Mercurial > repos > iuc > bcftools_view

annotate bcftools_view.xml @ 24:1a2ef636f48e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 784611c9caf2680d41414ca2880b93a69d719701
author iuc
date Sun, 18 Aug 2024 10:19:46 +0000
parents abc3ced31cd1
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_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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24
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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 ${section.known_or_novel}
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47 #end if
4
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48 #if str($section.min_alleles)
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49 --min-alleles ${section.min_alleles}
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50 #end if
4
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51 #if str($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 ${section.min_af}
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59 #end if
4
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60 #if str($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" />
8
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105 <expand macro="macro_restrict" />
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106 <expand macro="macro_restrict" type="target" label_type="Target" />
0
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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" label="Select Genotype" optional="True">
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125 <help>
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126 Include only sites with one or more homozygous (hom), heterozygous (het) or missing (miss) genotypes.
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127 When prefixed with ^, the logic is reversed.
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128 Please notice that if the input file doesn't have any genotype columns,
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129 then this option is ignored altogether.
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130 </help>
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131 <option value="hom">hom</option>
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132 <option value="het">het</option>
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133 <option value="miss">miss</option>
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134 <option value="^hom">^hom</option>
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135 <option value="^het">^het</option>
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136 <option value="^miss">^miss</option>
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137 </param>
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138 <param name="types" type="select" label="Select Types" multiple="true" optional="True">
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139 <help>
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140 List of variant types to select. Site is selected if any of the ALT alleles is of the type requested.
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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 <param name="exclude_types" type="select" label="Exclude Types" multiple="true" optional="True">
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147 <help>
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148 List of variant types to exclude. Site is excluded if any of the ALT alleles is of the type requested.
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149 Types are determined by comparing the REF and ALT alleles in the VCF record.
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150 </help>
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151 <expand macro="macro_types_options" />
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152 </param>
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153
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154
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155 <param name="known_or_novel" type="select" label="filter known or novel ID" optional="true">
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156 <option value="--novel">(-k) print novel sites only (ID column is ".")</option>
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157 <option value="--known">(-n) print known sites only (ID column is not ".")</option>
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158 </param>
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159
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160 <param name="min_alleles" type="integer" label="Min Alleles" optional="True"
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161 help="(-m) Minimum number of alleles listed in REF and ALT (e.g. -m2)" />
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162 <param name="max_alleles" type="integer" label="Max Alleles" optional="True"
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163 help="(-M) Maximum number of alleles listed in REF and ALT (e.g. -M2 for biallelic sites)" />
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164
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165 <param name="phased" type="select" label="filter phased" optional="true">
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166 <help>
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167 Haploid genotypes are considered phased. Missing genotypes considered unphased unless the phased bit is set.
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168 </help>
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169 <option value="--phased">(-p) print sites where all samples are phased</option>
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170 <option value="--exclude-phased">(-P) exclude sites where all samples are phased</option>
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171 </param>
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172
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173 <!-- TODO optional select for type: nref,alt1,minor,major,sum -->
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174 <param name="min_af" type="float" label="Min Af" optional="True"
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175 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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176 <param name="max_af" type="float" label="Max Af" optional="True"
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177 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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178
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179 <param name="uncalled" type="select" label="filter on genotype uncalled" optional="true">
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180 <option value="--uncalled">uncalled - print sites without a called genotype</option>
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181 <option value="--exclude-uncalled">exclude-uncalled - exclude sites without a called genotype</option>
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182 </param>
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183
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184 <param name="private" type="select" label="filter on private" optional="true">
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185 <help><![CDATA[
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186 Private: Where only the subset samples carry an non-reference allele.
