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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="1.1.1">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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6
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16 <xml name="function_components">
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7
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17 <repeat name="function_component_repeat" title="Call a function" min="1" default="1">
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18 <param type="select" name="function_name" multiple="false" label="==== Call function ====">
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19 <option value="ggplot" selected="false">ggplot</option>
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20 <option value="aes" selected="false">ggplot</option>
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21 <option value="read.table" selected="false">read.table</option>
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22 <option value="write.csv" selected="false">write.csv</option>
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23 </param>
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4
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24 <expand macro="function_arguments" />
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25 <param type="select" name="operator" label="connect to next function">
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26 <option value="%>%" selected="false">pipe (%>%)</option>
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27 <option value="+" selected="false">plus (+)</option>
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28 </param>
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4
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29 </repeat>
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30 </xml>
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31
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32 <xml name="function_arguments">
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33 <repeat name="regular_argument_value" title="Argument value: from user input" min="0" default="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="argument value" />
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2
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36 <param type="select" name="argument_type" label="argument type">
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37 <option value="string" selected="true">string</option>
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38 <option value="numeric" selected="false">numeric</option>
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39 <option value="boolean" selected="false">boolean</option>
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40 <option value="variable" selected="false">variable</option>
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2
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41 </param>
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42 </repeat>
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43 <repeat name="rdata_argument_value" title="Argument value: from RData" min="0" default="0">
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44 <param type="text" name="argument" label="argument" />
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8
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45 <param type="data" format="rdata" name="argument_value" optional="false" label="RData output" />
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46 </repeat>
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47 </xml>
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48
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49
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50 <!--output set-->
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51 <xml name="output_set">
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52 <data format="html" name="report" label="${tool.name} report"/>
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53 <data format="txt" name="tool_help_doc" label="${tool.name} help doc"/>
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54 <data format="txt" name="tool_log" label="${tool.name} log" />
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55 </xml>
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56
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57
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58 <!--shell command fragment-->
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59 <xml name="shell_command">
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60 <command><![CDATA[
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61
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62 ############ 1. create a directory to store all files
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63 mkdir -p $report.files_path &&
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64
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65
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66 ############ 2. save the tool installation directory to an environment variable
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67 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
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68
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69
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70 ############ 3. save user inputs into arguments.txt
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71
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72 ############ 3.1 table header
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73 echo 'function|input_type|argument|argument_value|argument_value_type|operator' > $report.files_path/arguments.txt &&
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74
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75
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76 ############ 3.2 loop through function component repeat
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77 #for $fun_component in $function_components:
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78 #for reg_arg in $fun_component.regular_argument_value
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79 echo '$fun_component.function_name|regular|$reg_arg.argument|$arg_arg.argument_value|$arg_arg.argument_value_type|$fun_component.operator' >> $report.files_path/arguments.txt &&
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80 #end for
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81
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82 #for rdata_arg in $fun_component.rdata_argument_value
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83 echo '$fun_component.function_name|rdata|$rdata_arg.argument|$arg_arg.argument_value|rdata|$fun_component.operator' >> $report.files_path/arguments.txt &&
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84 #end for
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85
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86 ############ output_set
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87 ## '$report'
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88 ## '$report.files_path'
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89 ## '$tool_help_doc'
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90 ## '$tool_log'
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91 #######################
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92 export REPORT='$report' &&
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93 export REPORT_FILES_PATH='$report.files_path' &&
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94 export TOOL_HELP_DOC='$tool_help_doc' &&
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95 export TOOL_LOG='$tool_log' &&
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96
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97
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98 ############ run render R script to render R markdowns
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99 Rscript '${__tool_directory__}/elastic_tool_render.R'
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100
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101 ]]></command>
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102 </xml>
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103
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104 <!--tool citations-->
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105 <xml name="citations">
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106 <citation type="bibtex"><![CDATA[
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107 @article{allaire2016rmarkdown,
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108 title={rmarkdown: Dynamic Documents for R, 2016},
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109 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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110 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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111 journal={R package version 0.9},
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112 volume={6},
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113 year={2016}
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114 }
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115 ]]></citation>
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116 <citation type="bibtex"><![CDATA[
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117 @book{xie2015elastic,
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118 title={Dynamic Documents with R and knitr},
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119 author={Xie, Yihui},
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120 volume={29},
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121 year={2015},
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122 publisher={CRC Press}
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123 }
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124 ]]></citation>
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125 </xml>
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126 </macros>
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