--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/w4mcorcov_wrapper.R	Mon Oct 16 14:56:52 2017 -0400
@@ -0,0 +1,169 @@
+#!/usr/bin/env Rscript
+
+# This script assumes that it is being executed in a current working directory containing the following files:
+#   - w4mcorcov_lib.R
+#   - w4mcorcov_input.R
+#   - w4mcorcov_calc.R
+
+## constants
+##----------
+
+modNamC <- "w4mcorcov" ## module name
+
+topEnvC <- environment()
+nl <- "\n"
+
+## options
+##--------
+
+strAsFacL <- options()$stringsAsFactors
+options(stringsAsFactors = FALSE)
+
+## subroutines
+##----------
+
+source("w4mcorcov_lib.R")
+source("w4mcorcov_util.R")
+source("w4mcorcov_input.R")
+source("w4mcorcov_salience.R")
+source("w4mcorcov_calc.R")
+source("w4mcorcov_output.R")
+
+## log file
+##---------
+
+my_log <- function(x, ...) { cat(paste(iso8601.znow(), " ", x, ..., nl, sep=""))}
+my_fatal <- function(x, ...) { 
+  my_log("ERROR: ", x, ...)
+  quit(save = "no", status = 11, runLast = TRUE)
+}
+
+my_log("Start of the '", modNamC, "' Galaxy module call: ")
+
+
+########
+# MAIN #
+########
+
+argVc <- unlist(parseCommandArgs(evaluate=FALSE))
+my_env <- new.env()
+
+##------------------------------
+## Initializing
+##------------------------------
+
+## arguments
+##----------
+
+# files
+
+my_env$dataMatrix_in        <- as.character(argVc["dataMatrix_in"])
+my_env$sampleMetadata_in    <- as.character(argVc["sampleMetadata_in"])
+my_env$variableMetadata_in  <- as.character(argVc["variableMetadata_in"])
+my_env$contrast_detail      <- as.character(argVc["contrast_detail"])
+my_env$contrast_corcov      <- as.character(argVc["contrast_corcov"])
+my_env$contrast_salience    <- as.character(argVc["contrast_salience"])
+# print(sprintf("contrast_salience: %s", my_env$contrast_salience))
+
+# other parameters
+
+my_env$tesC            <- as.character(argVc["tesC"])
+my_env$facC            <- as.character(argVc["facC"])
+my_env$pairSigFeatOnly <- as.logical(argVc["pairSigFeatOnly"])
+my_env$levCSV          <- as.character(argVc["levCSV"])
+my_env$matchingC       <- as.character(argVc["matchingC"])
+my_env$labelFeatures   <- as.logical(argVc["labelFeatures"])
+
+tsv_action_factory <- function(file, colnames, append) {
+  return (
+    function(tsv) {
+      write.table(
+        x = tsv
+      , file = file
+      , sep = "\t"
+      , quote = FALSE
+      , row.names = FALSE
+      , col.names = colnames
+      , append = append
+      )
+    }
+  )
+}
+
+corcov_tsv_colnames <- TRUE
+corcov_tsv_append   <- FALSE
+corcov_tsv_action <- function(tsv) {
+  tsv_action_factory(
+    file     = my_env$contrast_corcov
+  , colnames = corcov_tsv_colnames
+  , append   = corcov_tsv_append
+  )(tsv)
+  corcov_tsv_colnames <<- FALSE
+  corcov_tsv_append   <<- TRUE
+}
+
+salience_tsv_colnames <- TRUE
+salience_tsv_append   <- FALSE
+salience_tsv_action <- function(tsv) {
+  tsv_action_factory(
+    file     = my_env$contrast_salience
+  , colnames = salience_tsv_colnames
+  , append   = salience_tsv_append
+  )(tsv)
+  salience_tsv_colnames <<- FALSE
+  salience_tsv_append   <<- TRUE
+}
+
+my_log( "--------------------------  Reading input data  --------------------------")
+
+# read_inputs is defined in w4mcorcov_input.R
+my_result <- read_inputs(input_env = my_env, failure_action = my_log)
+
+if ( is.logical(my_result) && my_result) {
+  my_log( "--------------------------  Beginning data processing  --------------------------")
+
+  # receiver for result of the call to corcov_calc
+  my_result <- NULL
+
+  # compute and plot the correlation_vs_covariance details plot
+  #   The parameter settings here are generally taken from bioconductor ropls::plot.opls source.
+  marVn <- c(4.6, 4.1, 2.6, 1.6)
+  old_par <- par(
+    font      = 2         # bold font face
+  , font.axis = 2         # bold font face for axis
+  , font.lab  = 2         # bold font face for x and y labels
+  , lwd       = 2         # line-width - interpretation is device spcific
+  , mar       = marVn     # margins
+  , pch       = 18        # black diamond plot-character, see help for graphics::points
+  # , mfrow     = c(2,2)    # two rows by two columns
+  , pty       = "s"       # force plots to be square
+  )
+  plot2pdf(
+    file.name = my_env$contrast_detail
+  , width  = 8
+  , height = 8
+  , plot.function = function() {
+      # plot layout four plots per page
+      layout(matrix(1:4, byrow = TRUE, nrow = 2))
+      my_result <<- corcov_calc(
+          calc_env            = my_env
+        , failure_action      = my_fatal
+        , progress_action     = my_log
+        , corcov_tsv_action   = corcov_tsv_action
+        , salience_tsv_action = salience_tsv_action
+        )
+    }
+  )
+  par(old_par)
+  
+  my_log( "--------------------------  Finished data processing  --------------------------")
+}
+
+my_log( "End of the '", modNamC, "' Galaxy module call")
+
+if (is.logical(my_result) && my_result) {
+  quit(save = "no", status = 0, runLast = TRUE)
+} else {
+  my_log("failure :(")
+  quit(save = "no", status = 10, runLast = TRUE)
+}