--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mirdeep2_mapper_render.R	Tue Aug 08 13:14:41 2017 -0400
@@ -0,0 +1,153 @@
+##======= 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$FASTQ_READS = c('reads', 'r', '1', 'character')
+spec_list$REFERENCE_GENOME = c('reference_genome', 'g', 1, 'character')
+spec_list$ECHO = c('echo', 'e', '1', 'character')
+
+##--------2. output report and report site directory --------------
+spec_list$OUTPUT_HTML = c('mirdeep2_mapper', 'o', '1', 'character')
+spec_list$OUTPUT_DIR = c('mirdeep2_mapper_dir', 'd', '1', 'character')
+spec_list$READS_COLLAPSED = c('reads_collapsed', 'm', '1', 'character')
+spec_list$READ_X_COLLAPSED_VS_GENOME = c('reads_collapsed_vs_genome', 'n', '1', 'character')
+spec_list$REPORT_LOG = c("report_log", 't', '1', 'character')
+
+##---------other parameters---------------
+spec_list$PARSE_TO_FASTA = c('parse_to_fasta', 'b', '1', 'character')
+spec_list$CLEAN_ENTRIES = c('clean_entries', 'c', '1', 'character')
+spec_list$CLIP_3_ADAPTER = c('clip_3_adapter', 'f', '2', 'character')
+spec_list$DISCARD_SHORTER_READS = c('discard_shorter_reads', 'h', '1', 'character')
+spec_list$COLLAPSE_READS_OR_NOT = c('collapse_reads_or_not', 'j', '1', 'character')
+spec_list$MAP_WITH_ONE_MISMATCH = c('map_with_one_mismatch', 'k', '1', 'character')
+spec_list$MAP_UP_TO_POSITION = c('map_up_to_position', 'l', '1', 'character')
+
+##--------3. Rmd templates sitting in the tool directory ----------
+
+## _site.yml and index.Rmd files
+spec_list$SITE_YML = c('site_yml', 's', 1, 'character')
+spec_list$INDEX_Rmd = c('index_rmd', 'i', 1, 'character')
+
+## other Rmd body template files
+spec_list$MIRDEEP2_MAPPER_RMD = c('mirdeep2_mapper_rmd', 'p', '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(plotly)
+# library(formattable)
+library(htmltools)
+
+
+#----- 1. create the report directory ------------------------
+paste0('mkdir -p ', opt$mirdeep2_mapper_dir) %>%
+  system()
+
+#----- 2. generate Rmd files with Rmd templates --------------
+#   a. templates without placeholder variables:
+#         copy templates from tool directory to the working directory.
+#   b. templates with placeholder variables:
+#         substitute variables with user input values and place them in the working directory.
+
+
+#----- mirdeep2_mapper.Rmd -----------------------
+readLines(opt$mirdeep2_mapper_rmd) %>%
+  (function(x) {
+    gsub('ECHO', opt$echo, x)
+  }) %>%
+  (function(x) {
+    gsub('FASTQ_READS', opt$reads, x)
+  }) %>% 
+  (function(x) {
+    gsub('REFERENCE_GENOME', opt$reference_genome, x)
+  }) %>%
+  (function(x) {
+    gsub('PARSE_TO_FASTA', opt$parse_to_fasta, x)
+  }) %>%
+  (function(x) {
+    gsub('CLEAN_ENTRIES', opt$clean_entries, x)
+  }) %>%
+  (function(x) {
+    gsub('CLIP_3_ADAPTER', opt$clip_3_adapter, x)
+  }) %>%
+  (function(x) {
+    gsub('DISCARD_SHORTER_READS', opt$discard_shorter_reads, x)
+  }) %>%
+  (function(x) {
+    gsub('COLLAPSE_READS', opt$collapse_reads, x)
+  }) %>%
+  (function(x) {
+    gsub('MAP_WITH_ONE_MISMATCH', opt$map_with_one_mismatch, x)
+  }) %>%
+  (function(x) {
+    gsub('MAP_UP_TO_POSITION', opt$map_up_to_position, x)
+  }) %>%
+  (function(x) {
+    gsub('OUTPUT_DIR', opt$mirdeep2_mapper_dir, x)
+  }) %>%
+  (function(x) {
+    fileConn = file('mirdeep2_mapper.Rmd')
+    writeLines(x, con=fileConn)
+    close(fileConn)
+  })
+
+
+#------ 3. render all Rmd files with render() --------
+render('mirdeep2_mapper.Rmd', output_file = opt$mirdeep2_mapper)
+
+
+#-------4. manipulate outputs -----------------------------
+#   a. copy non-site files
+file.copy('reads_collapsed.fa', opt$reads_collapsed, recursive=TRUE)
+file.copy('reads_collapsed_vs_genome.arf', opt$reads_collapsed_vs_genome, recursive=TRUE)
+file.copy('report.log', opt$report_log, recursive=TRUE)
+
+
+
+
+