--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/w4mclstrpeakpics_wrapper.R	Sun Jun 18 23:25:58 2017 -0400
@@ -0,0 +1,134 @@
+#!/usr/bin/env Rscript
+
+library(batch) ## parseCommandArgs
+
+########
+# MAIN #
+########
+
+argVc <- unlist(parseCommandArgs(evaluate=FALSE))
+
+##------------------------------
+## Initializing
+##------------------------------
+
+## options
+##--------
+
+strAsFacL <- options()$stringsAsFactors
+options(stringsAsFactors = FALSE)
+
+## libraries
+##----------
+
+# begin HACK - suppress " Can't find a usable init.tcl ...  probably means that Tcl wasn't installed properly" issue
+library("gsubfn")
+options(gsubfn.engine = "R")
+# end HACK
+
+r_package_archive <- as.character(argVc["r_package_archive"])
+install.packages(r_package_archive, repos = NULL, type = "source")
+suppressMessages( library("w4mclstrpeakpics") )
+
+## constants
+##----------
+
+modNamC <- "w4mclsltrpeakpics" ## module name
+
+topEnvC <- environment()
+flgC <- "\n"
+
+## functions
+##----------
+
+
+## log file
+##---------
+
+my_print <- function(x, ...) { cat(c(x, ...))}
+
+my_print("\nStart of the '", modNamC, "' Galaxy module call: ",
+    format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
+
+## arguments
+##----------
+
+# files
+
+output_pdf                  <- as.character(argVc["output_pdf"])
+output_tsv                  <- as.character(argVc["output_tsv"])
+output_rdata                <- as.character(argVc["output_rdata"])
+data_matrix_path            <- as.character(argVc["data_matrix_path"])
+variable_metadata_path      <- as.character(argVc["variable_metadata_path"])
+sample_metadata_path        <- as.character(argVc["sample_metadata_path"])
+  
+# other parameters
+
+sample_selector_column_name <- as.character(argVc["sample_selector_column_name"])
+sample_selector_value       <- as.character(argVc["sample_selector_value"])
+  
+##------------------------------
+## Computation
+##------------------------------
+
+# from 'demo(error.catching)'
+tryCatch.W.E <- function(expr) {
+  W <- NULL
+  w.handler <- function(w){
+    # warning handler
+    W <<- w
+    invokeRestart("muffleWarning")
+  }
+  list(
+    value = withCallingHandlers(
+      tryCatch(expr, error = function(e) e)
+    , warning = w.handler
+    )
+  , warning = W
+  )
+}
+
+result <- cluster_peak_assessment(
+  sample_selector_column_name = sample_selector_column_name
+, sample_selector_value       = sample_selector_value      
+, sample_metadata_path        = sample_metadata_path  
+, variable_metadata_path      = variable_metadata_path
+, data_matrix_path            = data_matrix_path      
+, output_pdf                  = output_pdf            
+, output_tsv                  = output_tsv            
+, output_rdata                = output_rdata                 
+, failure_action              = my_print
+)
+
+
+my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ",
+    as.character(result), "\n", sep = "")
+
+##--------
+## Closing
+##--------
+
+my_print("\nEnd of '", modNamC, "' Galaxy module call: ",
+    as.character(Sys.time()), "\n", sep = "")
+
+#sink()
+
+if (!file.exists(output_pdf)) {
+  print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, output_pdf))
+}
+
+if (!file.exists(output_tsv)) {
+  print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, output_tsv))
+}
+
+if (!file.exists(output_rdata)) {
+  print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, output_rdata))
+}
+
+# 'stop' causes Rscript to return a non-zero exit code
+if( !result ) {
+  stop(sprintf("ERROR %s::w4m_filter_by_sample_class - method failed", modNamC))
+}
+
+# exit with status code zero
+q(save = "no", status = 0, runLast = FALSE)