Mercurial > repos > iuc > bcftools_cnv

annotate bcftools_cnv.xml @ 18:fb888de59f92 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author iuc
date Tue, 20 Sep 2022 12:20:24 +0000
parents 3f5c2434dd2b
children 9aa28226b77c
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f8d5042afdfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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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>Call copy number variation from VCF B-allele frequency (BAF) and Log R Ratio intensity (LRR) values</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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3f5c2434dd2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit af43d9cf6824f88726900857116f333ff4cdd336"
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8 <expand macro="bio_tools" />
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9 <expand macro="requirements">
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10 <expand macro="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[
f8d5042afdfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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14 @PREPARE_ENV@
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15 @PREPARE_INPUT_FILE@
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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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20 bcftools @EXECUTABLE@
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21
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22 #set $output_dir = 'cnv_tmp'
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23 --output-dir $output_dir
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25 ## General section
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26 #set $query_sample = str($query_sample).strip()
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27 #set $control_sample = str($control_sample).strip()
acbd780cf753 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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28 #if $control_sample:
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29 -c '$control_sample'
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30 #end if
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31 #if $query_sample:
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32 -s '$query_sample'
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33 #end if
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34 @AF_FILE@
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35 #if str($plotting.generate_plots) != 'none':
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36 -p ${plotting.plot_threshold}
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37 #end if
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39 ## HMM section
f8d5042afdfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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40 #set $section = $sec_hmm
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41 --aberrant "${section.aberrant_query},${section.aberrant_control}"
acbd780cf753 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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42 #if str($section.aberrant_optimization.do_optimize) == 'yes':
acbd780cf753 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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43 --optimize ${section.aberrant_optimization.lower_bound}
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44 #end if
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45 --BAF-weight ${section.score_usage.baf_weight}
acbd780cf753 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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46 --BAF-dev "${section.score_usage.baf_dev_query},${section.score_usage.baf_dev_control}"
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47 --LRR-weight ${section.score_usage.lrr_weight}
acbd780cf753 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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48 #if str($section.score_usage.compute_on) == 'baf+lrr':
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49 --LRR-dev "${section.score_usage.lrr_dev_query},${section.score_usage.lrr_dev_control}"
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50 --LRR-smooth-win ${section.score_usage.lrr_smooth_win}
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51 #end if
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52 #if $section.same_prob:
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53 --same-prob ${section.same_prob}
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54 #end if
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55 #if $section.err_prob:
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56 --err-prob ${section.err_prob}
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57 #end if
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58 #if $section.xy_prob:
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59 --xy-prob ${section.xy_prob}
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60 #end if
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62 ## Filter section
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63 #set $section = $sec_restrict
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64 @REGIONS@
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65 @TARGETS@
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67 ## Primary Input/Outputs
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68 @INPUT_FILE@
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70 && mv $output_dir/cn.*.tab '$output_cn'
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71 #if $control_sample:
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72 && mv ${output_dir}/summary.tab '$output_summary'
acbd780cf753 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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73 #else:
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74 && mv ${output_dir}/summary.*.tab '$output_summary'
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75 #end if
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76
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77 #if str($plotting.generate_plots) != 'none':
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78 ## collect all generated plots and embed them in html as base-64 encoded data
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79 && (echo '<html><body><head><title>Copy-number variation plots (bcftools cnv)</title><style type="text/css">
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80 @media print {
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81 img {
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82 max-width:100% !important;
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83 page-break-inside: avoid;
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84 }
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85 </style>' > $output_plots;
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86 for plot in $output_dir/*.png; do
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87 [ -f "\$plot" ] || break;
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88 echo '<div><img src="data:image/png;base64,' >> $output_plots;
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89 python -m base64 \$plot >> $output_plots;
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90 echo '" /></div><hr>' >> $output_plots;
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91 done;
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92 echo '</body></html>' >> $output_plots;)
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93 #end if
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94
0
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95 ]]>
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96 </command>
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97 <inputs>
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98 <expand macro="macro_input" />
9
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99 <param argument="-s" name="query_sample" type="text" label="Query Sample" optional="True" help="The name (as used in the input) of the query sample in the input. Can be ommitted if, and only if, there is only one sample in the input." />
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100 <param argument="-c" name="control_sample" type="text" label="Control Sample" optional="True" help="The name (as used in the input) of an optional control sample to compare against. Note: The pairwise calling mode represents the real strength of the tool as it helps to reduce the number of false calls and also allows one to distinguish between normal and novel copy number variation." />
