diff w4mclassfilter_wrapper.R @ 0:bab3a658f74e draft

planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/w4mclassfilter_wrapper.R	Tue May 09 18:34:35 2017 -0400
@@ -0,0 +1,148 @@
+#!/usr/bin/env Rscript
+
+library(batch) ## parseCommandArgs
+
+########
+# MAIN #
+########
+
+argVc <- unlist(parseCommandArgs(evaluate=FALSE))
+
+##------------------------------
+## Initializing
+##------------------------------
+
+## options
+##--------
+
+strAsFacL <- options()$stringsAsFactors
+options(stringsAsFactors = FALSE)
+
+## libraries
+##----------
+
+suppressMessages(library(w4mclassfilter))
+
+if(packageVersion("w4mclassfilter") < "0.98.0")
+    stop("Please use 'w4mclassfilter' versions of 0.98.0 and above")
+
+## constants
+##----------
+
+modNamC <- "w4mclassfilter" ## module name
+
+topEnvC <- environment()
+flgC <- "\n"
+
+## functions
+##----------
+
+flgF <- function(tesC,
+                 envC = topEnvC,
+                 txtC = NA) { ## management of warning and error messages
+
+    tesL <- eval(parse(text = tesC), envir = envC)
+
+    if(!tesL) {
+
+        #sink(NULL)
+        stpTxtC <- ifelse(is.na(txtC),
+                          paste0(tesC, " is FALSE"),
+                          txtC)
+
+        stop(stpTxtC,
+             call. = FALSE)
+
+    }
+
+} ## flgF
+
+
+## log file
+##---------
+
+information <- as.character(argVc["information"])
+
+#sink(information)
+
+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
+
+dataMatrix_in <- as.character(argVc["dataMatrix_in"])
+dataMatrix_out <- as.character(argVc["dataMatrix_out"])
+
+sampleMetadata_in <- as.character(argVc["sampleMetadata_in"])
+sampleMetadata_out <- as.character(argVc["sampleMetadata_out"])
+
+variableMetadata_in <- as.character(argVc["variableMetadata_in"])
+variableMetadata_out <- as.character(argVc["variableMetadata_out"])
+
+# other parameters
+
+sampleclassNames <- as.character(argVc["sampleclassNames"])
+# if (sampleclassNames == "NONE_SPECIFIED") {
+#     sampleclassNames <- as.character(c())
+# 
+# } else {
+#     sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]]
+# }
+sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]]
+inclusive <- as.logical(argVc["inclusive"])
+# print(sprintf("inclusive = '%s'", as.character(inclusive)))
+classnameColumn <- as.character(argVc["classnameColumn"])
+samplenameColumn <- as.character(argVc["samplenameColumn"])
+
+##------------------------------
+## Computation
+##------------------------------
+
+result <- w4m_filter_by_sample_class(
+  dataMatrix_in        = dataMatrix_in
+, sampleMetadata_in    = sampleMetadata_in
+, variableMetadata_in  = variableMetadata_in
+, dataMatrix_out       = dataMatrix_out
+, sampleMetadata_out   = sampleMetadata_out
+, variableMetadata_out = variableMetadata_out
+, classes              = sampleclassNames
+, include              = inclusive
+, class_column         = classnameColumn
+, samplename_column    = samplenameColumn
+, 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(dataMatrix_out)) {
+  print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, dataMatrix_out))
+}# else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, dataMatrix_out)) }
+
+if (!file.exists(variableMetadata_out)) {
+  print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, variableMetadata_out))
+} # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, variableMetadata_out)) }
+
+if (!file.exists(sampleMetadata_out)) {
+  print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, sampleMetadata_out))
+} # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, sampleMetadata_out)) }
+
+if( !result ) {
+  stop(sprintf("ERROR %s::w4m_filter_by_sample_class - method failed", modNamC))
+}
+
+rm(list = ls())