Mercurial > repos > jjohnson > bcftools_cnv

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sun, 26 Jun 2016 15:47:04 -0400
parents b50e0b926cde
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b50e0b926cde planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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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@.0">
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3 <description>Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R Ratio intensity (LRR)</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">cnv</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="version_command" />
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10 <command detect_errors="aggressive"><![CDATA[
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11 @PREPARE_ENV@
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12 @PREPARE_INPUT_FILE@
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13 #set $section = $sec_restrict
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14 @PREPARE_TARGETS_FILE@
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15
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16 bcftools @EXECUTABLE@
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17
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18 --output-dir cnv_tmp
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19
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20 ## General section
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21 #set $section = $sec_general
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22 #if $section.control_sample:
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23 --control-sample "${section.control_sample}"
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24 #end if
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25 #if $section.query_sample:
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26 --query-sample "${section.query_sample}"
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27 #end if
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28 @AF_FILE@
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29
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30 #if $section.plot_threshold:
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31 --plot-threshold "${section.plot_threshold}"
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32 #end if
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33
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34 ## HMM section
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35 #set $section = $sec_hmm
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36 #if $section.aberrant_query or $section.aberrant_control:
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37 #set $query_val = #if $section.aberrant_query then $section.aberrant_query else '1.0'#
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38 #set $control_val = #if $section.aberrant_control then $section.aberrant_control else '1.0'#
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39 --aberrant "${query_val},${control_val}"
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40 #end if
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41 #if $section.BAF_weight:
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42 --BAF-weight "${section.BAF_weight}"
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43 #end if
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44 #if $section.BAF_dev_query or $section.BAF_dev_control:
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45 #set $query_val = #if $section.BAF_dev_query then $section.BAF_dev_query else '1.0'#
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46 #set $control_val = #if $section.BAF_dev_control then $section.BAF_dev_control else '1.0'#
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47 --BAF-dev "${query_val},${control_val}"
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48 #end if
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49 #if $section.LRR_weight:
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50 --LRR-weight "${section.LRR_weight}"
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51 #end if
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52 #if $section.LRR_dev_query or $section.LRR_dev_control:
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53 #set $query_val = #if $section.LRR_dev_query then $section.LRR_dev_query else '1.0'#
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54 #set $control_val = #if $section.LRR_dev_control then $section.LRR_dev_control else '1.0'#
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55 --LRR-dev "${query_val},${control_val}"
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56 #end if
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57 #if $section.LRR_smooth_win:
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58 --LRR-smooth-win "${section.LRR_smooth_win}"
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59 #end if
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60 #if $section.optimize:
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61 --optimize "${section.optimize}"
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62 #end if
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63 #if $section.same_prob:
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64 --same-prob "${section.same_prob}"
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65 #end if
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66 #if $section.err_prob:
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67 --err-prob "${section.err_prob}"
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68 #end if
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69 #if $section.xy_prob:
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70 --xy-prob "${section.xy_prob}"
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71 #end if
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72
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73 ## Filter section
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74 #set $section = $sec_restrict
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75 @REGIONS@
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76 @TARGETS@
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77
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78 ## Primary Input/Outputs
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79 @INPUT_FILE@
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80 && mv $output_dir/cn.*.tab "$output_cn"
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81 && mv $output_dir/dat.*.tab "$output_dat"
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82 && mv $output_dir/summary.*.tab "$output_summary"
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83 ## && python $output_dir/plot.*.py
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84 ]]>
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85 </command>
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86 <inputs>
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87 <param name="output_dir" type="hidden" value="cnv_tmp"/>
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88 <expand macro="macro_input" />
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89 <section name="sec_restrict" expanded="false" title="Restrict to">
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90 <expand macro="macro_regions" />
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91 <expand macro="macro_targets" />
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92 </section>
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93 <param name="reference_fasta" type="data" format="fasta" label="Reference Fasta" />
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94 <section name="sec_general" expanded="true" title="General Options">
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95 <param name="query_sample" type="text" label="Query Sample" optional="True" help="Query samply name" />
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96 <param name="control_sample" type="text" label="Control Sample" optional="True" help="Optional control sample name to highlight differences" />
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97 <expand macro="macro_AF_file" />
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98 <param name="plot_threshold" type="float" label="Plot Threshold" optional="True" help="Plot aberrant chromosomes with quality at least 'float'" />
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99 </section>
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100 <section name="sec_hmm" expanded="false" title="HMM Options">
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101 <param name="err_prob" type="float" value="1e-4" label="Err Prob" optional="True" help="Uniform error probability" />
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102 <param name="optimize" type="float" value="" imin="0." max="1." label="Optimize" optional="True" >
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103 <help>
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104 Iteratively estimate the fraction of aberrant cells, down to the given fraction.
