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annotate elastic_expose_to_list_paired_collection.xml @ 4:9ff33a3631fa draft

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author mingchen0919
date Mon, 02 Apr 2018 08:32:59 -0400
parents 5838300fc1aa
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="elastic_expose_to_list_paired_collection" name="expose data (list:paired)" version="1.0.1">
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3 <macros>
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4 <import>elastic_tool_wrappers_macros.xml</import>
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5 </macros>
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6 <description/>
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7 <requirements>
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8 <expand macro="rmarkdown_requirements"/>
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9 </requirements>
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10 <expand macro="stdio"/>
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11 <command><![CDATA[
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13 ############ first, create a directory to store all files
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14 mkdir -p $report.files_path &&
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17 ############ save the tool installation directory to an environment variable
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18 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
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21 #########################
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22 ##
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23 ## save user input option/argument pairs into a file
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24 ##
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25 #########################
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27 ## first line will be the header
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28 echo 'tool_output_dir|relative_path' > '$report.files_path/options_and_arguments.txt' &&
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32 ####################################################
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33 ## loop through repeats to get option/argument pairs
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34 ####################################################
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37 ############ option_argument_path_relative_to_a_tool
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38 #for i in $option_argument_path_relative_to_a_tool_repeat:
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39 #set $item = str($i.a_tool_output_dir) + "|" + str($i.value)
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40 echo '$item' >> '$report.files_path/options_and_arguments.txt' &&
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41 #end for
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44 ############ output_set
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45 ## '$report'
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46 ## '$report.files_path'
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47 #######################
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48 export REPORT='$report' &&
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49 export TOOL_LOG='$tool_log' &&
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50 export REPORT_FILES_PATH='$report.files_path' &&
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53 ############ run render R script to render R markdowns
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54 Rscript '${__tool_directory__}/list_paired_render.R'
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56 ]]></command>
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57 <inputs>
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58 <repeat name="option_argument_path_relative_to_a_tool_repeat" title="INPUT DATA PATH: relative to a tool output directory" min="0" default="0">
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59 <param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/>
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60 <param type="text" name="value" optional="true" label="relative path"/>
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61 </repeat>
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62 </inputs>
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63 <outputs>
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64 <data format="html" name="report" label="${tool.name} report ${on_string}"/>
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65 <data format="txt" name="tool_log" label="${tool.name} log ${on_string}"/>
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66 <collection type="list:paired" name="list_paired_collection">
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67 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?" directory="list_paired"/>
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68 </collection>
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69 </outputs>
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70 <citations>
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71 <expand macro="citations"/>
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72 </citations>
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73 </tool>