--- a/profia_wrapper.R	Wed May 03 10:49:08 2017 -0400
+++ b/profia_wrapper.R	Mon Jan 22 11:32:41 2018 -0500
@@ -95,9 +95,43 @@
 
 cat("\n", stpI, ") Peak detection step ('proFIAset'):\n", sep = "")
 
-fiaset <- proFIAset(directory,
-                    ppm = as.numeric(argVc["ppmN"]),
-                    parallel = TRUE)
+if("sizeMinN" %in% names(argVc) && argVc["sizeMinN"] != "none") {
+    if("scanMaxI" %in% names(argVc) && argVc["scanMaxI"] != "none") {
+        fiaset <- proFIAset(directory,
+                            ppm = as.numeric(argVc["ppmN"]),
+                            dmz = as.numeric(argVc["dmzN"]),
+                            bandCoverage = as.numeric(ifelse("bandCoverageN" %in% names(argVc), argVc["bandCoverageN"], "0.3")),
+                            sizeMin = as.numeric(argVc["sizeMinN"]),
+                            scanmin = as.numeric(ifelse("scanMinI" %in% names(argVc), argVc["scanMinI"], "1")),
+                            scanmax = as.numeric(argVc["scanMaxI"]),
+                            parallel = TRUE)
+    } else {
+        fiaset <- proFIAset(directory,
+                            ppm = as.numeric(argVc["ppmN"]),
+                            dmz = as.numeric(argVc["dmzN"]),
+                            bandCoverage = as.numeric(ifelse("bandCoverageN" %in% names(argVc), argVc["bandCoverageN"], "0.3")),
+                            sizeMin = as.numeric(argVc["sizeMinN"]),
+                            scanmin = as.numeric(ifelse("scanMinI" %in% names(argVc), argVc["scanMinI"], "1")),
+                            parallel = TRUE)
+    }
+} else {
+    if("scanMaxI" %in% names(argVc) && argVc["scanMaxI"] != "none") {
+        fiaset <- proFIAset(directory,
+                            ppm = as.numeric(argVc["ppmN"]),
+                            dmz = as.numeric(argVc["dmzN"]),
+                            bandCoverage = as.numeric(ifelse("bandCoverageN" %in% names(argVc), argVc["bandCoverageN"], "0.3")),
+                            scanmin = as.numeric(ifelse("scanMinI" %in% names(argVc), argVc["scanMinI"], "1")),
+                            scanmax = as.numeric(argVc["scanMaxI"]),
+                            parallel = TRUE)
+    } else {
+        fiaset <- proFIAset(directory,
+                            ppm = as.numeric(argVc["ppmN"]),
+                            dmz = as.numeric(argVc["dmzN"]),
+                            bandCoverage = as.numeric(ifelse("bandCoverageN" %in% names(argVc), argVc["bandCoverageN"], "0.3")),
+                            scanmin = as.numeric(ifelse("scanMinI" %in% names(argVc), argVc["scanMinI"], "1")),
+                            parallel = TRUE)
+    }
+}
 
 stpI <- stpI + 1
 
@@ -105,6 +139,7 @@
 
 fiaset <- group.FIA(fiaset,
                     ppmGroup = as.numeric(argVc["ppmGroupN"]),
+                    dmz = as.numeric(argVc["dmzGroupN"]),
                     fracGroup = as.numeric(argVc["fracGroupN"]))
 
 stpI <- stpI + 1
@@ -116,17 +151,23 @@
 
 stpI <- stpI + 1
 
-kI <- as.integer(argVc["kI"])
 
-if(kI > 0) {
+if(argVc["imputeC"] == "randomForest") {
+
+    cat("\n", stpI, ") Imputing missing values ('impute.randomForest'):\n", sep = "")
 
-    cat("\n", stpI, ") Imputing missing values ('imputeMissingValues.WKNN_TN'):\n", sep = "")
+    set.seed(123)
 
-    fiaset <- imputeMissingValues.WKNN_TN(fiaset,
-                                          k = kI)
+    fiaset <- impute.randomForest(fiaset,
+                                  parallel = FALSE)
+
+    set.seed(NULL)
 
     stpI <- stpI + 1
 }
+###TODO Fix the error message to set 'parallel' to TRUE: You must register a 'foreach' parallel backend to run 'missForest' in parallel. Set 'parallelize' to 'no' to compute serially.
+###TODO add the impute.KNN_TN method
+
 
 options(warn = optWrnN)
 
@@ -205,6 +246,21 @@
 cat("\nEnd of '", modNamC, "' Galaxy module call: ",
     as.character(Sys.time()), "\n", sep = "")
 
+cat("\n\n\n============================================================================")
+cat("\nAdditional information about the call:\n")
+cat("\n1) Parameters:\n")
+print(cbind(value = argVc))
+
+cat("\n2) Session Info:\n")
+sessioninfo <- sessionInfo()
+cat(sessioninfo$R.version$version.string,"\n")
+cat("Main packages:\n")
+for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
+cat("Other loaded packages:\n")
+for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
+
+cat("============================================================================\n")
+
 sink()
 
 rm(list = ls())