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##======= Handle arguments from command line ========
# setup R error handline to go to stderr
options(show.error.messages=FALSE,
error=function(){
    cat(geterrmessage(), file=stderr())
    quit("no", 1, F)
})

# we need that to not crash galaxy with an UTF8 error on German LC settings.
loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")

# suppress warning
options(warn = -1)

options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
args = commandArgs(trailingOnly=TRUE)

suppressPackageStartupMessages({
    library(getopt)
    library(tools)
})

# 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.
spec_list=list()

##------- 1. input data ---------------------
spec_list$COUNT_FILES = c('count_files', 'c', '1', 'character')
spec_list$ECHO = c('echo', 'e', '1', 'character')
spec_list$SAMPLE_TABLE = c('sample_table', 's', '1', 'character')
spec_list$DESIGN_FORMULA = c('design_formula', 'p', '1', 'character')

##--------2. output report and report site directory --------------
spec_list$OUTPUT_HTML = c('deseq_html', 'o', '1', 'character')
spec_list$OUTPUT_DIR = c('deseq_dir', 'd', '1', 'character')
spec_list$WORKSPACE = c('deseq_workspace', 'w', '1', 'character')

##--------3. Rmd templates sitting in the tool directory ----------

spec_list$DESEQ_RMD = c('deseq_rmd', 'D', '1', 'character')



##------------------------------------------------------------------

spec = t(as.data.frame(spec_list))
opt = getopt(spec)
# arguments are accessed by long flag name (the first column in the spec matrix)
#                        NOT by element name in the spec_list
# example: opt$help, opt$expression_file
##====== End of arguments handling ==========

#------ Load libraries ---------
library(rmarkdown)
library(plyr)
library(stringr)
library(dplyr)
library(highcharter)
library(DT)
library(reshape2)
# library(Kmisc)
library(plotly)
library(formattable)
library(htmltools)


#----- 1. create the report directory ------------------------
system(paste0('mkdir -p ', opt$deseq_dir))


#----- 2. generate Rmd files with Rmd templates --------------
#   a. templates without placeholder variables:
#         copy templates from tool directory to the working directory.
#   b. templates with placeholder variables:
#         substitute variables with user input values and place them in the working directory.


#----- 01 DESeq.Rmd -----------------------
readLines(opt$deseq_rmd) %>%
    (function(x) {
        gsub('ECHO', opt$echo, x)
    }) %>%
    (function(x) {
      gsub('DESEQ_WORKSPACE', opt$deseq_workspace, x)
    }) %>%
    (function(x) {
      gsub('DESIGN_FORMULA', opt$design_formula, x)
    }) %>%
    (function(x) {
        gsub('OUTPUT_DIR', opt$deseq_dir, x)
    }) %>%
    (function(x) {
        fileConn = file('DESeq.Rmd')
        writeLines(x, con=fileConn)
        close(fileConn)
    })


#------ 3. render all Rmd files --------
render('DESeq.Rmd', output_file = opt$deseq_html)


#-------4. manipulate outputs -----------------------------
# document file
# file.copy('DESeq.html', opt$deseq_html, recursive = TRUE)