--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rmarkdown_report_render.R	Fri Dec 14 00:21:26 2018 -0500
@@ -0,0 +1,161 @@
+##============ Sink warnings and errors to a file ==============
+## use the sink() function to wrap all code within it.
+##==============================================================
+zz = file(paste0(Sys.getenv('REPORT_FILES_PATH'), '/r_rendering.log.txt'))
+sink(zz)
+sink(zz, type = 'message')
+
+#============== preparation ====================================
+# import libraries
+#------------------------------------------------------------------
+# ADD MORE LIBRARIES HERE IF YOUR TOOL DEPENDS ON OTHER R LIBRARIES
+#------------------------------------------------------------------
+library('getopt')
+library('rmarkdown')
+library('htmltools')
+library('ggplot2')
+library('plotly')
+library('DESeq2')
+library('pheatmap')
+#------------------------------------------------------------------
+options(stringsAsFactors = FALSE)
+
+
+# define two helper functions
+#-----: helper function 1
+#' \code{getopt_specification_matrix} returns a getopt specification matrix.
+#'
+#' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data.
+#' The first column are short flags, the second column are argument masks, the third column
+#' is data types. The fourth column are variable names used in the tool XML. These three columns are required.
+#' @param gtg_name the name of a running GTG.
+getopt_specification_matrix = function(specification_file,
+                                       gtg_name = 'gtg',
+                                       tool_dir = Sys.getenv('TOOL_INSTALL_DIR')) {
+  df = read.csv(
+    paste0(tool_dir, '/', specification_file),
+    header = TRUE,
+    stringsAsFactors = FALSE
+  )
+  # check if there are duplicated short flags
+  short_flags = df[, 1]
+  if (length(unique(short_flags)) < length(short_flags)) {
+    cat('----Duplicated short flags found ----\n')
+    cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n')
+    stop('Duplicated short flags are not allowed.')
+  }
+  
+  # use short flags to generate long flags
+  long_flags = paste0('X_', df[, 1])
+  
+  # specification matrix
+  df2 = data.frame(
+    long_flags = long_flags,
+    short_flags = df[, 1],
+    argument_mask = df[, 2],
+    data_type = df[, 3]
+  )
+  
+  as.matrix(df2)
+}
+
+#-----: helper function 2
+#' \code{file_tree} generate file tree of a directory in the format of HTML lists.
+#'
+#' @param dir the path to the directory for generating the file tree.
+#' @param output_dir the REPORT_FILES_PATH folder name, which has the name style: dataset_NUMBER_files.
+# define a recursive function to build html string of the file tree
+file_tree = function(dir = '.') {
+  # get the OUTPUT_DIR folder data: dataset_NUMBER_files
+  report_files_path = Sys.getenv('REPORT_FILES_PATH')
+  output_dir = tail(strsplit(report_files_path, '/')[[1]], 1)
+  
+  files = list.files(path = dir,
+                     recursive = FALSE,
+                     full.names = TRUE)
+  # files also include directorys, need to remove directorys
+  files = files[!dir.exists(files)]
+  dirs = list.dirs(path = dir,
+                   recursive = FALSE,
+                   full.names = TRUE)
+  tags$ul({
+    if (length(files) > 0) {
+      lapply(files, function(x) {
+        path_end = tail(strsplit(x, '/')[[1]], 1)
+        href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
+        li_item = tags$li(tags$a(path_end, href = href_path))
+        li_item$attribs = list('data-jstree' = '{"icon":"jstree-file"}')
+        li_item
+      })
+    }
+  },
+  {
+    if (length(dirs) > 0) {
+      lapply(dirs, function(x) {
+        path_end = tail(strsplit(x, '/')[[1]], 1)
+        # hide vakata-jstree-3.3.5 folder
+        if (!(path_end %in% c('vakata-jstree-3.3.5', 'rmarkdown_report_files', 'site_libs'))) {
+          # x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
+          li_item = tags$li(path_end, file_tree(x))
+          li_item$attribs = list('data-jstree' = '{"icon":"jstree-folder"}')
+          li_item
+        }
+      })
+    }
+  })
+}
+#----------------- end of help functions -------------------------
+
+
+# import getopt specification matrix from a csv file
+opt = getopt(getopt_specification_matrix('command-line-arguments.csv',
+                                         tool_dir = Sys.getenv('TOOL_INSTALL_DIR')))
+# define environment variables for all input values. this is useful when we
+# want to use input values by other programming language in r markdown
+do.call(Sys.setenv, opt[-1])
+#===============================================================
+
+
+#======================== render Rmd files =========================
+# copy jstree javascript library to tool output directory
+file.copy(
+  from = paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/vakata-jstree-3.3.5'),
+  to = Sys.getenv('REPORT_FILES_PATH'),
+  recursive = TRUE
+)
+
+# if '_site.yml' file exists, this tool is assumed to render a website.
+# otherwise, it renders a single html.
+if (file.exists(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/_site.yml'))) {
+  # render a website
+  system(command = 'cp -r ${TOOL_INSTALL_DIR}/*.Rmd ${REPORT_FILES_PATH}')
+  system(command = 'cp -r ${TOOL_INSTALL_DIR}/_site.yml ${REPORT_FILES_PATH}')
+  render_site(input = Sys.getenv('REPORT_FILES_PATH'))
+} else {
+  # render a single html
+  system(command = 'cp -r ${TOOL_INSTALL_DIR}/rmarkdown_report.Rmd ${REPORT_FILES_PATH}')
+  # add a few lines to 'rmarkdown_report.Rmd' to generate file tree outputs
+  jstree_lines = '
+## Outputs
+
+```{r, echo=FALSE}
+tags$div(id="jstree", file_tree(Sys.getenv(\'REPORT_FILES_PATH\')))
+```'
+  write(
+    x = jstree_lines,
+    append = TRUE,
+    file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd')
+  )
+  render(input = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd'))
+}
+#===============================================================
+
+
+#============== expose outputs to galaxy history ===============
+system(command = 'sh ${TOOL_INSTALL_DIR}/expose-outputs-to-galaxy-history.sh')
+#===============================================================
+
+
+##--------end of code rendering .Rmd templates----------------
+sink()
+##=========== End of sinking output=============================