="2" />
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296 <param name="max_alleles" value="2" />
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297 <param name="min_af" value="0.3" />
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298 <param name="max_af" value="0.7" />
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299 <param name="header" value="--header-only" />
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300 <param name="output_type" value="v" />
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301 <output name="output_file">
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302 <assert_contents>
4
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303 <has_text text="##bcftools_viewCommand" />
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304 <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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305 </assert_contents>
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306 </output>
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307 </test>
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308 <test>
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309 <param name="input_file" ftype="vcf" value="view.vcf" />
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310 <param name="uncalled" value="--uncalled" />
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311 <param name="header" value="--no-header" />
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312 <param name="output_type" value="v" />
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313 <output name="output_file">
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314 <assert_contents>
4
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315 <not_has_text text="##bcftools_viewCommand" />
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316 <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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317 </assert_contents>
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318 </output>
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319 </test>
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320 <test>
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321 <param name="input_file" ftype="vcf" value="view.vcf" />
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322 <param name="exclude_types" value="snps" />
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323 <param name="drop_genotypes" value="true" />
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324 <param name="output_type" value="v" />
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325 <output name="output_file">
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326 <assert_contents>
4
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327 <not_has_text text="##FORMAT=&lt;ID=GT" />
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328 <not_has_text text="rs62584840" />
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329 <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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330 </assert_contents>
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331 </output>
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332 </test>
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333 </tests>
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334 <help><![CDATA[
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335 =====================================
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336 bcftools @EXECUTABLE@
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337 =====================================
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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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 VCF/BCF conversion, view, subset and filter VCF/BCF files.
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340
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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341 @REGIONS_HELP@
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342 @TARGETS_HELP@
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343 @EXPRESSIONS_HELP@
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344
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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345 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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346
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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347 @BCFTOOLS_WIKI@
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348 ]]>
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349 </help>
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350 <expand macro="citations" />
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351 </tool>