diff profia_wrapper.R @ 3:5215be2bdc9e draft

planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29

--- a/profia_wrapper.R	Thu Jun 29 09:21:32 2017 -0400
+++ b/profia_wrapper.R	Tue Jan 09 12:44:23 2018 -0500
@@ -1,262 +1,266 @@
-#!/usr/bin/env Rscript
-
-library(batch) ## parseCommandArgs
-
-argVc <- unlist(parseCommandArgs(evaluate=FALSE))
-
-##------------------------------
-## Initializing
-##------------------------------
-
-
-## libraries
-##----------
-
-suppressMessages(library(proFIA))
-
-
-## constants
-##----------
-
-modNamC <- "proFIA" ## module name
-
-
-## log file
-##---------
-
-sink(argVc["information"])
-
-cat("\nStart of the '", modNamC, "' Galaxy module call: ",
-    format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
-
-
-## arguments
-##----------
-
-
-if("zipfile" %in% names(argVc)) {
-    
-    zipfile <- argVc["zipfile"]
-
-    ## We unzip automatically the raw files from the zip file
-    
-    if(exists("zipfile") && (zipfile!="")) {
-        if(!file.exists(zipfile)){
-            error_message=paste("Cannot access the Zip file:", zipfile)
-            print(error_message)
-            stop(error_message)
-        }
-
-        ## unzip
-
-        suppressWarnings(unzip(zipfile, unzip="unzip"))
-        
-        ## get the directory name
-        
-        filesInZip=unzip(zipfile, list=T);
-        directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
-        directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
-        directory = "."
-        if (length(directories) == 1) directory = directories
-        
-        cat("files_root_directory\t",directory,"\n")
-        
-    }
-
-} else if ("library" %in% names(argVc)) {
-
-    directory <- argVc["library"]
-    
-    if(!file.exists(directory)) {
-        
-        error_message=paste("Cannot access the directory:", directory,". Please check that the directory really exists.")
-        print(error_message)
-        stop(error_message)
-        
-    }
-    
-} else {
-
-    error_message <- "No zipfile nor input library available"
-    print(error_message)
-    stop(error_message)
-
-}
-
-##------------------------------
-## Computations
-##------------------------------
-
-
-optWrnN <- options()$warn
-options(warn = -1)
-
-stpI <- 1
-
-cat("\n", stpI, ") Peak detection step ('proFIAset'):\n", sep = "")
-
-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 = FALSE)
-    } 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 = FALSE)
-    }
-} 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 = FALSE)
-    } 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 = FALSE)
-    }
-}
-
-stpI <- stpI + 1
-
-cat("\n", stpI, ") Peak alignment ('group.FIA'):\n", sep = "")
-
-fiaset <- group.FIA(fiaset,
-                    ppmGroup = as.numeric(argVc["ppmGroupN"]),
-                    dmz = as.numeric(argVc["dmzGroupN"]),
-                    fracGroup = as.numeric(argVc["fracGroupN"]))
-
-stpI <- stpI + 1
-
-cat("\n", stpI, ") Creating the peak table ('makeDataMatrix'):\n", sep = "")
-
-fiaset <- makeDataMatrix(fiaset,
-                         maxo = FALSE)
-
-stpI <- stpI + 1
-
-kI <- as.integer(argVc["kI"])
-
-
-###TODO add the two method for imputation.
-if(kI > 0) {
-
-    cat("\n", stpI, ") Imputing missing values ('imputeMissingValues.WKNN_TN'):\n", sep = "")
-
-    fiaset <- imputeMissingValues.WKNN_TN(fiaset,
-                                          k = kI)
-
-    stpI <- stpI + 1
-}
-
-options(warn = optWrnN)
-
-
-##------------------------------
-## Ending
-##------------------------------
-
-
-## Plotting
-##---------
-
-cat("\n", stpI, ") Plotting ('plot'):\n", sep = "")
-
-pdf(argVc["figure"])
-
-plot(fiaset)
-
-dev.off()
-
-stpI <- stpI + 1
-
-## Printing
-##---------
-
-cat("\n", stpI, ") Printing ('show'):\n", sep = "")
-
-fiaset
-
-stpI <- stpI + 1
-
-## Exporting
-##----------
-
-cat("\n", stpI, ") Exporting ('exportDataMatrix', 'exportSampleMetadata', 'exportVariableMetadata'):\n", sep = "")
-
-datMN <- exportDataMatrix(fiaset)
-samDF <- exportSampleMetadata(fiaset)
-varDF <- exportVariableMetadata(fiaset)
-
-if(nrow(datMN) == nrow(samDF) && ncol(datMN) == nrow(varDF)) {
-    datDF <- as.data.frame(t(datMN))
-} else {
-    datDF <- as.data.frame(datMN)
-}
-rownames(varDF) <- rownames(datDF)
-
-datDF <- cbind.data.frame(dataMatrix = rownames(datDF),
-                          datDF)
-write.table(datDF,
-            file = argVc["dataMatrix_out"],
-            quote = FALSE,
-            row.names = FALSE,
-            sep = "\t")
-
-samDF <- cbind.data.frame(sampleMetadata = samDF[, "sampleID"],
-                          class = samDF[, "class"])
-write.table(samDF,
-            file = argVc["sampleMetadata_out"],
-            quote = FALSE,
-            row.names = FALSE,
-            sep = "\t")
-
-varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
-                          varDF)
-write.table(varDF,
