--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/collection_paired_render.R	Tue Sep 26 13:33:22 2017 -0400
@@ -0,0 +1,88 @@
+##======= 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.
+##------- 1. input data ---------------------
+spec_list=list()
+spec_list$FORWARD_INPUT = c('forward_input', 'L', '1', 'character')
+spec_list$REVERSE_INPUT = c('reverse_input', 'R', '1', 'character')
+spec_list$ECHO = c('echo', 'e', '1', 'character')
+spec_list$FORMAT = c('format', 'f', '1', 'character')
+##--------2. output report and outputs --------------
+spec_list$OUTPUT_HTML = c('paired_collection_html', 'r', '1', 'character')
+spec_list$OUTPUT_DIR = c('paired_collection_dir', 'd', '1', 'character')
+##--------3. Rmd templates in the tool directory ----------
+spec_list$PAIRED_COLLECTION_RMD = c('paired_collection_rmd', 't', '1', 'character')
+
+spec = t(as.data.frame(spec_list))
+opt = getopt(spec)
+##====== End of arguments handling ==========
+
+#------ Load libraries ---------
+library(rmarkdown)
+library(htmltools)
+library(dplyr)
+
+#----- 1. create the report directory ------------------------
+system(paste0('mkdir -p ', opt$paired_collection_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 paired_collection.Rmd -----------------------
+readLines(opt$paired_collection_rmd) %>%
+  (function(x) {
+    gsub('ECHO', opt$echo, x)
+  }) %>%
+  (function(x) {
+    gsub('FORMAT', opt$format, x)
+  }) %>%
+  (function(x) {
+    gsub('FORWARD_INPUT', opt$forward_input, x)
+  }) %>%
+  (function(x) {
+    gsub('REVERSE_INPUT', opt$reverse_input, x)
+  }) %>%
+  (function(x) {
+    gsub('OUTPUT_DIR', opt$paired_collection_dir, x)
+  }) %>%
+  (function(x) {
+    fileConn = file('paired_collection.Rmd')
+    writeLines(x, con=fileConn)
+    close(fileConn)
+  })
+
+#------ 3. render all Rmd files --------
+render('paired_collection.Rmd', output_file = opt$paired_collection_html)
+
+
+#-------4. manipulate outputs -----------------------------