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101 <expand macro="macro_AF_file" />
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102 <conditional name="plotting">
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103 <param name="generate_plots" type="select" label="Plot results?">
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104 <option value="all">Yes, plot results for all chromosomes</option>
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105 <option value="some">Yes, but plot only chromosomes with above-threshold quality of CNV status estimate</option>
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106 <option value="none">No, do not generate plots</option>
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107 </param>
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108 <when value="all">
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109 <param name="plot_threshold" type="hidden" value="0" />
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110 </when>
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111 <when value="some">
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112 <param argument="-p" name="plot_threshold" type="float" value="0"
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113 label="Plot Threshold"
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114 help="Plot aberrant chromosomes with quality at least 'float'" />
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115 </when>
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116 <when value="none" />
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117 </conditional>
0
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118 <section name="sec_restrict" expanded="false" title="Restrict to">
9
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119 <expand macro="macro_restrict" />
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120 <expand macro="macro_restrict" type="target" label_type="Target" />
0
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121 </section>
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122 <section name="sec_hmm" expanded="false" title="HMM Options">
9
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123 <param argument="--aberrant" name="aberrant_query" type="float" value="1" min="0" max="1"
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124 label="Estimated purity of the query sample"
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125 help="Estimate of the fractional contribution of the desired query tissue to the (possibly control-contaminated) query sample (default: 1 = no contamination with control tissue)" />
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126 <param argument="--aberrant" name="aberrant_control" type="float" value="1" min="0" max="1"
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127 label="Estimated purity of the control sample"
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128 help="Estimate of the fractional contribution of the desired control tissue to the (possibly query-contaminated) control sample (default: 1 = no contamination with query tissue)" />
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129 <conditional name="aberrant_optimization">
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130 <param name="do_optimize" type="select"
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131 label="Adjust sample purity estimates based on data?"
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132 help="Instead of treating your specified estimates of the sample purities as fixed values, the tool can use them as starting values for an iterative optimization that tries to estimate the sample purities from the data. Note: With estimate optimization enabled the final estimates will be reported as cell fraction (CF) estimates in the summary report.">
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133 <option value="no">No, leave sample purities as specified</option>
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134 <option value="yes">Yes, adjust purity estimates</option>
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135 </param>
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136 <when value="no" />
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137 <when value="yes">
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138 <param argument="--optimize" name="lower_bound" type="float" value="0.3" min="1e-9" max="1"
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139 label="Lower bound for adjusted estimate"
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140 help="Constrains the final adjusted purity estimates not to be smaller than this value." />
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141 </when>
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142 </conditional>
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143 <conditional name="score_usage">
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144 <param name="compute_on" type="select" label="Use BAF and LRR annotations to call CNVs?"
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145 help="Using LRR information in addition to BAF values is the default and helps in dealing with random noise in the data. However, the tool is also able to call CNVs from BAF values alone in case your input does not feature LRR information.">
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146 <option value="baf+lrr">Yes (requires input with both BAF and LRR subfields)</option>
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147 <option value="baf">No, use BAF values exclusively</option>
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148 </param>
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149 <when value="baf+lrr">
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150 <param argument="--BAF-weight" name="baf_weight" type="float" value="1" min="0" max="1"
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151 label="Baf Weight" help="relative contribution from BAF" />
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152
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153 <param argument="--BAF-dev" name="baf_dev_query" type="float" value="0.04" min="0" max="1"
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154 label="Query sample BAF deviation"
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155 help="Expected BAF deviation in the query sample (default: 0.04)" />
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156 <param argument="--BAF-dev" name="baf_dev_control" type="float" value="0.04" min="0" max="1"
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157 label="Control sample BAF deviation"
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158 help="Expected BAF deviation in the control sample (default: 0.04)" />
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159
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160 <param argument="--LRR-weight" name="lrr_weight" type="float" value="0.2" min="0" max="1"
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161 label="LRR Weight"
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162 help="Relative contribution from LRR. This option can have a big effect on the number of calls produced. With truly random noise (such as in simulated data), the value should be set high (1.0), but in the presence of systematic noise when LRR values are not informative, lower values result in cleaner calls (default: 0.2)." />
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163 <param argument="--LRR-dev" name="lrr_dev_query" type="float" value="0.2" min="0" max="1"
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164 label="Query sample LRR Deviation"
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165 help="Expected LRR deviation in the query sample (default: 0.2)" />
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166 <param argument="--LRR-dev" name="lrr_dev_control" type="float" value="0.2" min="0" max="1"
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167 label="Control sample LRR Deviation"
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168 help="Expected LRR deviation in the control sample (default: 0.2)" />
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169 <param argument="--LRR-smooth-win" name="lrr_smooth_win" type="integer" value="10"
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170 label="LRR Smoothing Window"
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171 help="Window of LRR moving average smoothing (default: 10)" />
