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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_one_dataset">
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26 <repeat name="option_argument_one_dataset_repeat" title="OPTION and ARGUMENT: input one 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="true" multiple="false" label="value"/>
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29 </repeat>
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30 </xml>
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31 <xml name="option_argument_multiple_datasets">
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32 <repeat name="option_argument_multiple_datasets_repeat" title="OPTION and ARGUMENT: input multiple datasets" min="0" default="0">
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33 <param type="text" name="flag" optional="true" label="flag" />
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34 <param name="value" type="data" optional="true" multiple="true" label="value" />
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35 </repeat>
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36 </xml>
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37 <xml name="option_argument_path_relative_to_upstream_tool">
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38 <repeat name="option_argument_path_relative_to_upstream_tool_repeat" title="OPTION and ARGUMENT: path relative to upstream tool" min="0" default="0">
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39 <param type="text" name="flag" optional="true" label="flag" />
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40 <param name="upstream_tool_output_dir" type="data" optional="true" multiple="false" label="upstream tool output directory"/>
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41 <param type="text" name="value" optional="true" label="value" />
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42 </repeat>
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43 </xml>
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44
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45 <!--input values: string, float and integer-->
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46 <xml name="option_argument_string">
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47 <repeat name="option_argument_string_repeat" title="OPTION and ARGUMENT: input string" min="0" default="0">
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48 <param type="text" name="flag" label="flag" />
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49 <param type="text" name="value" label="value" />
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50 </repeat>
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51 </xml>
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52 <xml name="option_argument_float">
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53 <repeat name="option_argument_float_repeat" title="OPTION and ARGUMENT: input float" min="0" default="0">
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54 <param type="text" name="flag" label="flag" />
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55 <param type="text" name="value" label="value" />
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56 </repeat>
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57 </xml>
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58 <xml name="option_argument_integer">
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59 <repeat name="option_argument_integer_repeat" title="OPTION and ARGUMENT: input integer" min="0" default="0">
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60 <param type="text" name="flag" label="flag" />
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61 <param type="text" name="value" label="value" />
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62 </repeat>
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63 </xml>
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64
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65 <!--output set-->
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66 <xml name="output_set">
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67 <data format="html" name="report" label="${tool.name} report"/>
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68 <data format="txt" name="tool_help_doc" label="${tool.name} help doc"/>
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69 <data format="txt" name="tool_output_dir" label="${tool.name} output directory"/>
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70 <data format="txt" name="tool_log" label="${tool.name} log" />
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71 </xml>
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72
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73
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74 <!--shell command fragment-->
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75 <xml name="shell_command">
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76 <command><![CDATA[
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77
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78 ############ first, create a directory to store all files
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79 mkdir -p $report.files_path && cd $report.files_path &&
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80
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81
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82 ############ save the tool installation directory to an environment variable
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83 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
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84
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85
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86 #########################
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87 ##
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88 ## save user input option/argument pairs into a file
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89 ##
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90 #########################
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91
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92 ## first line will be the header
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93 echo 'type|flag|value' > options_and_arguments.txt &&
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94
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95 ############ tool_name
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96 ##-t '$tool_name'
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97 echo "tool_name|tool_flag|${tool_name}" >> options_and_arguments.txt &&
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98
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99 ####################################################
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100 ## loop through repeats to get option/argument pairs
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101 ####################################################
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102
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103 ############ option_argument_one_dataset
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104 #for i in $option_argument_one_dataset_repeat:
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105 #set $item = 'one_dataset|' + str($i.flag) + "|" + str($i.value)
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106 echo '$item' >> options_and_arguments.txt &&
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107 #end for
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108
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109 ############ option_argument_multiple_datasets
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110 #for i in $option_argument_multiple_datasets_repeat:
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111 #set $item = 'multiple_datasets|' + str($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_path_relative_to_upstream_tool
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116 #for i in $option_argument_path_relative_to_upstream_tool_repeat:
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117 #set $item = 'path_relative_to_upstream_tool|' + str($i.flag) + "|" + str($i.value)
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118 echo '$item' >> options_and_arguments.txt &&
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119 #end for
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120
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121 ############ option_argument_string
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122 #for i in $option_argument_string_repeat:
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123 #set $item = 'string|' + str($i.flag) + "|" + str($i.value)
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124 echo '$item' >> options_and_arguments.txt &&
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125 #end for
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126
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127 ############ option_argument_float
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128 #for i in $option_argument_float_repeat:
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129 #set $item = 'float|' + str($i.flag) + "|" + str($i.value)
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130 echo '$item' >> options_and_arguments.txt &&
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131 #end for
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132
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133
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134 ############ option_argument_integer
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135 #for i in $option_argument_integer_repeat:
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136 #set $item = 'integer|' + str($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
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141 ############ output_set
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142 ## '$report'
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143 ## '$report.files_path'
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144 ## '$tool_help_doc'
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145 ## '$tool_output_dir'
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146 ## '$tool_log'
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147 #######################
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148 export REPORT='$report' &&
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149 export REPORT_FILES_PATH='$report.files_path' &&
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150 export TOOL_HELP_DOC='$tool_help_doc' &&
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151 export TOOL_OUTPUT_DIR='$tool_output_dir' &&
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152 export TOOL_LOG='$tool_log' &&
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153
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154
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155 ############ save tool files path to a tool output so that it can be accessed from galaxy history
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156 echo '$report.files_path' > $tool_output_dir &&
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157
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158 ############ run render R script to render R markdowns
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159 Rscript '${__tool_directory__}/dynamic_tool_render.R'
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160
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161 ]]></command>
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162 </xml>
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163
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164 <!--tool citations-->
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165 <xml name="citations">
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166 <citation type="bibtex"><![CDATA[
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167 @article{allaire2016rmarkdown,
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168 title={rmarkdown: Dynamic Documents for R, 2016},
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169 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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170 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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171 journal={R package version 0.9},
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172 volume={6},
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173 year={2016}
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174 }
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175 ]]></citation>
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176 <citation type="bibtex"><![CDATA[
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177 @book{xie2015dynamic,
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178 title={Dynamic Documents with R and knitr},
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179 author={Xie, Yihui},
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180 volume={29},
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181 year={2015},
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182 publisher={CRC Press}
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183 }
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184 ]]></citation>
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185 </xml>
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186 </macros> |
