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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <macros>
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3 <xml name="rmarkdown_requirements">
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4 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
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5 <requirement type="package" version="1.6">r-rmarkdown</requirement>
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6 </xml>
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7 <xml name="stdio">
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8 <stdio>
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9 <regex match="XXX" source="stderr" level="warning" description="Check the tool log output file for more details."/>
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10 </stdio>
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11 </xml>
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12 <!--Tool name-->
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13 <xml name="tool_name">
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14 <param type="select" name="tool_name" multiple="false" label="Tool name">
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15 <option value="cp" selected="false">cp</option></param>
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16 </xml>
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17 <!--OPTION/ARGUMENT PAIRS and INPUT types-->
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18 <!--input files-->
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19 <xml name="option_argument_single_dataset">
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20 <repeat name="option_argument_single_dataset_repeat" title="INPUT DATA FROM HISTORY: single data set" min="0" default="0">
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21 <param type="text" name="flag" optional="true" label="flag"/>
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22 <param name="value" type="data" optional="false" multiple="false" label="value"/>
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23 </repeat>
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24 </xml>
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25 <xml name="option_argument_multiple_datasets">
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26 <repeat name="option_argument_multiple_datasets_repeat" title="INPUT DATA FROM HISTORY: multiple data sets" min="0" default="0">
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27 <param type="text" name="flag" optional="true" label="flag"/>
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28 <param name="value" type="data" optional="false" multiple="true" label="value"/>
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29 <param type="select" name="delimiter" multiple="false" label="file delimiter">
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30 <option value=" " selected="false">space</option>
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31 <option value="," selected="false">comma</option>
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32 </param>
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33 </repeat>
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34 </xml>
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35 <!--input path-->
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36 <xml name="option_argument_path_relative_to_a_tool">
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37 <repeat name="option_argument_path_relative_to_a_tool_repeat" title="INPUT DATA PATH: relative to a tool output directory" min="0" default="0">
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38 <param type="text" name="flag" optional="true" label="flag"/>
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39 <param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/>
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40 <param type="text" name="value" optional="true" label="value"/>
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41 </repeat>
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42 </xml>
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43 <xml name="option_argument_path_relative_to_this_tool">
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44 <repeat name="option_argument_path_relative_to_this_tool_repeat" title="OUTPUT PATH: relative to this tool output directory" min="0" default="0">
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45 <param type="text" name="flag" optional="true" label="flag"/>
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46 <param type="text" name="value" optional="false" label="value"/>
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47 <param type="select" name="path_type" multiple="false" label="path type">
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48 <option value="file_path" selected="false">file path</option>
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49 <option value="dir_path" selected="false">directory path</option>
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50 </param>
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51 </repeat>
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52 </xml>
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53 <!--input values: string, float and integer-->
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54 <xml name="option_argument_string_float_integer">
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55 <repeat name="option_argument_string_float_integer_repeat" title="INPUT VALUE: string/float/integer" min="0" default="0">
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56 <param type="text" name="flag" label="flag"/>
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57 <param type="text" name="value" label="value"/>
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58 </repeat>
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59 </xml>
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60 <!--output set-->
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61 <xml name="output_set">
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62 <data format="html" name="report" label="${tool.name} report"/>
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63 <data format="txt" name="tool_help_doc" label="${tool.name} help doc"/>
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64 <data format="txt" name="tool_output_dir" label="${tool.name} output directory"/>
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65 <data format="txt" name="tool_log" label="${tool.name} log"/>
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66 <data name="asis">
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67 <discover_datasets pattern="__name_and_ext__" directory="${report.files_path}/asis_dir"/>
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68 </data>
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69 <collection type="list" name="expose_to_list">
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70 <discover_datasets pattern="__name_and_ext__" directory="${report.files_path}/list_dir" />
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71 </collection>
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72 <collection type="paired" name="expose_to_pair">
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73 <discover_datasets pattern="__name_and_ext__" directory="${report.files_path}/pair_dir" />
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74 </collection>
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75 <collection type="list:paired" name="expose_to_list_pairs">
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76 <discover_datasets pattern="(?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)\.(?P<ext>[^\._]+)?"
