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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="1.2.1">r-tidyverse</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="function_name">
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18 <param type="select" name="function_name" multiple="false" label="Tool name">
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19 </param>
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20 </xml>
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21
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22 <!--input values: string, float and integer-->
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23 <xml name="function_arguments">
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2
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24 <repeat name="regular_argument_value" title="INPUT VALUE: string/numeric/boolean" min="0" default="0">
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0
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25 <param type="text" name="argument" label="argument" />
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26 <param type="text" name="argument_value" label="argument value" />
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2
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27 <param type="select" name="argument_type" label="argument type">
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28 <option value="string" selected="true">string</option>
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29 <option value="numeric" selected="true">numeric</option>
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30 <option value="boolean" selected="true">boolean</option>
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31 </param>
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0
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32 </repeat>
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2
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33 <repeat name="rdata_argument_value" title="INPUT VALUE: from RData" min="0" default="0">
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0
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34 <param type="text" name="argument" label="argument" />
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35 <param type="text" name="argument_value" label="RData output" />
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36 </repeat>
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2
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37 <repeat name="function_argument_value" title="INPUT VALUE: from function output" min="0" default="0">
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0
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38 <param type="text" name="argument" label="argument" />
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2
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39 <expand macro="function_name" />
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40 <expand macro="nested_function_arguments" />
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0
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41 </repeat>
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42 <param type="select" name="connection" label="connection function">
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43 <option value="%>%" selected="false">pipe (%>%)</option>
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44 <option value="+" selected="false">plus (+)</option>
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45 </param>
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46 </xml>
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47
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48 <xml name="nested_function_arguments">
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2
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49 <repeat name="regular_argument_value" title="INPUT VALUE: string/numeric/boolean" min="0" default="0">
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0
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50 <param type="text" name="argument" label="argument" />
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51 <param type="text" name="argument_value" label="argument value" />
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2
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52 <param type="select" name="argument_type" label="argument type">
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53 <option value="string" selected="true">string</option>
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54 <option value="numeric" selected="true">numeric</option>
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55 <option value="boolean" selected="true">boolean</option>
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56 </param>
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0
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57 </repeat>
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2
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58 <repeat name="rdata_argument_value" title="INPUT VALUE: from RData" min="0" default="0">
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0
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59 <param type="text" name="argument" label="argument" />
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60 <param type="text" name="argument_value" label="RData output" />
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61 </repeat>
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62 </xml>
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63
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64 <!--<!–OPTION/ARGUMENT PAIRS and INPUT types–>-->
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65 <!--<!–input files–>-->
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66 <!--<xml name="option_argument_single_dataset">-->
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67 <!--<repeat name="option_argument_single_dataset_repeat" title="INPUT DATA FROM HISTORY: single data set" min="0" default="0">-->
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68 <!--<param type="text" name="flag" optional="true" label="flag" />-->
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69 <!--<param name="value" type="data" optional="false" multiple="false" label="value"/>-->
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70 <!--</repeat>-->
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71 <!--</xml>-->
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72
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73 <!--<xml name="option_argument_multiple_datasets">-->
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74 <!--<repeat name="option_argument_multiple_datasets_repeat" title="INPUT DATA FROM HISTORY: multiple data sets" min="0" default="0">-->
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75 <!--<param type="text" name="flag" optional="true" label="flag" />-->
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76 <!--<param name="value" type="data" optional="false" multiple="true" label="value"/>-->
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77 <!--<param type="select" name="delimiter" multiple="false" label="file delimiter">-->
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78 <!--<option value=" " selected="false">space</option>-->
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79 <!--<option value="," selected="false">comma</option>-->
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80 <!--</param>-->
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81 <!--</repeat>-->
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82 <!--</xml>-->
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83
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84 <!--<!–input path–>-->
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85 <!--<xml name="option_argument_path_relative_to_a_tool">-->
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86 <!--<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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87 <!--<param type="text" name="flag" optional="true" label="flag" />-->
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88 <!--<param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/>-->
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89 <!--<param type="text" name="value" optional="true" label="value" />-->
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90 <!--</repeat>-->
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91 <!--</xml>-->
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92 <!--<xml name="option_argument_path_relative_to_this_tool">-->
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93 <!--<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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94 <!--<param type="text" name="flag" optional="true" label="flag" />-->
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95 <!--<param type="text" name="value" optional="false" label="value" />-->
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96 <!--<param type="select" name="path_type" multiple="false" label="path type">-->
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97 <!--<option value="file_path" selected="false">file path</option>-->
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98 <!--<option value="dir_path" selected="false">directory path</option>-->
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99 <!--</param>-->
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100 <!--</repeat>-->
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101 <!--</xml>-->
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102
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103
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104
