Mercurial > repos > iuc > bcftools_stats

annotate bcftools_stats.xml @ 21:999c1918479b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 868f4386992de55d25da197660a43a913a09c8df
author iuc
date Wed, 14 Aug 2024 16:38:47 +0000
parents bf8325a07ce7
children 591cc8518033
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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="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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3 <description>Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">stats</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="bio_tools" />
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9 <expand macro="requirements">
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10 <expand macro="samtools_requirement"/>
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11 <expand macro="matplotlib_requirement" />
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12 <requirement type="package" version="0.12.0">tectonic</requirement>
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13 </expand>
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14 <expand macro="version_command" />
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15 <command detect_errors="aggressive"><![CDATA[
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16 @PREPARE_ENV@
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17 #set $input_files = [$input_file]
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18 #if $inputB_file:
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19 #silent $input_files.append($inputB_file)
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20 #end if
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21 @PREPARE_INPUT_FILES@
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22 #set $section = $sec_restrict
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23 @PREPARE_TARGETS_FILE@
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24 @PREPARE_REGIONS_FILE@
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25 ## Stats section
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26 #set $section = $sec_default.reference_source
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27 @PREPARE_FASTA_REF@
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28 #set $section = $sec_default
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29 @PREPARE_EXONS_FILE@
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31 bcftools @EXECUTABLE@
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33 ## Stats section
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34 #set $section = $sec_default.reference_source
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35 @FASTA_REF@
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36 #set $section = $sec_default
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37 @EXONS_FILE@
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38 ${section.first_allele_only}
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39 #if $section.depth.set_depth == 'yes':
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40 --depth ${section.depth.depth_min},${section.depth.depth_max},${section.depth.depth_bin_size}
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41 #end if
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42 #if $section.user_tstv:
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43 --user-tstv '${section.user_tstv}'
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44 #end if
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45 #if $section.afbins.afbins_select == 'af_bins_list':
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46 --af-bins '$section.afbins.af_bins_list'
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47 #elif $section.afbins.afbins_select == 'af_bins_file':
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48 --af-bins '$section.afbins.af_bins_file'
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49 #end if
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50 #if $section.af_tag:
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51 --af-tag '${section.af_tag}'
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52 #end if
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53 #if len($input_vcfs) == 1:
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54 ${section.split_by_ID}
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55 #end if
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56 ${section.verbose}
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57
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58 ## Stats section
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59 #set $section = $sec_restrict
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60 @APPLY_FILTERS@
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61 @COLLAPSE@
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62 @REGIONS@
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63 @SAMPLES@
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64 @TARGETS@
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65 @INCLUDE@
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66 @EXCLUDE@
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67
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68 ## Primary Input/Outputs
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69 @INPUT_FILES@
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70 > '$output_file'
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71 #if $plot_title:
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72 && plot-vcfstats
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73 -p 'plot_tmp/'
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74 -T '$plot_title'
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75 -s
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76 '$output_file'
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77 || (printf "The content of plot_tmp/plot-vcfstats.log is:\n" >&2 && cat plot_tmp/plot-vcfstats.log >&2 && exit 1)
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78 #end if
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79 ]]></command>
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80 <inputs>
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81 <expand macro="macro_input" />
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82 <param name="inputB_file" type="data" format="vcf,vcf_bgzip,bcf" optional="true" label="Optional VCF/BCF Data to compare against" help="When this second dataset is also specified, separate stats for intersection and the complements are generated" />
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83 <section name="sec_restrict" expanded="false" title="Restrict to">
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84 <expand macro="macro_samples" />
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85 <expand macro="macro_apply_filters" />
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86 <expand macro="macro_collapse" />
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87 <expand macro="macro_restrict" />
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88 <expand macro="macro_restrict" type="target" label_type="Target" />
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89 <expand macro="macro_include" />
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90 <expand macro="macro_exclude" />
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91 </section>
19
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92 <section name="sec_default" expanded="true" title="Stats options">
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93 <param name="first_allele_only" type="boolean" truevalue="--1st-allele-only" falsevalue="" label="First allele only"
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94 help="Include only first allele at multiallelic sites" />
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95 <conditional name="depth">
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96 <param name="set_depth" type="select" label="Depth distribution">
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97 <option value="no">Use depth defaults</option>
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98 <option value="yes">Set depth values</option>
