--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rmarkdown_feature_counts_render.R	Fri Dec 29 15:03:18 2017 -0500
@@ -0,0 +1,118 @@
+##============ 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')
+
+  ##============== load packages ===============================
+  library(getopt)
+  library(rmarkdown)
+  library(htmltools)
+  library(dplyr)
+  library(Rsubread)
+  library(DT)
+  ##============================================================
+
+  ##---------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$e = c('echo', 'e', '1', 'logical')
+  args_list$a = c('input_bam_paths', 'a', '1', 'character')
+  args_list$N = c('input_bam_names', 'N', '1', 'character')
+  args_list$b = c('annot_inbuilt', 'b', '1', 'character')
+  args_list$c = c('annot_ext', 'c', '1', 'character')
+  args_list$f = c('isGTFAnnotationFile', 'f', '1', 'logical')
+  args_list$g = c('gtf_feature_type', 'g', '1', 'character')
+  args_list$h = c('gtf_attr_type', 'h', '1', 'character')
+  args_list$i = c('chr_aliases', 'i', '2', 'character')
+  args_list$j = c('use_meta_features', 'j', '1', 'logical')
+  args_list$k = c('allow_multi_overlap', 'k', '1', 'logical')
+  args_list$l = c('min_overlap', 'l', '1', 'integer')
+  args_list$m = c('largest_overlap', 'm', '1', 'logical')
+  args_list$n = c('read_extension_5', 'n', '1', 'integer')
+  args_list$o = c('read_extension_3', 'o', '1', 'integer')
+  args_list$p = c('read_2_pos', 'p', '1', 'character')
+  args_list$q = c('count_multi_mapping_reads', 'q', '1', 'logical')
+  args_list$u = c('fraction', 'u', '1', 'logical')
+  args_list$v= c('min_mqs', 'v', '1', 'integer')
+  args_list$w= c('split_only', 'w', '1', 'logical')
+  args_list$x= c('non_split_only', 'x', '1', 'logical')
+  args_list$y= c('primary_only', 'y', '1', 'logical')
+  args_list$z= c('ignore_dup', 'z', '1', 'logical')
+  args_list$A= c('strand_specific', 'A', '1', 'integer')
+  args_list$B= c('junc_counts', 'B', '1', 'logical')
+  args_list$C= c('genome', 'C', '1', 'character')
+  args_list$D= c('is_paired_end', 'D', '1', 'logical')
+  args_list$E= c('require_both_ends_mapped', 'E', '1', 'logical')
+  args_list$F= c('check_frag_length', 'F', '1', 'logical')
+  args_list$G= c('min_frag_length', 'G', '1', 'integer')
+  args_list$H= c('max_frag_length', 'H', '1', 'integer')
+  args_list$I= c('count_chimeric_fragments', 'I', '1', 'logical')
+  args_list$J= c('auto_sort', 'J', '1', 'logical')
+  args_list$K= c('n_threads', 'K', '1', 'integer')
+  args_list$L= c('max_mop', 'L', '1', 'integer')
+  args_list$M= c('report_reads', 'M', '1', 'logical')
+  
+  ##--------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=============================