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187 ( Ignored if samples are not included )
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188 ]]></help>
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189 <option value="--private">(-x) private - print sites where only the subset samples carry an non-reference allele</option>
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190 <option value="--exclude-private">(-X) exclude-private - exclude sites where only the subset samples carry an non-reference allele</option>
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191 </param>
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192
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193 </section>
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194
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195 <section name="sec_output" expanded="false" title="Output Options">
4
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196 <param name="drop_genotypes" type="boolean" truevalue="--drop-genotypes" falsevalue="" label="Drop Genotypes"
0
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197 help="Drop individual genotype information (after subsetting if -s option set)" />
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198 <param name="header" type="select" label="output header" optional="true">
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199 <option value="--no-header">(-h) no-header</option>
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200 <option value="--header-only">(-H) header-only</option>
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201 </param>
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202 <param name="compression_level" type="integer" min="0" max="9" label="Compression Level" optional="True"
0
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203 help="Compression level: 0 uncompressed, 1 best speed, 9 best compression" />
4
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204 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets File"
0
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205 help="Inverts the query/filtering applied by Targets File" />
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206 </section>
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207 <expand macro="macro_select_output_type" />
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208 </inputs>
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209 <outputs>
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210 <expand macro="macro_vcf_output" />
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211 </outputs>
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212 <tests>
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213 <test>
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214 <param name="input_file" ftype="vcf" value="view.vcf" />
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215 <param name="min_ac" value="1" />
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216 <param name="max_ac" value="1" />
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217 <param name="samples" value="NA00002" />
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218 <param name="types" value="snps" />
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219 <param name="output_type" value="v" />
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220 <output name="output_file">
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221 <assert_contents>
4
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222 <has_text text="rs2298108" />
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223 <not_has_text text="rs6111385" />
0
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224 </assert_contents>
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225 </output>
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226 </test>
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227 <test>
7
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228 <param name="input_file" ftype="bcf" value="view.bcf" />
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229 <param name="min_ac" value="1" />
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230 <param name="max_ac" value="1" />
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231 <param name="samples" value="NA00002" />
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232 <param name="types" value="snps" />
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233 <param name="output_type" value="v" />
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234 <output name="output_file">
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235 <assert_contents>
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236 <has_text text="rs2298108" />
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237 <not_has_text text="rs6111385" />
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238 </assert_contents>
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239 </output>
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240 </test>
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241 <test>
0
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242 <param name="input_file" ftype="vcf" value="view.vcf" />
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243 <param name="known_or_novel" value="--novel" />
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244 <param name="private" value="--exclude-private" />
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245 <param name="samples" value="NA00003" />
21
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246 <section name="sec_restrict">
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247 <conditional name="regions">
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248 <param name="regions_src" value="regions"/>
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249 <repeat name="regions">
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250 <param name="chrom" value="Y" />
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251 <param name="start" value="20" />
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252 </repeat>
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253 </conditional>
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254 </section>
0
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255 <param name="output_type" value="v" />
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256 <output name="output_file">
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257 <assert_contents>
4
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258 <has_text text="8657215" />
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259 <not_has_text text="rs6111385" />
0
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260 </assert_contents>
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261 </output>
17
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262 <assert_command>
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263 <has_text text="--regions 'Y:20-'"/>
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264 </assert_command>
0
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265 </test>
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266 <test>
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267 <param name="input_file" ftype="vcf" value="view.vcf" />
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268 <param name="known_or_novel" value="--known" />
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269 <param name="private" value="--exclude-private" />
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270 <param name="apply_filters" value="PASS" />
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271 <param name="samples" value="NA00003" />
21
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272 <section name="sec_restrict">
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diff changeset
273 <conditional name="regions">
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274 <param name="regions_src" value="regions"/>
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275 <repeat name="regions">
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parents: 18
diff changeset
276 <param name="chrom" value="Y" />
abc3ced31cd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 96c0663be587b73bdf09ddf060cb559f28f9eba7
iuc
parents: 18
diff changeset
277 <param name="start" value="20" />
abc3ced31cd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 96c0663be587b73bdf09ddf060cb559f28f9eba7
iuc
parents: 18
diff changeset
278 </repeat>
abc3ced31cd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 96c0663be587b73bdf09ddf060cb559f28f9eba7
iuc
parents: 18
diff changeset
279 </conditional>
abc3ced31cd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 96c0663be587b73bdf09ddf060cb559f28f9eba7
iuc
parents: 18
diff changeset
280 </section>
0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
281 <param name="output_type" value="v" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
282 <output name="output_file">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
283 <assert_contents>
21
abc3ced31cd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 96c0663be587b73bdf09ddf060cb559f28f9eba7
iuc
parents: 18
diff changeset
284 <has_text text="Minimum number of alternate bases" />
4
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 2
diff changeset
285 <not_has_text text="8657215" />
0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
286 </assert_contents>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
287 </output>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
288 </test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
289 <test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
290 <param name="input_file" ftype="vcf" value="view.vcf" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
291 <param name="private" value="--private" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
292 <param name="samples" value="NA00003" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
293 <param name="output_type" value="v" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
294 <output name="output_file">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
295 <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
296 <has_text text="rs62584840" />
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 2
diff changeset
297 <not_has_text text="8657215" />
0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
298 </assert_contents>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
299 </output>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
300 </test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
301 <test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
302 <param name="input_file" ftype="vcf" value="view.vcf" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
303 <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
parents:
diff changeset
304 <param name="output_type" value="v" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
305 <output name="output_file">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
306 <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
307 <has_text text="rs5939407" />
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 2
diff changeset
308 <not_has_text text="8657215" />
