Mercurial > repos > mingchen0919 > elastic_expose_data

annotate list_paired_render.R @ 7:23cbb0daf18d draft default tip

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planemo upload commit d1d9c6fc42729b4194adac13d1b71062bf19ad0b-dirty
author mingchen0919
date Mon, 02 Apr 2018 10:53:05 -0400
parents 52ecc1cfd205
children
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1 ##============ Sink warnings and errors to a file ==============
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2 ## use the sink() function to wrap all code within it.
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3 ##==============================================================
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4 zz = file(Sys.getenv('TOOL_LOG'))
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5 sink(zz)
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6 sink(zz, type = 'message')
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8 #------------import libraries--------------------
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9 options(stringsAsFactors = FALSE)
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10
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11 library(rmarkdown)
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12 library(stringr)
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13 #------------------------------------------------
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14
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15 #------------------------------------------------
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16 options_and_arguments = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'),
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17 sep = '|', header = TRUE)
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19 #------------------------------------------------
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20 # create three folders within working directory
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21 dir.create('list_paired')
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23 #-----------------render Rmd--------------
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24 # copy R markdown file to working directory and render it within the working directory.
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25 render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/list_paired.Rmd'),
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26 output_file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/report.html'))
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28 # for some unknow reason, directly using REPORT as the input value for output_file parameter
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29 # in the render function can cause empty report file when the tool runs in batch mode.
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30 # the solution is to render the rmarkdown to a explicitly specified file and then copy the
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31 # file to ${REPORT}
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32 system(command = 'cp ${REPORT_FILES_PATH}/report.html ${REPORT}')
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33 system(command = 'sh ${REPORT_FILES_PATH}/script.sh')
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35 # rename files so that all files have the name pattern BASENAME_forward.EXT and BASENAME_reverse.EXT
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36 from_files = list.files('list_paired', full.names = TRUE)
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37 to_files = str_replace_all(from_files, c('_1', '_2'), c('_forward', '_reverse'))
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38 file.rename(from = from_files, to = to_files)
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39 #------------------------------------------
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42 ##--------end of code rendering .Rmd templates----------------
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43 sink()
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44 ##=========== End of sinking output=============================