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105 Lowering this value from the default 1.0 to say, 0.3, can help discover more events but also increases noise.
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106 </help>
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107 </param>
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108 <param name="same_prob" type="float" value="" min="0." max="1." label="Same Prob" optional="True">
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109 <help>
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110 The prior probability of the query and the control sample being the same.
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111 Setting to 0 calls both independently, setting to 1 forces the same copy number state in both.
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112 </help>
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113 </param>
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114 <param name="xy_prob" type="float" value="" min="0." max="1." label="Xy Prob" default="1e-9" optional="True">
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115 <help>
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116 The HMM probability of transition to another copy number state.
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117 Increasing this value leads to smaller and more frequent calls.
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118 </help>
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119 </param>
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120
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121 <param name="aberrant_query" type="float" value="" min="0." max="1." label="Aberrant Query" optional="true"
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122 help="Fraction of aberrant cells in query, defaults to 1." />
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123 <param name="aberrant_control" type="float" value="" min="0." max="1." label="Aberrant Control" optional="true"
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124 help="Fraction of aberrant cells in control, defaults to 1." />
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125 <param name="BAF_weight" type="float" value="1." min="0." max="1." label="Baf Weight" optional="True" help="relative contribution from BAF" />
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126
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127 <param name="BAF_dev_query" type="float" value="" min="0." max="1." label="Baf Query Deviation" optional="true"
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128 help="Expected BAF deviation in query, defaults to: 0.04" />
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129 <param name="BAF_dev_control" type="float" value="" min="0." max="1." label="Baf Control Deviation" optional="true"
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130 help="Expected BAF deviation in control, defaults to: 0.04" />
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131
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132 <param name="LRR_weight" type="float" default="" label="LRR Weight" optional="True" >
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133 <help>
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134 Relative contribution from LRR.
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135 With noisy data, this option can have big effect on the number of calls produced.
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136 In truly random noise (such as in simulated data), the value should be set high (1.0), i
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137 but in the presence of systematic noise when LRR are not informative, lower values result in cleaner calls (0.2).
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138 </help>
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139 </param>
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140 <param name="LRR_dev_query" type="float" value="" min="0." max="1." label="LRR Query Deviation"
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141 help="Expected LRR deviation in query, default is: 0.2" />
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142 <param name="LRR_dev_control" type="float" value="" min="0." max="1." label="LRR Control Deviation"
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143 help="Expected LRR deviation in control, default is: 0.2" />
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144 <param name="LRR_smooth_win" type="integer" label="Lrr Smooth Win" default="10" optional="True"
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145 help="Window of LRR moving average smoothing" />
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146
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147 </section>
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148 </inputs>
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149 <outputs>
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150 <data name="output_cn" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.cn"/>
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151 <data name="output_dat" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.dat"/>
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152 <data name="output_summary" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.summary"/>
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153 <!-- add plot output -->
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154 <!-- script has png per chr, html of images or collect into pdf?
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155 <data name="output_plots" format="" />
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156 -->
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157 </outputs>
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158 <tests />
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159 <help><![CDATA[
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160 =====================================
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161 bcftools @EXECUTABLE@
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162 =====================================
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163
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164 Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R Ratio intensity (LRR).
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165 The HMM considers the following copy number states: CN 2 (normal), 1 (single-copy loss), 0 (complete loss), 3 (single-copy gain)
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166
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167 @REGIONS_HELP@
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168 @TARGETS_HELP@
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169
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170 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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171
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172 @BCFTOOLS_WIKI@
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173 ]]>
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174 </help>
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175 <expand macro="citations" />
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176 </tool>