Mercurial > repos > mingchen0919 > elastic_expose_data
annotate elastic_expose_to_list_collection.xml @ 4:9ff33a3631fa draft
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author | mingchen0919 |
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date | Mon, 02 Apr 2018 08:32:59 -0400 |
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1 <?xml version="1.0" encoding="UTF-8"?> |
3 | 2 <tool id="elastic_expose_to_list_collection" name="expose data (list)" 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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12 |
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13 ############ first, create a directory to store all files |
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14 mkdir -p $report.files_path && |
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15 |
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16 |
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17 ############ save the tool installation directory to an environment variable |
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18 export TOOL_INSTALL_DIR='${__tool_directory__}' && |
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19 |
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20 |
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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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26 |
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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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29 |
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30 |
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31 |
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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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35 |
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36 |
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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' >> '$report.files_path/options_and_arguments.txt' && |
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41 #end for |
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42 |
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43 |
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44 ############ output_set |
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45 ## '$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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51 |
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52 |
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53 ############ run render R script to render R markdowns |
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54 Rscript '${__tool_directory__}/list_render.R' |
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55 |
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56 ]]></command> |
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57 <inputs> |
2
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58 <repeat name="option_argument_path_relative_to_a_tool_repeat" title="INPUT DATA PATH: relative to a tool output directory" min="0" default="0"> |
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59 <param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/> |
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60 <param type="text" name="value" optional="true" label="relative path"/> |
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61 </repeat> |
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62 </inputs> |
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63 <outputs> |
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64 <data format="html" name="report" label="${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" name="list_collection"> |
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67 <discover_datasets pattern="__name_and_ext__" directory="list" /> |
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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> |