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1 <tool id="elastic_fastq_dump" name="elastic fastq-dump" version="1.0.1">
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2 <macros>
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3 <import>elastic_tool_macros.xml</import>
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4 </macros>
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5 <expand macro="tool_description"/>
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6 <requirements>
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3
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7 <expand macro="tool_requirements"/>
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8 </requirements>
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9 <stdio>
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10 <regex match="XXX" source="stderr" level="warning"
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11 description="Check the tool log output file for more details."/>
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12 </stdio>
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13 <command><![CDATA[
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14
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15 ############ first, create a directory to store all files
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16 mkdir -p $report.files_path &&
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17
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18
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19 ############ save the tool installation directory to an environment variable
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20 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
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21
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22
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23 #########################
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24 ##
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25 ## save user input option/argument pairs into a file
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26 ##
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27 #########################
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28
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29 ## first line will be the header
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30 echo 'type|option|value|path_type' > $report.files_path/options_and_arguments.txt &&
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31
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32 ############ tool_name
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33 ##-t '$tool_name'
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34 echo "tool_name|not available|${tool_name}|not available" >> $report.files_path/options_and_arguments.txt &&
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35
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36 ####################################################
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37 ## loop through repeats to get option/argument pairs
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38 ####################################################
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39
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40 ############ option_argument_single_dataset
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41 #for i in $option_argument_single_dataset_repeat:
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42 #set $item = 'single_dataset|' + str($i.option) + "|" + str($i.value) + "|"
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43 echo '$item' >> $report.files_path/options_and_arguments.txt &&
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44 #end for
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45
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46 ############ option_argument_multiple_datasets
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47 #for i in $option_argument_multiple_datasets_repeat:
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48 #set $item = 'multiple_datasets|' + str($i.option) + "|" + str($i.value).replace(',', str($i.delimiter)) + "|"
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49 echo '$item' >> $report.files_path/options_and_arguments.txt &&
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50 #end for
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51
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52
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53 ############ option_argument_path_relative_to_a_tool
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54 #for i in $option_argument_path_relative_to_a_tool_repeat:
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55 #set $item = 'path_relative_to_a_tool|' + str($i.option) + "|" + str($i.value) + "|" + str($i.a_tool_output_dir)
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56 echo '$item' >> $report.files_path/options_and_arguments.txt &&
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57 #end for
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58
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59 ############ option_argument_path_relative_to_this_tool
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60 #for i in $option_argument_path_relative_to_this_tool_repeat:
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61 #set $item = 'path_relative_to_this_tool|' + str($i.option) + "|" + $report.files_path + '/' + str($i.value) + "|" + str($i.path_type)
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62 echo '$item' >> $report.files_path/options_and_arguments.txt &&
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63 #end for
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64
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65 ############ option_argument_string_float_integer
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66 #for i in $option_argument_string_float_integer_repeat:
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67 #set $item = 'value|' + str($i.option) + "|" + str($i.value) + "|"
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68 echo '$item' >> $report.files_path/options_and_arguments.txt &&
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69 #end for
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70
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71 ############ output_set
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72 ## '$report'
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73 ## '$report.files_path'
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74 ## '$tool_output_dir'
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75 ## '$tool_log'
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76 #######################
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77 export REPORT='$report' &&
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78 export REPORT_FILES_PATH='$report.files_path' &&
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79 export TOOL_OUTPUT_DIR='$tool_output_dir' &&
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80 export TOOL_LOG='$tool_log' &&
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81
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82
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83 ############ run render R script to render R markdowns
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84 Rscript '${__tool_directory__}/elastic_tool_render.R'
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85
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86 ]]></command>
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87 <inputs>
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88 <param type="select" name="tool_name" multiple="false" label="Tool name">
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89 <expand macro="tool_options"/>
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90 </param>
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91 <repeat name="option_argument_single_dataset_repeat" title="DATA FROM HISTORY: single data set" min="0"
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92 default="0">
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93 <param type="text" name="option" optional="true" label="option"/>
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94 <param name="value" type="data" optional="false" multiple="false" label="value"/>
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95 </repeat>
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4
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96 <repeat name="option_argument_multiple_datasets_repeat" title="DATA FROM HISTORY: multiple data sets"
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97 min="0" default="0">
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98 <param type="text" name="option" optional="true" label="option"/>
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99 <param name="value" type="data" optional="false" multiple="true" label="value"/>
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100 <param type="select" name="delimiter" multiple="false" label="file delimiter">
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101 <option value=" " selected="false">space</option>
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102 <option value="," selected="false">comma</option>
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103 </param>
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104 </repeat>
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105 <repeat name="option_argument_path_relative_to_a_tool_repeat"
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4
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106 title="DATA PATH: relative to other tool output directory" min="0" default="0">
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107 <param type="text" name="option" optional="true" label="option"/>
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108 <param name="a_tool_output_dir" type="data" optional="false" multiple="false"
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109 label="a tool output directory"/>
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110 <param type="text" name="value" optional="true" label="value"/>
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111 </repeat>
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112 <repeat name="option_argument_path_relative_to_this_tool_repeat"
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4
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113 title="DATA PATH: relative to this tool output directory" min="0" default="0">
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1
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114 <param type="text" name="option" optional="true" label="option"/>
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115 <param type="text" name="value" optional="false" label="value"/>
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116 <param type="select" name="path_type" multiple="false" label="path type">
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117 <option value="file_path" selected="false">file path</option>
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118 <option value="dir_path" selected="false">directory path</option>
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119 </param>
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120 </repeat>
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4
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121 <repeat name="option_argument_string_float_integer_repeat" title="INPUT VALUE: string/float/integer" min="0"
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122 default="0">
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123 <param type="text" name="option" label="option"/>
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124 <param type="text" name="value" label="value"/>
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125 </repeat>
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1
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126 </inputs>
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127 <outputs>
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128 <data format="html" name="report" label="${tool.name} report ${on_string}"/>
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129 <data format="txt" name="tool_output_dir" label="${tool.name} output directory ${on_string}"/>
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130 <data format="txt" name="tool_log" label="${tool.name} log ${on_string}"/>
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131 </outputs>
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132 <citations>
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4
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133 <expand macro="citations"/>
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1
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134 </citations>
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135 </tool>
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