Mercurial > repos > iuc > bcftools_stats

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