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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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9
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17 <repeat name="function_components" 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="geom_point" selected="false">geom_point</option>
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21 <option value="aes" selected="false">ggplot</option>
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22 <option value="read.table" selected="false">read.table</option>
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23 <option value="write.csv" selected="false">write.csv</option>
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24 </param>
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4
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25 <expand macro="function_arguments" />
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26 </repeat>
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27 </xml>
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28
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29 <xml name="function_arguments">
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30 <repeat name="function_arguments" title="argument name/value pairs" min="0" default="0">
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31 <conditional name="argument_type">
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32 <param name="argument_type_selector" type="select" label="Argument type">
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33 <option value="value" selected="false">user input value</option>
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34 <option value="rdata" selected="false">value from RData output</option>
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35 </param>
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36 <when value="value">
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37 <param type="text" name="argument_name" label="argument name" />
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38 <param type="text" name="argument_value" label="argument value" />
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39 </when>
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40 <when value="rdata">
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41 <param type="text" name="argument_name" label="argument name" />
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42 <param type="data" format="rdata" name="argument_value" optional="false" label="RData output" />
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43 </when>
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44 </conditional>
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45 </repeat>
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46 <param type="select" name="operator" label="connect to next function">
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47 <sanitizer>
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48 <valid initial="string.printable"/>
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49 </sanitizer>
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50 <option value="%>%" selected="true">pipe (%>%)</option>
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51 <option value="+" selected="false">plus (+)</option>
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52 </param>
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53 </xml>
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54
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55
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56 <!--output set-->
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57 <xml name="output_set">
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58 <data format="html" name="report" label="${tool.name} report"/>
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59 <data format="rdata" name="tool_rdata_output" label="${tool.name} RData output ${on_string}"/>
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60 <data format="txt" name="tool_log" label="${tool.name} log" />
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61 </xml>
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62
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63
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64 <!--shell command fragment-->
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65 <xml name="shell_command">
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66 <command><![CDATA[
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67
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68 ############ 1. create a directory to store all files
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69 mkdir -p $report.files_path &&
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70
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71
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72 ############ 2. save the tool installation directory to an environment variable
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73 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
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74
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75
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76 ############ 3. save user inputs into arguments.txt
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77
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78 ############ 3.1 table header
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79 echo 'row_type|function_name|argument_name|argument_value|argument_value_type|operator' > $report.files_path/arguments.txt &&
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80
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81
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82 ############ 3.2 loop through function component repeat
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83 #for fun_component in $function_components:
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84 echo 'func|$fun_component.function_name||||' >> $report.files_path/arguments.txt &&
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85
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86 Rscript -e 'library(tidyverse); help($fun_component.function_name)' >> $report.files_path/$fun_component.function_name-help.txt &&
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87
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88 #for argument in $fun_component.function_arguments:
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89 echo 'argument||$argument.argument_type.argument_name|$argument.argument_type.argument_value|$argument.argument_type.argument_type_selector|' >> $report.files_path/arguments.txt &&
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90 #end for
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91 echo 'operator|||||$fun_component.operator' >> $report.files_path/arguments.txt &&
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92 #end for
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93
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94 ############ output_set
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95 ## '$report'
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96 ## '$report.files_path'
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97 ## '$tool_help_doc'
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98 ## '$tool_log'
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99 #######################
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100 export REPORT='$report' &&
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101 export REPORT_FILES_PATH='$report.files_path' &&
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102 export TOOL_RDATA_OUTPUT='$tool_rdata_output' &&
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103 export TOOL_LOG='$tool_log' &&
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104
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105
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106 ############ run render R script to render R markdowns
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107 Rscript '${__tool_directory__}/elastic_r_package_render.R'
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108
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109 ]]></command>
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110 </xml>
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111
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112 <!--tool citations-->
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113 <xml name="citations">
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114 <citation type="bibtex"><![CDATA[
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115 @article{allaire2016rmarkdown,
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116 title={rmarkdown: Dynamic Documents for R, 2016},
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117 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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118 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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119 journal={R package version 0.9},
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120 volume={6},
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121 year={2016}
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122 }
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123 ]]></citation>
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124 <citation type="bibtex"><![CDATA[
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125 @book{xie2015elastic,
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126 title={Dynamic Documents with R and knitr},
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127 author={Xie, Yihui},
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128 volume={29},
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129 year={2015},
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130 publisher={CRC Press}
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131 }
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132 ]]></citation>
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133 </xml>
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134 </macros>
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