--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DESeq_visualization_render.R	Mon Aug 07 18:11:15 2017 -0400
@@ -0,0 +1,112 @@
+##======= 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$ECHO = c('echo', 'e', '1', 'character')
+spec_list$DESEQ_WORKSPACE = c('deseq_workspace', 'w', '1', 'character')
+spec_list$SAMPLE_TABLE = c('sample_table', 's', '1', 'character')
+spec_list$INTGROUPS_PCA = c('intgroups_pca', 'p', '1', 'character')
+spec_list$INTGROUPS_MDS = c('intgroups_mds', 'm', '1', 'character')
+
+##--------2. output report and report site directory --------------
+spec_list$OUTPUT_HTML = c('deseq_visualization_html', 'o', '1', 'character')
+spec_list$OUTPUT_DIR = c('deseq_visualization_dir', 'd', '1', 'character')
+
+##--------3. Rmd templates sitting in the tool directory ----------
+
+spec_list$DESEQ_VISUALIZATION_RMD = c('deseq_visualization_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$deseq_visualization_dir))
+
+
+#----- 2. generate Rmd files with Rmd templates --------------
+#   a. templates without placeholder variables:
+#         copy templates from tool directory to the working directory.
+#   b. templates with placeholder variables:
+#         substitute variables with user input values and place them in the working directory.
+
+
+#----- 01 DESeq_visualization.Rmd -----------------------
+readLines(opt$deseq_visualization_rmd) %>%
+  (function(x) {
+    gsub('ECHO', opt$echo, x)
+  }) %>%
+  (function(x) {
+    gsub('DESEQ_WORKSPACE', opt$deseq_workspace, x)
+  }) %>%
+  (function(x) {
+    gsub('INTGROUPS_PCA', opt$intgroups_pca, x)
+  }) %>%
+  (function(x) {
+    gsub('INTGROUPS_MDS', opt$intgroups_mds, x)
+  }) %>%
+  (function(x) {
+    gsub('OUTPUT_DIR', opt$deseq_visualization_dir, x)
+  }) %>%
+  (function(x) {
+    fileConn = file('DESeq_visualization.Rmd')
+    writeLines(x, con=fileConn)
+    close(fileConn)
+  })
+
+
+#------ 3. render all Rmd files --------
+render('DESeq_visualization.Rmd', output_file = opt$deseq_visualization_html)
+
+
+#-------4. manipulate outputs -----------------------------