0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
309 </assert_contents>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
310 </output>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
311 </test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
312 <test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
313 <param name="input_file" ftype="vcf" value="view.vcf" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
314 <param name="phased" value="--phased" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
315 <param name="output_type" value="v" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
316 <output name="output_file">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
317 <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
318 <has_text text="rs78249411" />
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 2
diff changeset
319 <not_has_text text="rs6111385" />
0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
320 </assert_contents>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
321 </output>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
322 </test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
323 <test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
324 <param name="input_file" ftype="vcf" value="view.vcf" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
325 <param name="phased" value="--exclude-phased" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
326 <param name="output_type" value="v" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
327 <output name="output_file">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
328 <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
329 <has_text text="rs6111385" />
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 2
diff changeset
330 <not_has_text text="rs78249411" />
0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
331 </assert_contents>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
332 </output>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
333 </test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
334 <test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
335 <param name="input_file" ftype="vcf" value="view.vcf" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
336 <param name="min_alleles" value="2" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
337 <param name="max_alleles" value="2" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
338 <param name="min_af" value="0.3" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
339 <param name="max_af" value="0.7" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
340 <param name="header" value="--header-only" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
341 <param name="output_type" value="v" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
342 <output name="output_file">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
343 <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
344 <has_text text="##bcftools_viewCommand" />
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 2
diff changeset
345 <not_has_text text="rs78249411" />
0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
346 </assert_contents>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
347 </output>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
348 </test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
349 <test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
350 <param name="input_file" ftype="vcf" value="view.vcf" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
351 <param name="uncalled" value="--uncalled" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
352 <param name="header" value="--no-header" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
353 <param name="output_type" value="v" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
354 <output name="output_file">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
355 <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
356 <not_has_text text="##bcftools_viewCommand" />
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 2
diff changeset
357 <has_text text="5464562" />
0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
358 </assert_contents>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
359 </output>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
360 </test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
361 <test>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
362 <param name="input_file" ftype="vcf" value="view.vcf" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
363 <param name="exclude_types" value="snps" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
364 <param name="drop_genotypes" value="true" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
365 <param name="output_type" value="v" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
366 <output name="output_file">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
367 <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
368 <not_has_text text="##FORMAT=&lt;ID=GT" />
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 2
diff changeset
369 <not_has_text text="rs62584840" />
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 2
diff changeset
370 <has_text text="2343543" />
0
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371 </assert_contents>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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372 </output>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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373 </test>
13
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374 <test>
98d5499ead46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
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375 <param name="input_file" ftype="vcf" value="view.vcf" />
98d5499ead46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
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376 <param name="phased" value="--phased" />
98d5499ead46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
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377 <param name="output_type" value="v" />
98d5499ead46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
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378 <param name="select_genotype" value="^het" />
98d5499ead46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
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379 <output name="output_file">
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380 <assert_contents>
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381 <has_text text="--genotype ^het" />
98d5499ead46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
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382 <has_text text="rs78249411" />
98d5499ead46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
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383 <not_has_text text="3048719" />
98d5499ead46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
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384 </assert_contents>
98d5499ead46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
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385 </output>
98d5499ead46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
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386 </test>
18
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387 <!-- Test region overlap option -->
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388 <test>
3ca3de4e5291 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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389 <param name="input_file" ftype="vcf" value="view.vcf" />
3ca3de4e5291 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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390 <param name="min_ac" value="1" />
3ca3de4e5291 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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391 <param name="max_ac" value="1" />
3ca3de4e5291 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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392 <param name="samples" value="NA00002" />
3ca3de4e5291 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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393 <param name="types" value="snps" />
3ca3de4e5291 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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394 <param name="output_type" value="v" />
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395 <section name="sec_restrict">
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396 <param name="regions_overlap" value="1"/>
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397 </section>
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398 <output name="output_file">
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399 <assert_contents>
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400 <has_text text="rs2298108" />
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401 <not_has_text text="rs6111385" />
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402 </assert_contents>
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403 </output>
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404 <assert_command>
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405 <has_text text="--regions-overlap" />
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406 </assert_command>
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407 </test>
0
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408 </tests>
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409 <help><![CDATA[
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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410 =====================================
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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411 bcftools @EXECUTABLE@
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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412 =====================================
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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413
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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414 VCF/BCF conversion, view, subset and filter VCF/BCF files.
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415
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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416 @REGIONS_HELP@
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417 @TARGETS_HELP@
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418 @EXPRESSIONS_HELP@
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419
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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420 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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421
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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422 @BCFTOOLS_WIKI@
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423 ]]>
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424 </help>
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425 <expand macro="citations" />
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426 </tool>