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99 </param>
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100 <when value="no"/>
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101 <when value="yes">
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102 <param name="depth_min" type="integer" value="0" min="0" label="Depth min"/>
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103 <param name="depth_max" type="integer" value="500" min="1" label="Depth max" />
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104 <param name="depth_bin_size" type="integer" value="1" min="1" label="Depth bin size" />
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105 </when>
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106 </conditional>
8
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107 <conditional name="reference_source">
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108 <param name="reference_source_selector" type="select" label="Choose a reference genome">
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109 <option value="">Run without a reference genome</option>
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110 <option value="cached">Use a built-in genome</option>
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111 <option value="history">Use a genome from the history</option>
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112 </param>
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113 <when value="" />
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114 <when value="cached">
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115 <param name="fasta_ref" type="select" label="Reference genome">
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116 <options from_data_table="fasta_indexes">
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117 <filter type="data_meta" column="dbkey" key="dbkey" ref="input_file" />
8
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118 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
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119 </options>
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120 </param>
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121 </when>
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122 <when value="history">
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123 <param name="fasta_ref" type="data" format="fasta" label="Reference genome" />
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124 </when>
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125 </conditional>
0
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126 <expand macro="macro_exons_file" />
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127 <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split by ID (ignored on multiple inputs)"
0
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128 help="Collect stats for sites with ID separately (known vs novel)" />
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129 <param name="user_tstv" type="text" value="" optional="true" label="User Tstv"
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130 help="Collect Ts/Tv stats for any tag using the given binning: TAG[:min:max:binsize]" >
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131 <validator type="regex" message="TAG optionally followed by :min:max:binsize">^([^ \t\n\r\f\v:,](:\d+:\d+:\d+)?)?$</validator>
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132 </param>
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133 <conditional name="afbins">
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134 <param name="afbins_select" type="select" label="Set af-bins">
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135 <option value="default">Use default</option>
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136 <option value="af_bins_list">Enter bins</option>
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137 <option value="af_bins_file">Read bins from file</option>
5
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138 </param>
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139 <when value="default"/>
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140 <when value="af_bins_list">
19
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141 <param name="af_bins_list" type="text" value="0.1,0.5,1" label="List of allele frequency bins" help="e.g. 0.1,0.5,1">
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142 <validator type="regex" message="Comma-separated list of floats of increasing value">^[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?(,[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?)*$</validator>
5
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143 </param>
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144 </when>
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145 <when value="af_bins_file">
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146 <param name="af_bins_file" type="data" format="tabular" label="File listing the allele frequency bins one per line"/>
5
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147 </when>
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148 </conditional>
19
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149 <param name="af_tag" type="text" value="" optional="true" label="Allele frequency tag to use, by default estimated from AN,AC or GT">
5
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150 <validator type="regex" message="TAG">^\w*$</validator>
0
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151 </param>
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152 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Verbose"
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153 help="Produce verbose per-site and per-sample output" />
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154 </section>
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155 <param name="plot_title" type="text" value="" optional="true" label="Create a plots pdf with this title">
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156 <validator type="regex" message="">^\w.*\w$</validator>
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157 </param>
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158 </inputs>
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159 <outputs>
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160 <data name="output_file" format="txt" label="${tool.name} on ${on_string}: txt" />
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161 <data name="output_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF" from_work_dir="plot_tmp/summary.pdf">
0
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162 <filter>plot_title</filter>
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163 </data>
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164 </outputs>
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165 <tests>
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166 <test expect_num_outputs="1">
7
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167 <param name="input_file" ftype="vcf" value="stats.b.vcf" />
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168 <param name="inputB_file" ftype="vcf" value="stats.a.vcf" />
0
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169 <output name="output_file">
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170 <assert_contents>
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171 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
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172 <has_text_matching expression="SN\t1\tnumber of samples:\t3"/>
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173 </assert_contents>
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174 </output>
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175 </test>
20
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176 <test expect_num_outputs="1">
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177 <param name="input_file" ftype="vcf" value="mpileup.vcf" />
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178 <section name="sec_default">
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179 <expand macro="test_using_reference" select_from="cached" ref="mpileup" />
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180 </section>
