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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="2.3.4.1">bowtie2</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="bowtie2" selected="false">bowtie2</option><option value="bowtie2-build" selected="false">bowtie2-build</option><option value="bowtie2-inspect" selected="false">bowtie2-inspect</option></param>
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17 </xml>
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18 <!--OPTION/ARGUMENT PAIRS and INPUT types-->
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19 <!--input files-->
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20 <xml name="option_argument_single_dataset">
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21 <repeat name="option_argument_single_dataset_repeat" title="INPUT DATA FROM HISTORY: single data set" min="0" default="0">
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22 <param type="text" name="flag" optional="true" label="flag"/>
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23 <param name="value" type="data" optional="false" multiple="false" label="value"/>
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24 </repeat>
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25 </xml>
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26 <xml name="option_argument_multiple_datasets">
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27 <repeat name="option_argument_multiple_datasets_repeat" title="INPUT DATA FROM HISTORY: multiple data sets" min="0" default="0">
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28 <param type="text" name="flag" optional="true" label="flag"/>
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29 <param name="value" type="data" optional="false" multiple="true" label="value"/>
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30 <param type="select" name="delimiter" multiple="false" label="file delimiter">
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31 <option value=" " selected="false">space</option>
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32 <option value="," selected="false">comma</option>
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33 </param>
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34 </repeat>
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35 </xml>
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36 <!--input path-->
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37 <xml name="option_argument_path_relative_to_a_tool">
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38 <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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39 <param type="text" name="flag" optional="true" label="flag"/>
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40 <param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a 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 <xml name="option_argument_path_relative_to_this_tool">
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45 <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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46 <param type="text" name="flag" optional="true" label="flag"/>
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47 <param type="text" name="value" optional="false" label="value"/>
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48 <param type="select" name="path_type" multiple="false" label="path type">
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49 <option value="file_path" selected="false">file path</option>
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50 <option value="dir_path" selected="false">directory path</option>
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51 </param>
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52 </repeat>
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53 </xml>
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54 <!--input values: string, float and integer-->
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55 <xml name="option_argument_string_float_integer">
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56 <repeat name="option_argument_string_float_integer_repeat" title="INPUT VALUE: string/float/integer" min="0" default="0">
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57 <param type="text" name="flag" label="flag"/>
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58 <param type="text" name="value" label="value"/>
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59 </repeat>
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60 </xml>
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61 <!--output set-->
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62 <xml name="output_set">
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63 <data format="html" name="report" label="${tool.name} report"/>
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64 <data format="txt" name="tool_help_doc" label="${tool.name} help doc"/>
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65 <data format="txt" name="tool_output_dir" label="${tool.name} output directory"/>
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66 <data format="txt" name="tool_log" label="${tool.name} log"/>
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67 </xml>
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68 <!--shell command fragment-->
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69 <xml name="shell_command">
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70 <command><![CDATA[
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71
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72 ############ first, create a directory to store all files
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73 mkdir -p $report.files_path &&
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74
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75
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76 ############ save the tool installation directory to an environment variable
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77 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
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78
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79
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80 #########################
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81 ##
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82 ## save user input option/argument pairs into a file
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83 ##
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84 #########################
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85
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86 ## first line will be the header
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87 echo 'type|flag|value|path_type' > $report.files_path/options_and_arguments.txt &&
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88
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89 ############ tool_name
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90 ##-t '$tool_name'
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91 echo "tool_name|not available|${tool_name}|not available" >> $report.files_path/options_and_arguments.txt &&
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92
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93 ####################################################
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94 ## loop through repeats to get option/argument pairs
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95 ####################################################
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96
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97 ############ option_argument_single_dataset
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98 #for i in $option_argument_single_dataset_repeat:
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99 #set $item = 'single_dataset|' + str($i.flag) + "|" + str($i.value) + "|"
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100 echo '$item' >> $report.files_path/options_and_arguments.txt &&
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101 #end for
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102
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103 ############ option_argument_multiple_datasets
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104 #for i in $option_argument_multiple_datasets_repeat:
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105 #set $item = 'multiple_datasets|' + str($i.flag) + "|" + str($i.value).replace(',', str($i.delimiter)) + "|"
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106 echo '$item' >> $report.files_path/options_and_arguments.txt &&
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107 #end for
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108
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109
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110 ############ option_argument_path_relative_to_a_tool
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111 #for i in $option_argument_path_relative_to_a_tool_repeat:
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112 #set $item = 'path_relative_to_a_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.a_tool_output_dir)
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113 echo '$item' >> $report.files_path/options_and_arguments.txt &&
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114 #end for
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115
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116 ############ option_argument_path_relative_to_this_tool
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117 #for i in $option_argument_path_relative_to_this_tool_repeat:
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118 #set $item = 'path_relative_to_this_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.path_type)
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119 echo '$item' >> $report.files_path/options_and_arguments.txt &&
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120 #end for
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121
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122 ############ option_argument_string_float_integer
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123 #for i in $option_argument_string_float_integer_repeat:
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124 #set $item = 'value|' + str($i.flag) + "|" + str($i.value) + "|"
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125 echo '$item' >> $report.files_path/options_and_arguments.txt &&
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126 #end for
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127
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128 ############ output_set
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129 ## '$report'
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130 ## '$report.files_path'
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131 ## '$tool_help_doc'
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132 ## '$tool_output_dir'
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133 ## '$tool_log'
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134 #######################
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135 export REPORT='$report' &&
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136 export REPORT_FILES_PATH='$report.files_path' &&
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137 export TOOL_HELP_DOC='$tool_help_doc' &&
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138 export TOOL_OUTPUT_DIR='$tool_output_dir' &&
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139 export TOOL_LOG='$tool_log' &&
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140
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141
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142 ############ run render R script to render R markdowns
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143 Rscript '${__tool_directory__}/elastic_tool_render.R'
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144
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145 ]]></command>
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146 </xml>
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147 <!--tool citations-->
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148 <xml name="citations">
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149 <citation type="bibtex"><![CDATA[
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150 @article{allaire2016rmarkdown,
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151 title={rmarkdown: Dynamic Documents for R, 2016},
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152 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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153 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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154 journal={R package version 0.9},
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155 volume={6},
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156 year={2016}
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157 }
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158 ]]></citation>
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159 <citation type="bibtex"><![CDATA[
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160 @book{xie2015elastic,
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161 title={Dynamic Documents with R and knitr},
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162 author={Xie, Yihui},
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163 volume={29},
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164 year={2015},
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165 publisher={CRC Press}
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166 }
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167 ]]></citation>
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168 </xml>
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169 </macros>
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