Mercurial > repos > mingchen0919 > dynamic_star

annotate dynamic_tool_wrappers_macros.xml @ 2:a9579c344a90 draft default tip

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planemo upload commit 8f84e3911c6ff4103c0ad5fb8dd774f80d9b2559
author mingchen0919
date Fri, 23 Mar 2018 21:50:16 -0400
parents ddc3c3527f49
children
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1 <macros>
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2
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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 <requirement type="package" version="2.5.4a">star</requirement>
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7 </xml>
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8
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9 <xml name="stdio">
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10 <stdio>
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11 <regex match="XXX" source="stderr" level="warning"
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12 description="Check the tool log output file for more details."/>
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13 </stdio>
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14 </xml>
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15
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16 <!--Tool name-->
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17 <xml name="tool_name">
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18 <param type="select" name="tool_name" multiple="false" label="Tool name">
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19 <option value="STAR" selected="false">STAR</option>
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20 </param>
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21 </xml>
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22
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23 <!--OPTION/ARGUMENT PAIRS and INPUT types-->
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24 <!--input files-->
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25 <xml name="option_argument_single_dataset">
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26 <repeat name="option_argument_single_dataset_repeat" title="INPUT SINGLE DATASET" 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="false" label="value"/>
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29 </repeat>
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30 </xml>
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31
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32 <xml name="option_argument_multiple_datasets">
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33 <repeat name="option_argument_multiple_datasets_repeat" title="INPUT MULTIPLE DATASETS" min="0" default="0">
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34 <param type="text" name="flag" optional="true" label="flag" />
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35 <param name="value" type="data" optional="false" multiple="true" label="value"/>
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36 <param type="select" name="delimiter" multiple="false" label="file delimiter">
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37 <option value=" " selected="false">space</option>
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38 <option value="," selected="false">comma</option>
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39 </param>
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40 </repeat>
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41 </xml>
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42
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43 <!--input path-->
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44 <xml name="option_argument_path_relative_to_a_tool">
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45 <repeat name="option_argument_path_relative_to_a_tool_repeat" title="INPUT PATH: path relative to a tool" min="0" default="0">
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46 <param type="text" name="flag" optional="true" label="flag" />
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47 <param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/>
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48 <param type="text" name="value" optional="true" label="value" />
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49 </repeat>
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50 </xml>
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51 <xml name="option_argument_path_relative_to_this_tool">
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52 <repeat name="option_argument_path_relative_to_this_tool_repeat" title="INPUT PATH: path relative to this tool" min="0" default="0">
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53 <param type="text" name="flag" optional="true" label="flag" />
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54 <param type="text" name="value" optional="false" label="value" />
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55 <param type="select" name="path_type" multiple="false" label="path type">
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56 <option value="file_path" selected="false">file path</option>
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57 <option value="dir_path" selected="false">directory path</option>
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58 </param>
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59 </repeat>
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60 </xml>
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62 <!--input values: string, float and integer-->
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63 <xml name="option_argument_string_float_integer">
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64 <repeat name="option_argument_string_float_integer_repeat" title="INPUT VALUE: string/float/integer" min="0" default="0">
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65 <param type="text" name="flag" label="flag" />
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66 <param type="text" name="value" label="value" />
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67 </repeat>
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68 </xml>
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69
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70 <!--output set-->
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71 <xml name="output_set">
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72 <data format="html" name="report" label="${tool.name} report"/>
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73 <data format="txt" name="tool_help_doc" label="${tool.name} help doc"/>
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74 <data format="txt" name="tool_output_dir" label="${tool.name} output directory"/>
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75 <data format="txt" name="tool_log" label="${tool.name} log" />
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76 </xml>
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77
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78
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79 <!--shell command fragment-->
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80 <xml name="shell_command">
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81 <command><![CDATA[
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82
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83 ############ first, create a directory to store all files
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84 mkdir -p $report.files_path && cd $report.files_path &&
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85
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86
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87 ############ save the tool installation directory to an environment variable
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88 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
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89
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90
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91 #########################
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92 ##
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93 ## save user input option/argument pairs into a file
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94 ##
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95 #########################
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96
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97 ## first line will be the header
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98 echo 'type|flag|value|path_type' > options_and_arguments.txt &&
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99
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100 ############ tool_name
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101 ##-t '$tool_name'
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102 echo "tool_name|not available|${tool_name}|not available" >> options_and_arguments.txt &&
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103
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104 ####################################################
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105 ## loop through repeats to get option/argument pairs
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106 ####################################################
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107
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108 ############ option_argument_single_dataset
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109 #for i in $option_argument_single_dataset_repeat:
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110 #set $item = 'single_dataset|' + str($i.flag) + "|" + str($i.value) + "|"
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111 echo '$item' >> options_and_arguments.txt &&
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112 #end for
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113
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114 ############ option_argument_multiple_datasets
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115 #for i in $option_argument_multiple_datasets_repeat:
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116 #set $item = 'multiple_datasets|' + str($i.flag) + "|" + str($i.value).replace(',', str($i.delimiter)) + "|"
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117 echo '$item' >> options_and_arguments.txt &&
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118 #end for
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119
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120
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121 ############ option_argument_path_relative_to_a_tool
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122 #for i in $option_argument_path_relative_to_a_tool_repeat:
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123 #set $item = 'path_relative_to_a_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.a_tool_output_dir)
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124 echo '$item' >> options_and_arguments.txt &&
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125 #end for
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126
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127 ############ option_argument_path_relative_to_this_tool
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128 #for i in $option_argument_path_relative_to_this_tool_repeat:
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129 #set $item = 'path_relative_to_this_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.path_type)
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130 echo '$item' >> options_and_arguments.txt &&
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131 #end for
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132
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133 ############ option_argument_string_float_integer
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134 #for i in $option_argument_string_float_integer_repeat:
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135 #set $item = 'value|' + str($i.flag) + "|" + str($i.value) + "|"
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136 echo '$item' >> options_and_arguments.txt &&
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137 #end for
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138
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139 ############ output_set
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140 ## '$report'
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141 ## '$report.files_path'
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142 ## '$tool_help_doc'
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143 ## '$tool_output_dir'
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144 ## '$tool_log'
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145 #######################
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146 export REPORT='$report' &&
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147 export REPORT_FILES_PATH='$report.files_path' &&
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148 export TOOL_HELP_DOC='$tool_help_doc' &&
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149 export TOOL_OUTPUT_DIR='$tool_output_dir' &&
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150 export TOOL_LOG='$tool_log' &&
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151
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152
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153 ############ run render R script to render R markdowns
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154 Rscript '${__tool_directory__}/dynamic_tool_render.R'
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155
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156 ]]></command>
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157 </xml>
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158
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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{xie2015dynamic,
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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>