Mercurial > repos > mingchen0919 > aurora_skewer

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author mingchen0919
date Sun, 30 Dec 2018 13:56:16 -0500
parents 0358f6f78adf
children
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1 <tool name="aurora_skewer" id='aurora_skewer_report' version="2.0.1">
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2 <description>A fast and accurate adapter trimmer for next-generation sequencing single or paired end reads.
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3 </description>
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4 <requirements>
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5 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
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6 <requirement type="package" version="1.20.0">r-getopt</requirement>
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7 <requirement type="package" version="1.6">r-rmarkdown</requirement>
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8 <requirement type="package" version="0.2.2">skewer</requirement>
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9 <requirement type="package" version="4.5.6">r-plotly</requirement>
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10 </requirements>
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11 <command><![CDATA[
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12
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13 ######### each aurora tool generates a html file and have an files path directory associated with it.
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14 mkdir -p $report.files_path &&
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15
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16 ######### three important paths:
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17 ######### 1. path to tool installation directory
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18 ######### 2. path to report html
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19 ######### 3. path to files_path directory associated with the report output.
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20 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
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21 export REPORT='$report' &&
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22 export REPORT_FILES_PATH='$report.files_path' &&
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23
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24 ############ create a hidden file to store r markdown rendering log
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25 touch $report.files_path/.r_rendering.log.txt &&
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26
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27 ############ finally run the render.R script
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28 Rscript '${__tool_directory__}/rmarkdown_report_render.R'
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29
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30 -o $report
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31 -d $report.files_path
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32
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33 -A '$first_reads'
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34 -B '$second_reads'
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35 -x '$adapter_first_reads'
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36 -y '$adapter_second_reads'
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37 -m '$trimming_mode'
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38 -r '$maximum_allowed_error_rate'
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39 -D '$maximum_allowed_indel_error_rate'
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40 -q '$quality_trimming_3_end'
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41 -Q '$mean_quality'
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42 -l '$minimum_read_length'
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43 -j '$advanced_options.junction_adapter'
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44 -M '$advanced_options.tab_adapter'
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45 -b '$advanced_options.barcode'
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46 -c '$advanced_options.cut'
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47 -n '$advanced_options.filter_degenerative_reads'
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48 -u '$advanced_options.filter_undetermined_mate_pair_reads'
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49 -f '$advanced_options.format'
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50 -z '$advanced_options.compress'
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51 -E '$advanced_options.qiime'
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52 -F '$advanced_options.quiet'
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53 -i '$advanced_options.intelligent'
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54 -1 '$trimmed_r1'
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55 -2 '$trimmed_r2'
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56 -3 '$trimmed_s'
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57
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58
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59 ]]></command>
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60 <inputs>
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61 <param type="data" name="first_reads" label="First reads" optional="False" format="fastq,fastqsanger"
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62 multiple="False"/>
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63 <param type="data" name="second_reads" label="Second reads"
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64 help="If it is single end reads, ignore this input field and use the &quot;first reads&quot; field only."
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65 optional="True" format="fastq,fastqsanger" multiple="False"/>
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66 <param type="data" name="adapter_first_reads" argument="-x" label="Adapter sequence/file for the first reads."
