Mercurial > repos > mingchen0919 > elastic_expose_data
annotate elastic_expose_individuals.xml @ 4:9ff33a3631fa draft
planemo upload commit 979e0f1c28c74ca7df02ef20c2208e9677bc820a-dirty
| author | mingchen0919 |
|---|---|
| date | Mon, 02 Apr 2018 08:32:59 -0400 |
| parents | 5838300fc1aa |
| children |
| rev | line source |
|---|---|
| 3 | 1 <?xml version="1.0" encoding="UTF-8"?> |
| 2 <tool id="elastic_expose_individuals" name="expose data (individuals)" version="1.0.1"> | |
| 3 <macros> | |
| 4 <import>elastic_tool_wrappers_macros.xml</import> | |
| 5 </macros> | |
| 6 <description/> | |
| 7 <requirements> | |
| 8 <expand macro="rmarkdown_requirements"/> | |
| 9 </requirements> | |
| 10 <expand macro="stdio"/> | |
| 11 <command><![CDATA[ | |
| 12 | |
| 13 ############ first, create a directory to store all files | |
| 14 mkdir -p $report.files_path && | |
| 15 | |
| 16 | |
| 17 ############ save the tool installation directory to an environment variable | |
| 18 export TOOL_INSTALL_DIR='${__tool_directory__}' && | |
| 19 | |
| 20 | |
| 21 ######################### | |
| 22 ## | |
| 23 ## save user input option/argument pairs into a file | |
| 24 ## | |
| 25 ######################### | |
| 26 | |
| 27 ## first line will be the header | |
| 28 echo 'tool_output_dir|relative_path' > '$report.files_path/options_and_arguments.txt' && | |
| 29 | |
| 30 | |
| 31 | |
| 32 #################################################### | |
| 33 ## loop through repeats to get option/argument pairs | |
| 34 #################################################### | |
| 35 | |
| 36 | |
| 37 ############ option_argument_path_relative_to_a_tool | |
| 38 #for i in $option_argument_path_relative_to_a_tool_repeat: | |
| 39 #set $item = str($i.a_tool_output_dir) + "|" + str($i.value) | |
| 40 echo '$item' >> '$report.files_path/options_and_arguments.txt' && | |
| 41 #end for | |
| 42 | |
| 43 | |
| 44 ############ output_set | |
| 45 ## '$report' | |
| 46 ## '$report.files_path' | |
| 47 ####################### | |
| 48 export REPORT='$report' && | |
| 49 export TOOL_LOG='$tool_log' && | |
| 50 export REPORT_FILES_PATH='$report.files_path' && | |
| 51 | |
| 52 | |
| 53 ############ run render R script to render R markdowns | |
|
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9ff33a3631fa
planemo upload commit 979e0f1c28c74ca7df02ef20c2208e9677bc820a-dirty
mingchen0919
parents:
3
diff
changeset
|
54 Rscript '${__tool_directory__}/individuals_render.R' |
| 3 | 55 |
| 56 ]]></command> | |
| 57 <inputs> | |
| 58 <repeat name="option_argument_path_relative_to_a_tool_repeat" title="INPUT DATA PATH: relative to a tool output directory" min="1" default="1"> | |
| 59 <param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/> | |
| 60 <param type="text" name="value" optional="true" label="relative path"/> | |
| 61 </repeat> | |
| 62 </inputs> | |
| 63 <outputs> | |
|
4
9ff33a3631fa
planemo upload commit 979e0f1c28c74ca7df02ef20c2208e9677bc820a-dirty
mingchen0919
parents:
3
diff
changeset
|
64 <data format="html" name="report" label="${tool.name} report ${on_string}"> |
| 3 | 65 <discover_datasets pattern="__designation_and_ext__" directory="individual_outputs" visible="true"/> |
| 66 </data> | |
|
4
9ff33a3631fa
planemo upload commit 979e0f1c28c74ca7df02ef20c2208e9677bc820a-dirty
mingchen0919
parents:
3
diff
changeset
|
67 <data format="txt" name="tool_log" label="${tool.name} log ${on_string}"/> |
| 3 | 68 </outputs> |
| 69 <citations> | |
| 70 <expand macro="citations"/> | |
| 71 </citations> | |
| 72 </tool> |