comparison elastic_r_package_render.R @ 9:06f38d3febdc draft default tip

planemo upload

8:ea3271940757

#------------import libraries--------------------
options(stringsAsFactors = FALSE)

library(rmarkdown)
#------------------------------------------------

#------------------------------------------------
options_and_arguments = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'), 
                                   sep = '|', header = TRUE)


#-----------------render Rmd--------------
render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/elastic_tool.Rmd'),
       output_file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/report.html'))

# for some unknow reason, directly using REPORT as the input value for output_file parameter
# in the render function can cause empty report file when the tool runs in batch mode.
# the solution is to render the rmarkdown to a explicitly specified file and then copy the

9:06f38d3febdc

#------------import libraries--------------------
options(stringsAsFactors = FALSE)

library(rmarkdown)
library(tidyverse)
#------------------------------------------------

#------------------------------------------------
arguments = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/arguments.txt'),
                                   sep = '|', header = TRUE)


#-----------------render Rmd--------------
render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/elastic_r_package.Rmd'),
       output_file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/report.html'))

# for some unknow reason, directly using REPORT as the input value for output_file parameter
# in the render function can cause empty report file when the tool runs in batch mode.
# the solution is to render the rmarkdown to a explicitly specified file and then copy the