view htseq_count_render.R @ 0:10a460f61ac2 draft

planemo upload

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

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

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


#------------get arguments into R--------------------
# library(dplyr)
# getopt_specification_matrix(extract_short_flags('')) %>%
#   write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE)


spec_matrix = as.matrix()
opt = getopt(spec_matrix)
#----------------------------------------------------


#-----------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_DIR = ''
TOOL_DIR =   ''
RMD_NAME = ''
OUTPUT_REPORT = opt$X_o

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

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

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


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