view dynamic_tool_render.R @ 0:b49e227ec738 draft default tip

planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190

##============ Sink warnings and errors to a file ==============
## use the sink() function to wrap all code within it.
##==============================================================
zz = file('tool_log.txt')
sink(zz)
sink(zz, type = 'message')

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

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


#------------get arguments into R--------------------
# load helper function
source(paste0(Sys.getenv('TOOL_DIR'), '/helper.R'))
# import getopt specification matrix from a csv file
opt = getopt(getopt_specification_matrix('/dynamic_tool.csv'))
opt$X_T = Sys.getenv('TOOL_DIR')
#----------------------------------------------------


#-----------using passed arguments in R 
#           to define system environment variables---
do.call(Sys.setenv, opt[-1])
#----------------------------------------------------

#---------- often used variables ----------------
# OUTPUT_DIR: path to the output associated directory, which stores all outputs
# TOOL_DIR: path to the tool installation directory
OUTPUT_REPORT = opt$X_R
OUTPUT_DIR = opt$X_D
TOOL_DIR =   opt$X_T
RMD_NAME = 'dynamic_tool.Rmd'

# create the output associated directory to store all outputs
dir.create(OUTPUT_DIR, recursive = TRUE)

#-----------------render Rmd--------------
render(paste0(TOOL_DIR, '/', RMD_NAME), output_file = OUTPUT_REPORT)
#------------------------------------------

#==============the end==============


##--------end of code rendering .Rmd templates----------------
sink()
##=========== End of sinking output=============================