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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <macros>
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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="0.2.2">skewer</requirement>
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7 </xml>
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8 <xml name="stdio">
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9 <stdio>
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10 <regex match="XXX" source="stderr" level="warning" description="Check the tool log output file for more details."/>
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11 </stdio>
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12 </xml>
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13 <!--Tool name-->
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14 <xml name="tool_name">
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15 <param type="select" name="tool_name" multiple="false" label="Tool name">
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16 <option value="package" selected="false">skewer</option>
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17 </param>
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18 </xml>
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19 <!--OPTION/ARGUMENT PAIRS and INPUT types-->
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20 <!--input files-->
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21 <xml name="option_argument_single_dataset">
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22 <repeat name="option_argument_single_dataset_repeat" title="INPUT SINGLE DATASET" min="0" default="0">
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23 <param type="text" name="flag" optional="true" label="flag"/>
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24 <param name="value" type="data" optional="false" multiple="false" label="value"/>
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25 </repeat>
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26 </xml>
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27 <xml name="option_argument_multiple_datasets">
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28 <repeat name="option_argument_multiple_datasets_repeat" title="INPUT MULTIPLE DATASETS" min="0" default="0">
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29 <param type="text" name="flag" optional="true" label="flag"/>
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30 <param name="value" type="data" optional="false" multiple="true" label="value"/>
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31 <param type="select" name="delimiter" multiple="false" label="file delimiter">
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32 <option value=" " selected="false">space</option>
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33 <option value="," selected="false">comma</option>
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34 </param>
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35 </repeat>
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36 </xml>
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37 <!--input path-->
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38 <xml name="option_argument_path_relative_to_a_tool">
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39 <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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40 <param type="text" name="flag" optional="true" label="flag"/>
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41 <param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/>
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42 <param type="text" name="value" optional="true" label="value"/>
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43 </repeat>
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44 </xml>
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45 <xml name="option_argument_path_relative_to_this_tool">
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46 <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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47 <param type="text" name="flag" optional="true" label="flag"/>
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48 <param type="text" name="value" optional="false" label="value"/>
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49 <param type="select" name="path_type" multiple="false" label="path type">
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50 <option value="file_path" selected="false">file path</option>
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51 <option value="dir_path" selected="false">directory path</option>
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52 </param>
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53 </repeat>
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54 </xml>
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55 <!--input values: string, float and integer-->
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56 <xml name="option_argument_string_float_integer">
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57 <repeat name="option_argument_string_float_integer_repeat" title="INPUT VALUE: string/float/integer" min="0" default="0">
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58 <param type="text" name="flag" label="flag"/>
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59 <param type="text" name="value" label="value"/>
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60 </repeat>
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61 </xml>
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62 <!--output set-->
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63 <xml name="output_set">
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64 <data format="html" name="report" label="${tool.name} report"/>
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65 <data format="txt" name="tool_help_doc" label="${tool.name} help doc"/>
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66 <data format="txt" name="tool_output_dir" label="${tool.name} output directory"/>
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67 <data format="txt" name="tool_log" label="${tool.name} log"/>
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68 </xml>
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69 <!--shell command fragment-->
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70 <xml name="shell_command">
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71 <command><![CDATA[
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72
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73 ############ first, create a directory to store all files
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74 mkdir -p $report.files_path && cd $report.files_path &&
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75
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76
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77 ############ save the tool installation directory to an environment variable
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78 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
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79
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80
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81 #########################
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82 ##
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83 ## save user input option/argument pairs into a file
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84 ##
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85 #########################
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86
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87 ## first line will be the header
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88 echo 'type|flag|value|path_type' > options_and_arguments.txt &&
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89
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90 ############ tool_name
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91 ##-t '$tool_name'
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92 echo "tool_name|not available|${tool_name}|not available" >> options_and_arguments.txt &&
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93
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94 ####################################################
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95 ## loop through repeats to get option/argument pairs
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96 ####################################################
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97
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98 ############ option_argument_single_dataset
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99 #for i in $option_argument_single_dataset_repeat:
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100 #set $item = 'single_dataset|' + str($i.flag) + "|" + str($i.value) + "|"
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101 echo '$item' >> options_and_arguments.txt &&
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102 #end for
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103
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104 ############ option_argument_multiple_datasets
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105 #for i in $option_argument_multiple_datasets_repeat:
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106 #set $item = 'multiple_datasets|' + str($i.flag) + "|" + str($i.value).replace(',', str($i.delimiter)) + "|"
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107 echo '$item' >> options_and_arguments.txt &&
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108 #end for
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109
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110
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111 ############ option_argument_path_relative_to_a_tool
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112 #for i in $option_argument_path_relative_to_a_tool_repeat:
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113 #set $item = 'path_relative_to_a_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.a_tool_output_dir)
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114 echo '$item' >> options_and_arguments.txt &&
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115 #end for
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116
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117 ############ option_argument_path_relative_to_this_tool
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118 #for i in $option_argument_path_relative_to_this_tool_repeat:
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119 #set $item = 'path_relative_to_this_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.path_type)
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120 echo '$item' >> options_and_arguments.txt &&
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121 #end for
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122
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123 ############ option_argument_string_float_integer
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124 #for i in $option_argument_string_float_integer_repeat:
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125 #set $item = 'value|' + str($i.flag) + "|" + str($i.value) + "|"
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126 echo '$item' >> options_and_arguments.txt &&
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127 #end for
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128
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129 ############ output_set
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130 ## '$report'
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131 ## '$report.files_path'
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132 ## '$tool_help_doc'
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133 ## '$tool_output_dir'
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134 ## '$tool_log'
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135 #######################
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136 export REPORT='$report' &&
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137 export REPORT_FILES_PATH='$report.files_path' &&
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138 export TOOL_HELP_DOC='$tool_help_doc' &&
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139 export TOOL_OUTPUT_DIR='$tool_output_dir' &&
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140 export TOOL_LOG='$tool_log' &&
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141
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142
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143 ############ run render R script to render R markdowns
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144 Rscript '${__tool_directory__}/dynamic_tool_render.R'
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145
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146 ]]></command>
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147 </xml>
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148 <!--tool citations-->
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149 <xml name="citations">
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150 <citation type="bibtex"><![CDATA[
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151 @article{allaire2016rmarkdown,
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152 title={rmarkdown: Dynamic Documents for R, 2016},
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153 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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154 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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155 journal={R package version 0.9},
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156 volume={6},
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157 year={2016}
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158 }
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159 ]]></citation>
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160 <citation type="bibtex"><![CDATA[
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161 @book{xie2015dynamic,
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162 title={Dynamic Documents with R and knitr},
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163 author={Xie, Yihui},
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164 volume={29},
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165 year={2015},
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166 publisher={CRC Press}
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167 }
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168 ]]></citation>
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169 </xml>
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170 </macros>
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