view DESeq_render_ori.R @ 0:61c184384d02 draft default tip

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2

library(getopt)
library(rmarkdown)
library(htmltools)
library(dplyr)

##============ 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')
##---------below is the code for rendering .Rmd templates-----

##=============STEP 1: handle command line arguments==========
##
##============================================================
# column 1: the long flag name
# column 2: the short flag alias. A SINGLE character string
# column 3: argument mask
#           0: no argument
#           1: argument required
#           2: argument is optional
# column 4: date type to which the flag's argument shall be cast.
#           possible values: logical, integer, double, complex, character.
#-------------------------------------------------------------
#++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
# 1. short flag alias should match the flag in the command section in the XML file.
# 2. long flag name can be any legal R variable names
# 3. two names in args_list can have common string but one name should not be a part of another name.
#    for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
args_list=list()
##------- 1. input data ---------------------
args_list$ECHO = c('echo', 'e', '1', 'character')
##--------2. output report and outputs --------------
args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character')
##--------3. .Rmd templates in the tool directory ----------
args_list$TOOL_TEMPLATE_RMD = c('tool_template_rmd', 't', '1', 'character')
##-----------------------------------------------------------
opt = getopt(t(as.data.frame(args_list)))



##=======STEP 2: create report directory (optional)==========
##
##===========================================================
dir.create(opt$report_dir)

##=STEP 3: replace placeholders in .Rmd with argument values=
##
##===========================================================
#++ need to replace placeholders with args values one by one+
readLines(opt$tool_template_rmd) %>%
  (function(x) {
    gsub('ECHO', opt$echo, x)
  }) %>%
  (function(x) {
    gsub('REPORT_DIR', opt$output_dir, x)
  }) %>%
  (function(x) {
    fileConn = file('tool_template.Rmd')
    writeLines(x, con=fileConn)
    close(fileConn)
  })


##=============STEP 4: render .Rmd templates=================
##
##===========================================================
render('tool_template.Rmd', output_file = opt$report_html)


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