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181 <output name="output_file">
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182 <assert_contents>
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183 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
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184 <has_text_matching expression="SN\t0\tnumber of records:\t4103"/>
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185 <has_text_matching expression="ST\t0\tA>C\t16"/>
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186 </assert_contents>
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187 </output>
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188 </test>
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189 <test expect_num_outputs="2">
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190 <param name="input_file" ftype="vcf" value="mpileup.vcf" />
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191 <param name="plot_title" value="Plot for mpileup.vcf" />
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192 <output name="output_file">
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193 <assert_contents>
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194 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
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195 <has_text_matching expression="SN\t0\tnumber of records:\t4103"/>
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196 <has_text_matching expression="ST\t0\tA>C\t16"/>
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197 </assert_contents>
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198 </output>
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199 <output name="output_pdf" file="summary.pdf" compare="sim_size" delta="25000" />
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200 </test>
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201 <!-- Test region overlap option-->
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202 <test expect_num_outputs="1">
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203 <param name="input_file" ftype="vcf" value="stats.b.vcf" />
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204 <param name="inputB_file" ftype="vcf" value="stats.a.vcf" />
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205 <section name="sec_restrict">
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206 <param name="regions_overlap" value="1"/>
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207 </section>
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208 <output name="output_file">
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209 <assert_contents>
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210 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
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211 <has_text_matching expression="SN\t1\tnumber of samples:\t3"/>
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212 </assert_contents>
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213 </output>
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214 <assert_command>
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215 <has_text text="--regions-overlap" />
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216 </assert_command>
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217 </test>
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218 <!-- Test VCF.gz input file -> REQUIRES https://github.com/galaxyproject/galaxy/pull/14605
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219 <test expect_num_outputs="1">
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220 <param name="input_file" value="mpileup.vcf.gz" />
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221 <output name="output_file">
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222 <assert_contents>
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223 <has_text_matching expression="bcftools stats input0.vcf.gz"/>
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224 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
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225 <has_text_matching expression="SN\t0\tnumber of records:\t4103"/>
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226 </assert_contents>
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227 </output>
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228 </test>
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229 -->
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230 <!-- Test modification in samples option -->
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231 <test expect_num_outputs="1">
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232 <param name="input_file" ftype="vcf" value="mpileup.vcf" />
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233 <section name="sec_restrict">
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234 <param name="samples" value="-" />
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235 </section>
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236 <output name="output_file">
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237 <assert_contents>
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238 <has_text_matching expression="bcftools stats --samples - "/>
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239 <has_text_matching expression="PSC\t0\tHG00101\t0\t0\t0\t0\t0\t0\t4.8"/>
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240 <has_text_matching expression="PSI\t0\tHG00102\t0"/>
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241 </assert_contents>
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242 </output>
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243 </test>
0
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244 </tests>
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245 <help><![CDATA[
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246 =====================================
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247 bcftools @EXECUTABLE@
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248 =====================================
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249
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250 Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats.
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251
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252 When two files are given, the program generates separate stats for intersection and the complements.
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253 By default only sites are compared, -s/-S must given to include also sample columns.
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254
7
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255 When one VCF file is specified, then stats by non-reference allele frequency, depth distribution, stats by quality and per-sample counts, singleton stats, etc. are printed. When two VCF files are given, then stats such as concordance (Genotype concordance by non-reference allele frequency, Genotype concordance by sample, Non-Reference Discordance) and correlation are also printed. Per-site discordance (PSD) is also printed in --verbose mode.
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256
0
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257 @COLLAPSE_HELP@
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258 @REGIONS_HELP@
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259 @TARGETS_HELP@
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260 @EXPRESSIONS_HELP@
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261
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262 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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263
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264 @BCFTOOLS_WIKI@
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265 ]]>
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266 </help>
92e47ae9a121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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267 <expand macro="citations" />
92e47ae9a121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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268 </tool>