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77 directory="${report.files_path}/list_pairs_dir"/>
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78 </collection>
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79 </xml>
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80 <!--shell command fragment-->
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81 <xml name="shell_command">
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82 <command><![CDATA[
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83
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84 ############ first, create a directory to store all files
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85 mkdir -p $report.files_path && cd $report.files_path &&
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86
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87
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88 ############ save the tool installation directory to an environment variable
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89 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
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90
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91
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92 #########################
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93 ##
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94 ## save user input option/argument pairs into a file
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95 ##
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96 #########################
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97
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98 ## first line will be the header
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99 echo 'type|flag|value|path_type' > options_and_arguments.txt &&
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100
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101 ############ tool_name
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102 ##-t '$tool_name'
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103 echo "tool_name|not available|${tool_name}|not available" >> options_and_arguments.txt &&
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104
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105 ####################################################
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106 ## loop through repeats to get option/argument pairs
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107 ####################################################
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108
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109 ############ option_argument_single_dataset
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110 #for i in $option_argument_single_dataset_repeat:
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111 #set $item = 'single_dataset|' + str($i.flag) + "|" + str($i.value) + "|"
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112 echo '$item' >> options_and_arguments.txt &&
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113 #end for
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114
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115 ############ option_argument_multiple_datasets
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116 #for i in $option_argument_multiple_datasets_repeat:
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117 #set $item = 'multiple_datasets|' + str($i.flag) + "|" + str($i.value).replace(',', str($i.delimiter)) + "|"
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118 echo '$item' >> options_and_arguments.txt &&
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119 #end for
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120
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121
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122 ############ option_argument_path_relative_to_a_tool
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123 #for i in $option_argument_path_relative_to_a_tool_repeat:
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124 #set $item = 'path_relative_to_a_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.a_tool_output_dir)
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125 echo '$item' >> options_and_arguments.txt &&
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126 #end for
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127
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128 ############ option_argument_path_relative_to_this_tool
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129 #for i in $option_argument_path_relative_to_this_tool_repeat:
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130 #set $item = 'path_relative_to_this_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.path_type)
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131 echo '$item' >> options_and_arguments.txt &&
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132 #end for
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133
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134 ############ option_argument_string_float_integer
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135 #for i in $option_argument_string_float_integer_repeat:
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136 #set $item = 'value|' + str($i.flag) + "|" + str($i.value) + "|"
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137 echo '$item' >> options_and_arguments.txt &&
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138 #end for
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139
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140 ############ output_set
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141 ## '$report'
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142 ## '$report.files_path'
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143 ## '$tool_help_doc'
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144 ## '$tool_output_dir'
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145 ## '$tool_log'
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146 #######################
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147 export REPORT='$report' &&
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148 export REPORT_FILES_PATH='$report.files_path' &&
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149 export TOOL_HELP_DOC='$tool_help_doc' &&
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150 export TOOL_OUTPUT_DIR='$tool_output_dir' &&
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151 export TOOL_LOG='$tool_log' &&
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152
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153
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154 ############ run render R script to render R markdowns
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155 Rscript '${__tool_directory__}/elastic_tool_render.R'
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156
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157 ]]></command>
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158 </xml>
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159 <!--tool citations-->
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160 <xml name="citations">
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161 <citation type="bibtex"><![CDATA[
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162 @article{allaire2016rmarkdown,
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163 title={rmarkdown: Dynamic Documents for R, 2016},
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164 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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165 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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166 journal={R package version 0.9},
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167 volume={6},
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168 year={2016}
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169 }
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170 ]]></citation>
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171 <citation type="bibtex"><![CDATA[
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172 @book{xie2015elastic,
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173 title={Dynamic Documents with R and knitr},
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174 author={Xie, Yihui},
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175 volume={29},
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176 year={2015},
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177 publisher={CRC Press}
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178 }
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179 ]]></citation>
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180 </xml>
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181 </macros>
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