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172 </when>
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173 <when value="baf">
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174 <param argument="--BAF-dev" name="baf_dev_query" type="float" value="0.04" min="0" max="1"
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175 label="Query sample BAF deviation"
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176 help="Expected BAF deviation in the query sample (default: 0.04)" />
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177 <param argument="--BAF-dev" name="baf_dev_control" type="float" value="0.04" min="0" max="1"
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178 label="Control sample BAF deviation"
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179 help="Expected BAF deviation in the control sample (default: 0.04)" />
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180 <param name="baf_weight" type="hidden" value="1" />
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181 <param name="lrr_weight" type="hidden" value="0" />
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182 </when>
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183 </conditional>
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184 <param argument="--err-prob" name="err_prob" type="float" value="1e-4" label="Err Prob" help="Uniform error probability" />
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185 <param argument="--same-prob" name="same_prob" type="float" value="0.5" min="0" max="1" label="Same Prob">
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186 <help>
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187 The prior probability of the query and the control sample being the same.
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188 Setting to 0 calls both independently, setting to 1 forces the same copy number state in both. (default: 0.5)
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189 </help>
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190 </param>
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191 <param argument="--xy-prob" name="xy_prob" type="float" min="0." max="1." label="Xy Prob" value="1e-9">
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192 <help>
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193 The HMM probability of transition to another copy number state.
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194 Increasing this value leads to smaller and more frequent calls.
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195 </help>
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196 </param>
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197 </section>
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198 </inputs>
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199 <outputs>
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200 <data name="output_cn" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.cn"/>
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201 <data name="output_summary" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.summary"/>
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202 <data name="output_plots" format="html" label="${input_file.name.rsplit('.',1)[0]}.plots">
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203 <filter>plotting['generate_plots'] != 'none'</filter>
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204 </data>
0
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205 </outputs>
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206 <tests>
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207 <test expect_num_outputs="3">
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208 <param name="input_file" ftype="vcf" value="cnv.vcf" />
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209 <output name="output_summary" file="cnv_summary.tab" compare="re_match" />
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210 </test>
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211 <test expect_num_outputs="2">
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212 <param name="input_file" ftype="vcf" value="cnv.vcf" />
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213 <conditional name="plotting">
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214 <param name="generate_plots" value="none" />
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215 </conditional>
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216 <output name="output_summary" file="cnv_summary.tab" compare="re_match" />
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217 </test>
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218 <test expect_num_outputs="3">
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219 <param name="input_file" ftype="vcf" value="cnv.vcf" />
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220 <param name="query_sample" value="test" />
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221 <param name="control_sample" value="test" />
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222 <output name="output_summary" file="cnv_pairwise_summary.tab" compare="re_match" />
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223 </test>
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224 <test expect_num_outputs="2">
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225 <param name="input_file" ftype="vcf" value="cnv_baf_only.vcf" />
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226 <conditional name="plotting">
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227 <param name="generate_plots" value="none" />
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228 </conditional>
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229 <conditional name="score_usage">
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230 <param name="compute_on" value="baf" />
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231 </conditional>
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232 <output name="output_summary" file="cnv_summary.tab" compare="re_match" />
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233 </test>
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234 <!-- Test region overlap option -->
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235 <test expect_num_outputs="3">
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236 <param name="input_file" ftype="vcf" value="cnv.vcf" />
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237 <section name="sec_restrict">
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238 <param name="regions_overlap" value="1"/>
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239 </section>
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240 <output name="output_summary" file="cnv_summary.tab" compare="re_match" />
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241 <assert_command>
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242 <has_text text="--regions-overlap" />
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243 </assert_command>
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244 </test>
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245 </tests>
0
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246 <help><![CDATA[
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247 =====================================
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248 bcftools @EXECUTABLE@
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249 =====================================
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250
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251 Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R Ratio intensity (LRR).
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252 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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253
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254 @REGIONS_HELP@
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255 @TARGETS_HELP@
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256
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257 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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258
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259 @BCFTOOLS_WIKI@
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260 ]]>
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261 </help>
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262 <expand macro="citations" />
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263 </tool>