comparison dynamic_tool_render.R @ 2:a9579c344a90 draft default tip

planemo upload commit 8f84e3911c6ff4103c0ad5fb8dd774f80d9b2559

1:ddc3c3527f49

sink(zz, type = 'message')

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

library(getopt)
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'), '/dynamic_tool.Rmd'), 
       output_file = Sys.getenv('REPORT'))
#------------------------------------------


##--------end of code rendering .Rmd templates----------------
sink()

2:a9579c344a90

sink(zz, type = 'message')

#------------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'), '/dynamic_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
# file to ${REPORT}
system(command = 'cp ${REPORT_FILES_PATH}/report.html ${REPORT}')
#------------------------------------------


##--------end of code rendering .Rmd templates----------------
sink()