-            file = argVc["variableMetadata_out"],
-            quote = FALSE,
-            row.names = FALSE,
-            sep = "\t")
-
-
-## Closing
-##--------
-
-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$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
-
-cat("============================================================================\n")
-
-sink()
-
-rm(list = ls())
+#!/usr/bin/env Rscript
+
+library(batch) ## parseCommandArgs
+
+argVc <- unlist(parseCommandArgs(evaluate=FALSE))
+
+##------------------------------
+## Initializing
+##------------------------------
+
+
+## libraries
+##----------
+
+suppressMessages(library(proFIA))
+
+
+## constants
+##----------
+
+modNamC <- "proFIA" ## module name
+
+
+## log file
+##---------
+
+sink(argVc["information"])
+
+cat("\nStart of the '", modNamC, "' Galaxy module call: ",
+    format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
+
+
+## arguments
+##----------
+
+
+if("zipfile" %in% names(argVc)) {
+    
+    zipfile <- argVc["zipfile"]
+
+    ## We unzip automatically the raw files from the zip file
+    
+    if(exists("zipfile") && (zipfile!="")) {
+        if(!file.exists(zipfile)){
+            error_message=paste("Cannot access the Zip file:", zipfile)
+            print(error_message)
+            stop(error_message)
+        }
+
+        ## unzip
+
+        suppressWarnings(unzip(zipfile, unzip="unzip"))
+        
+        ## get the directory name
+        
+        filesInZip=unzip(zipfile, list=T);
+        directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
+        directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
+        directory = "."
+        if (length(directories) == 1) directory = directories
+        
+        cat("files_root_directory\t",directory,"\n")
+        
+    }
+
+} else if ("library" %in% names(argVc)) {
+
+    directory <- argVc["library"]
+    
+    if(!file.exists(directory)) {
+        
+        error_message=paste("Cannot access the directory:", directory,". Please check that the directory really exists.")
+        print(error_message)
+        stop(error_message)
+        
+    }
+    
+} else {
+
+    error_message <- "No zipfile nor input library available"
+    print(error_message)
+    stop(error_message)
+
+}
+
+##------------------------------
+## Computations
+##------------------------------
+
+
+optWrnN <- options()$warn
+options(warn = -1)
+
+stpI <- 1
+
+cat("\n", stpI, ") Peak detection step ('proFIAset'):\n", sep = "")
+
+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
+
+cat("\n", stpI, ") Peak alignment ('group.FIA'):\n", sep = "")
+
+fiaset <- group.FIA(fiaset,
+                    ppmGroup = as.numeric(argVc["ppmGroupN"]),
+                    dmz = as.numeric(argVc["dmzGroupN"]),
+                    fracGroup = as.numeric(argVc["fracGroupN"]))
+
+stpI <- stpI + 1
+
+cat("\n", stpI, ") Creating the peak table ('makeDataMatrix'):\n", sep = "")
+
+fiaset <- makeDataMatrix(fiaset,
+                         maxo = FALSE)
+
+stpI <- stpI + 1
+
+
+if(argVc["imputeC"] == "randomForest") {
+
+    cat("\n", stpI, ") Imputing missing values ('impute.randomForest'):\n", sep = "")
+
+    set.seed(123)
+
+    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)
+
+
+##------------------------------
+## Ending
+##------------------------------
+
+
+## Plotting
+##---------
+
+cat("\n", stpI, ") Plotting ('plot'):\n", sep = "")
+
+pdf(argVc["figure"])
+
+plot(fiaset)
+
+dev.off()
+
+stpI <- stpI + 1
+
+## Printing
+##---------
+
+cat("\n", stpI, ") Printing ('show'):\n", sep = "")
+
+fiaset
+
+stpI <- stpI + 1
+
+## Exporting
+##----------
+
+cat("\n", stpI, ") Exporting ('exportDataMatrix', 'exportSampleMetadata', 'exportVariableMetadata'):\n", sep = "")
+
+datMN <- exportDataMatrix(fiaset)
+samDF <- exportSampleMetadata(fiaset)
+varDF <- exportVariableMetadata(fiaset)
+
+if(nrow(datMN) == nrow(samDF) && ncol(datMN) == nrow(varDF)) {
+    datDF <- as.data.frame(t(datMN))
+} else {
+    datDF <- as.data.frame(datMN)
+}
+rownames(varDF) <- rownames(datDF)
+
+datDF <- cbind.data.frame(dataMatrix = rownames(datDF),
+                          datDF)
+write.table(datDF,
+            file = argVc["dataMatrix_out"],
+            quote = FALSE,
+            row.names = FALSE,
+            sep = "\t")
+
+samDF <- cbind.data.frame(sampleMetadata = samDF[, "sampleID"],
+                          class = samDF[, "class"])
+write.table(samDF,
+            file = argVc["sampleMetadata_out"],
+            quote = FALSE,
+            row.names = FALSE,
+            sep = "\t")
+
+varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
+                          varDF)
+write.table(varDF,
+            file = argVc["variableMetadata_out"],
+            quote = FALSE,
+            row.names = FALSE,
+            sep = "\t")
+
+
+## Closing
+##--------
+
+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())