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105 <!--output set-->
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106 <xml name="output_set">
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107 <data format="html" name="report" label="${tool.name} report"/>
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108 <data format="txt" name="tool_help_doc" label="${tool.name} help doc"/>
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109 <data format="txt" name="tool_output_dir" label="${tool.name} output directory"/>
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110 <data format="txt" name="tool_log" label="${tool.name} log" />
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111 </xml>
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112
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113
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114 <!--shell command fragment-->
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115 <xml name="shell_command">
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116 <command><![CDATA[
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117
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118 ############ first, create a directory to store all files
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119 mkdir -p $report.files_path &&
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120
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121
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122 ############ save the tool installation directory to an environment variable
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123 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
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124
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125
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126 #########################
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127 ##
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128 ## save user input option/argument pairs into a file
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129 ##
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130 #########################
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131
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132 ## first line will be the header
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133 echo 'type|flag|value|path_type' > $report.files_path/options_and_arguments.txt &&
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134
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135 ############ function_name
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136 ##-t '$function_name'
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137 echo "function_name|not available|${function_name}|not available" >> $report.files_path/options_and_arguments.txt &&
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138
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139 ####################################################
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140 ## loop through repeats to get option/argument pairs
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141 ####################################################
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142
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143 ############ option_argument_single_dataset
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144 #for i in $option_argument_single_dataset_repeat:
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145 #set $item = 'single_dataset|' + str($i.flag) + "|" + str($i.value) + "|"
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146 echo '$item' >> $report.files_path/options_and_arguments.txt &&
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147 #end for
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148
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149 ############ option_argument_multiple_datasets
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150 #for i in $option_argument_multiple_datasets_repeat:
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151 #set $item = 'multiple_datasets|' + str($i.flag) + "|" + str($i.value).replace(',', str($i.delimiter)) + "|"
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152 echo '$item' >> $report.files_path/options_and_arguments.txt &&
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153 #end for
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154
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155
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156 ############ option_argument_path_relative_to_a_tool
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157 #for i in $option_argument_path_relative_to_a_tool_repeat:
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158 #set $item = 'path_relative_to_a_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.a_tool_output_dir)
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159 echo '$item' >> $report.files_path/options_and_arguments.txt &&
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160 #end for
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161
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162 ############ option_argument_path_relative_to_this_tool
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163 #for i in $option_argument_path_relative_to_this_tool_repeat:
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164 #set $item = 'path_relative_to_this_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.path_type)
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165 echo '$item' >> $report.files_path/options_and_arguments.txt &&
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166 #end for
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167
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168 ############ option_argument_string_float_integer
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169 #for i in $option_argument_string_float_integer_repeat:
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170 #set $item = 'value|' + str($i.flag) + "|" + str($i.value) + "|"
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171 echo '$item' >> $report.files_path/options_and_arguments.txt &&
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172 #end for
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173
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174 ############ output_set
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175 ## '$report'
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176 ## '$report.files_path'
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177 ## '$tool_help_doc'
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178 ## '$tool_output_dir'
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179 ## '$tool_log'
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180 #######################
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181 export REPORT='$report' &&
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182 export REPORT_FILES_PATH='$report.files_path' &&
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183 export TOOL_HELP_DOC='$tool_help_doc' &&
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184 export TOOL_OUTPUT_DIR='$tool_output_dir' &&
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185 export TOOL_LOG='$tool_log' &&
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186
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187
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188 ############ run render R script to render R markdowns
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189 Rscript '${__tool_directory__}/elastic_tool_render.R'
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190
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191 ]]></command>
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192 </xml>
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193
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194 <!--tool citations-->
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195 <xml name="citations">
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196 <citation type="bibtex"><![CDATA[
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197 @article{allaire2016rmarkdown,
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198 title={rmarkdown: Dynamic Documents for R, 2016},
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199 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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200 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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201 journal={R package version 0.9},
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202 volume={6},
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203 year={2016}
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204 }
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205 ]]></citation>
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206 <citation type="bibtex"><![CDATA[
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207 @book{xie2015elastic,
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208 title={Dynamic Documents with R and knitr},
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209 author={Xie, Yihui},
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210 volume={29},
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211 year={2015},
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212 publisher={CRC Press}
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213 }
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214 ]]></citation>
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215 </xml>
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216 </macros>
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