--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rmarkdown_deseq2_count_matrix_render.R	Sat Dec 30 00:25:38 2017 -0500
@@ -0,0 +1,83 @@
+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$ECHO = c('echo', 'e', '1', 'character')
+  args_list$c = c('count_data', 'c', '1', 'character')
+  args_list$C = c('col_data', 'C', '1', 'character')
+  args_list$D = c('design_formula', 'D', '1', 'character')
+  args_list$k = c('contrast_condition', 'k', '1', 'character')
+  args_list$T = c('treatment', 'T', '1', 'character')
+  args_list$K = c('control', 'K', '1', 'character')
+  ##--------2. output report and outputs --------------
+  args_list$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$report_dir, x)
+    # }) %>%
+    (function(x) {
+      fileConn = file('tool_template.Rmd')
+      writeLines(x, con=fileConn)
+      close(fileConn)
+    })
+
+
+  ##=============STEP 4: render .Rmd templates=================
+  ##
+  ##===========================================================
+  render('tool_template.Rmd', output_file = opt$report_html)
+
+
+  ##--------end of code rendering .Rmd templates----------------
+sink()
+##=========== End of sinking output=============================