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67 optional="True" format="fasta,fa" multiple="False"/>
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68 <param type="data" name="adapter_second_reads" argument="-y" label="Adapter sequence/file for the second reads"
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69 optional="True" format="fasta,fa" multiple="False"/>
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70 <param type="select" name="trimming_mode" argument="-m" label="trimming mode" optional="False" multiple="False">
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71 <option value="None" selected="true">--select a model--</option>
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72 <option value="head" selected="false">5&#x2019; end trimming (single end reads)</option>
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73 <option value="tail" selected="false">3&#x2019; end trimming (single end reads)</option>
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74 <option value="any" selected="false">anywhere adapter detection and trimming (single end reads)</option>
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75 <option value="pe" selected="false">paired-end trimming</option>
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76 <option value="mp" selected="false">mate-pair trimming</option>
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77 <option value="ap" selected="false">amplicon trimming</option>
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78 </param>
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79 <param type="float" name="maximum_allowed_error_rate" argument="-r" label="Maximum allowed error rate"
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80 optional="False" value="0.1" min="0" max="0.5"/>
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81 <param type="float" name="maximum_allowed_indel_error_rate" argument="-d"
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82 label="Maximum allowed indel error rate"
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83 help="The valid range of indel error rate is [0, maximum allowed error rate]" optional="False"
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84 value="0.03" min="0"/>
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85 <param type="integer" name="quality_trimming_3_end" argument="-q" label="3&#x2019; end quality trimming"
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86 optional="False" value="0"/>
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87 <param type="integer" name="mean_quality" argument="-Q" label="Reads filtering by average quality"
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88 optional="False" value="0"/>
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89 <param type="integer" name="minimum_read_length" argument="-l"
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90 label="Minimum read length allowed after trimming" optional="False" value="18"/>
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91 <section name="advanced_options" title="Advanced options" expanded="False">
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92 <param type="data" name="junction_adapter" argument="-j"
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93 label="Junction adapter sequence/file for Nextera Mate Pair reads" optional="True" format="fasta,fa"
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94 multiple="False"/>
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95 <param type="text" name="tab_adapter" argument="-M"
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96 label="TAB delimited file indicates valid forward/reverse adapter pairing" optional="True"/>
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97 <param type="boolean" name="barcode" argument="-b"
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98 label="Whether to demultiplex reads according to adapters/primers" optional="False" checked="False"
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99 truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
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100 <param type="text" name="cut" argument="-c"
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101 label="To hard clip off the 5&#x2019; leading bases of the forward primer and reverse primer respectively as the barcodes in amplicon mode"
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102 optional="False" value="0, 0"/>
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103 <param type="boolean" name="filter_degenerative_reads" argument="-n"
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104 label="Whether to filter out highly degenerative reads" optional="False" checked="False"
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105 truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
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106 <param type="boolean" name="filter_undetermined_mate_pair_reads" argument="-u"
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107 label="Whether to filter out undetermined mate-pair reads" optional="False" checked="False"
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108 truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
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109 <param type="select" name="format" argument="-f" label="Format of FASTQ quality value" optional="False"
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110 multiple="False">
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111 <option value="sanger" selected="false">sanger</option>
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112 <option value="solexa" selected="false">solexa</option>
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113 <option value="auto" selected="true">auto</option>
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114 </param>
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115 <param type="boolean" name="compress" argument="-z" label="Whether to compress output in GZIP format"
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116 optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
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117 <param type="boolean" name="qiime" argument="-qiime" label="Whether to prepare files required by QIIME"
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118 optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
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119 <param type="boolean" name="quiet" argument="--quiet" label="Whether in quiet mode" optional="False"
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120 truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
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121 <param type="boolean" name="intelligent" argument="-i" label="Whether to intelligently redistribute reads"
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122 optional="False" checked="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
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123 </section>
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124 </inputs>
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125 <outputs>
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126 <data name="report" format="html" label="${tool.name} report on ${on_string}" hidden="false"/>
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127 <data name="trimmed_r1" format="fastq" label="${tool.name} trimmed first reads on ${on_string}" hidden="false"/>
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128 <data name="trimmed_r2" format="fastq" label="${tool.name} trimmed second reads on ${on_string}"
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129 hidden="false"/>
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130 <data name="trimmed_s" format="fastq" label="${tool.name} trimmed single end reads on ${on_string}"
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131 hidden="false"/>
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132 </outputs>
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133 <help>
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134 <![CDATA[Read the `tool manual <http://download2.nust.na/pub4/sourceforge/s/project/sk/skewer/skewer_manual.pdf>`_ if you are not sure what parameter values to use.]]></help>
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135 <citations>
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136 <citation type="bibtex"><![CDATA[
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137 @article{allaire2016rmarkdown,
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138 title={rmarkdown: Dynamic Documents for R, 2016},
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139 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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140 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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141 journal={R package version 0.9},
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142 volume={6},
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143 year={2016}
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144 }
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145 ]]></citation>
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146 <citation type="bibtex"><![CDATA[
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147 @book{xie2015dynamic,
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148 title={Dynamic Documents with R and knitr},
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149 author={Xie, Yihui},
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150 volume={29},
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151 year={2015},
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152 publisher={CRC Press}
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153 }
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154 ]]></citation>
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155 <citation type="bibtex"><![CDATA[
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156 @online{jstree,
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157 author={Bozhanov, Ivan},
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158 year = 2018,
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159 url = {https://www.jstree.com/}
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160 }
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161 ]]></citation>
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162 </citations>
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163 </tool>