Mercurial > repos > iuc > bcftools_stats

annotate bcftools_stats.xml @ 5:3afcc6474c79 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
author iuc
date Thu, 13 Apr 2017 17:43:15 -0400
parents 5129a2b2f316
children baa8823f8073
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@">
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3 <description>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="requirements">
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9 <expand macro="samtools_requirement"/>
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10 <requirement type="package" version="2.0.0">matplotlib</requirement>
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11 </expand>
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12 <expand macro="version_command" />
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13 <command detect_errors="aggressive"><![CDATA[
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14 @PREPARE_ENV@
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15 @PREPARE_INPUT_FILES@
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16 #set $section = $sec_restrict
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17 @PREPARE_TARGETS_FILE@
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18 @PREPARE_REGIONS_FILE@
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19 ## Stats section
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20 #set $section = $sec_default
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21 @PREPARE_FASTA_REF@
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22 @PREPARE_EXONS_FILE@
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24 bcftools @EXECUTABLE@
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26 ## Stats section
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27 #set $section = $sec_default
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28 @FASTA_REF@
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29 @EXONS_FILE@
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30 ${section.first_allele_only}
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31 #if $section.depth.set_depth == 'yes':
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32 --depth "${section.depth.depth_min},${section.depth.depth_max},${section.depth.depth_bin_size}"
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33 #end if
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34 #if $section.user_tstv:
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35 --user-tstv "${section.user_tstv}"
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36 #end if
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37 #if $section.afbins.afbins_select == 'af_bins_list':
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38 --af-bins $section.afbins.af_bins_list
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39 #elif $section.afbins.afbins_select == 'af_bins_file':
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40 --af-bins $section.afbins.af_bins_file
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41 #end if
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42 #if $section.af_tag:
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43 --af-tag "${section.af_tag}"
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44 #end if
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45 #if len($input_vcfs) == 1:
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46 ${section.split_by_ID}
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47 #end if
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48 ${section.verbose}
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49
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50 ## Stats section
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51 #set $section = $sec_restrict
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52 @APPLY_FILTERS@
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53 @COLLAPSE@
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54 @REGIONS@
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55 @SAMPLES@
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56 @TARGETS@
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57 @INCLUDE@
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58 @EXCLUDE@
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59
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60 ## Primary Input/Outputs
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61 @INPUT_FILES@
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62 > $output_file
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63 ## requires: matplotlib and pdflatex
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64 #if $plot_title:
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65 && plot-vcfstats -p 'plot_tmp/' -T $plot_title -s $output_file
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66 #end if
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67 ]]>
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68 </command>
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69 <inputs>
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70 <expand macro="macro_inputs" />
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71 <section name="sec_restrict" expanded="false" title="Restrict to">
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72 <expand macro="macro_samples" />
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73 <expand macro="macro_apply_filters" />
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74 <expand macro="macro_collapse" />
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75 <expand macro="macro_regions" />
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76 <expand macro="macro_targets" />
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77 <expand macro="macro_include" />
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78 <expand macro="macro_exclude" />
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79 </section>
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80 <section name="sec_default" expanded="true" title="Stats Options">
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81 <param name="first_allele_only" type="boolean" truevalue="--1st-allele-only" falsevalue="" label="1St Allele Only"
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82 help="Include only 1st allele at multiallelic sites" />
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83 <conditional name="depth">
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84 <param name="set_depth" type="select" label="depth distribution: min,max,bin_size [0,500,1]">
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85 <option value="no">use depth defaults</option>
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86 <option value="yes">set depth</option>
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87 </param>
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88 <when value="no"/>
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89 <when value="yes">
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90 <param name="depth_min" type="integer" value="0" min="0" label="Depth min"/>
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91 <param name="depth_max" type="integer" value="500" min="1" label="Depth max" />
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92 <param name="depth_bin_size" type="integer" value="1" min="1" label="Depth bin size" />
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93 </when>
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94 </conditional>
4
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95 <expand macro="macro_fasta_ref" />
0
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96 <expand macro="macro_exons_file" />
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97 <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split By Id (Ignored on multiple inputs)"
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98 help="Collect stats for sites with ID separately (known vs novel)" />
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99 <param name="user_tstv" type="text" value="" optional="true" label="User Tstv"
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100 help="Collect Ts/Tv stats for any tag using the given binning: TAG[:min:max:binsize]" >
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101 <validator type="regex" message="TAG optionally followed by :min:max:binsize">^([^ \t\n\r\f\v:,](:\d+:\d+:\d+)?)?$</validator>
5
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102 </param>
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103 <conditional name="afbins">
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104 <param name="afbins_select" type="select" label="Set af-bins">
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105 <option value="default">use default</option>
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106 <option value="af_bins_list">enter bins</option>
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107 <option value="af_bins_file">read bins from file</option>
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108 </param>
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109 <when value="default"/>
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110 <when value="af_bins_list">
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111 <param name="af_bins_list" type="text" value="0.1,0.5,1" label="list of allele frequency bins (e.g. 0.1,0.5,1)">
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112 <validator type="regex" message="comma-separated list of floats of increasing value">^[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?(,[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?)*$</validator>
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113 </param>
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114 </when>
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115 <when value="af_bins_file">
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116 <param name="af_bins_file" type="data" format="tabular" label="file listing the allele frequency bins one per line"/>
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117 </when>
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118 </conditional>
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119 <param name="af_tag" type="text" value="" optional="true" label="allele frequency tag to use, by default estimated from AN,AC or GT">
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120 <validator type="regex" message="TAG">^\w*$</validator>
0
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121 </param>
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122 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Verbose"
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123 help="Produce verbose per-site and per-sample output" />
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124 </section>
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125 <param name="plot_title" type="text" value="" optional="true" label="Create a plots pdf with this title">
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126 <validator type="regex" message="">^\w.*\w$</validator>
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127 </param>
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128 </inputs>
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129 <outputs>
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130 <data name="output_file" format="txt"/>
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131 <data name="output_pdf" format="pdf">
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132 <filter>plot_title</filter>
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133 </data>
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134 </outputs>
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135 <tests>
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136 <test>
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137 <param name="input_files" ftype="vcf" value="stats.b.vcf,stats.a.vcf" />
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138 <output name="output_file">
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139 <assert_contents>
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140 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
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141 <has_text_matching expression="SN\t1\tnumber of samples:\t3"/>
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142 </assert_contents>
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143 </output>
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144 </test>
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145 <test>
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146 <param name="input_files" ftype="vcf" value="mpileup.vcf" />
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147 <output name="output_file">
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148 <assert_contents>
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149 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
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150 <has_text_matching expression="SN\t0\tnumber of records:\t4103"/>
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151 <has_text_matching expression="ST\t0\tA>C\t16"/>
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152 </assert_contents>
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153 </output>
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154 </test>
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155 </tests>
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156 <help><![CDATA[
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157 =====================================
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158 bcftools @EXECUTABLE@
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159 =====================================
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160
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161 Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats.
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162
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163 When two files are given, the program generates separate stats for intersection and the complements.
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164 By default only sites are compared, -s/-S must given to include also sample columns.
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165
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166 @COLLAPSE_HELP@
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167 @REGIONS_HELP@
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168 @TARGETS_HELP@
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169 @EXPRESSIONS_HELP@
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170
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171 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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172
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173 @BCFTOOLS_WIKI@
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174 ]]>
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175 </help>
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176 <expand macro="citations" />
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177 </tool>