Mercurial > repos > mingchen0919 > elastic_expose_data
annotate elastic_tool_wrappers_macros.xml @ 1:16e0f4b7a286 draft
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
| author | mingchen0919 |
|---|---|
| date | Mon, 26 Mar 2018 18:40:39 -0400 |
| parents | a163532ab267 |
| children | 391394c022b8 |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0" encoding="UTF-8"?> |
| 2 <macros> | |
| 3 <xml name="rmarkdown_requirements"> | |
| 4 <requirement type="package" version="1.15.0.6-0">pandoc</requirement> | |
| 5 <requirement type="package" version="1.6">r-rmarkdown</requirement> | |
| 6 </xml> | |
| 7 <xml name="stdio"> | |
| 8 <stdio> | |
| 9 <regex match="XXX" source="stderr" level="warning" description="Check the tool log output file for more details."/> | |
| 10 </stdio> | |
| 11 </xml> | |
| 12 <!--OPTION/ARGUMENT PAIRS and INPUT types--> | |
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planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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13 |
| 0 | 14 <!--input path--> |
| 15 <xml name="option_argument_path_relative_to_a_tool"> | |
| 16 <repeat name="option_argument_path_relative_to_a_tool_repeat" title="INPUT DATA PATH: relative to a tool output directory" min="0" default="0"> | |
| 17 <param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/> | |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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18 <param type="text" name="value" optional="true" label="relative path"/> |
| 0 | 19 </repeat> |
| 20 </xml> | |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
mingchen0919
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21 |
| 0 | 22 <!--shell command fragment--> |
| 23 <xml name="shell_command"> | |
| 24 <command><![CDATA[ | |
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planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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25 echo $tool_name && |
| 0 | 26 |
| 27 ############ first, create a directory to store all files | |
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planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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28 mkdir -p $report.files_path && |
| 0 | 29 |
| 30 | |
| 31 ############ save the tool installation directory to an environment variable | |
| 32 export TOOL_INSTALL_DIR='${__tool_directory__}' && | |
| 33 | |
| 34 | |
| 35 ######################### | |
| 36 ## | |
| 37 ## save user input option/argument pairs into a file | |
| 38 ## | |
| 39 ######################### | |
| 40 | |
| 41 ## first line will be the header | |
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planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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42 echo 'tool_output_dir|relative_path' > '$report.files_path/options_and_arguments.txt' && |
| 0 | 43 |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
mingchen0919
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44 |
| 0 | 45 |
| 46 #################################################### | |
| 47 ## loop through repeats to get option/argument pairs | |
| 48 #################################################### | |
| 49 | |
| 50 | |
| 51 ############ option_argument_path_relative_to_a_tool | |
| 52 #for i in $option_argument_path_relative_to_a_tool_repeat: | |
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planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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53 #set $item = str($i.a_tool_output_dir) + "|" + str($i.value) |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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54 echo '$item' >> '$report.files_path/options_and_arguments.txt' && |
| 0 | 55 #end for |
| 56 | |
| 57 | |
| 58 ############ output_set | |
| 59 ## '$report' | |
| 60 ## '$report.files_path' | |
| 61 ####################### | |
| 62 export REPORT='$report' && | |
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planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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63 export TOOL_LOG='$tool_log' && |
| 0 | 64 export REPORT_FILES_PATH='$report.files_path' && |
| 65 | |
| 66 | |
| 67 ############ run render R script to render R markdowns | |
| 68 Rscript '${__tool_directory__}/elastic_tool_render.R' | |
| 69 | |
| 70 ]]></command> | |
| 71 </xml> | |
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planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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72 |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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73 <!--<xml name="output_set">--> |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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74 <!--<data format="html" name="report" label="${tool.name} report"/>--> |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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75 <!--<data format="txt" name="tool_log" label="${tool.name} log"/>--> |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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76 <!--<collection type="list" name="list_collection">--> |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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77 <!--<discover_datasets pattern="__name_and_ext__" directory="list" />--> |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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78 <!--</collection>--> |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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79 <!--<collection type="paired" name="list_collection">--> |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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80 <!--<discover_datasets pattern="__name_and_ext__" directory="paired_dir" />--> |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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81 <!--</collection>--> |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
mingchen0919
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82 <!--<collection type="list:paired" name="list_collection">--> |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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83 <!--<discover_datasets pattern="(?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)\.(?P<ext>[^\._]+)?"--> |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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84 <!--directory="list_paired"/>--> |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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85 <!--</collection>--> |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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86 <!--</xml>--> |
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16e0f4b7a286
planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d
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87 |
| 0 | 88 <!--tool citations--> |
| 89 <xml name="citations"> | |
| 90 <citation type="bibtex"><![CDATA[ | |
| 91 @article{allaire2016rmarkdown, | |
| 92 title={rmarkdown: Dynamic Documents for R, 2016}, | |
| 93 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff | |
| 94 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob}, | |
| 95 journal={R package version 0.9}, | |
| 96 volume={6}, | |
| 97 year={2016} | |
| 98 } | |
| 99 ]]></citation> | |
| 100 <citation type="bibtex"><![CDATA[ | |
| 101 @book{xie2015elastic, | |
| 102 title={Dynamic Documents with R and knitr}, | |
| 103 author={Xie, Yihui}, | |
| 104 volume={29}, | |
| 105 year={2015}, | |
| 106 publisher={CRC Press} | |
| 107 } | |
| 108 ]]></citation> | |
| 109 </xml> | |
| 110 </macros> |