diff checkformat_wrapper.R @ 0:059eb452931e draft

planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/checkformat_wrapper.R	Tue Oct 24 08:44:02 2017 -0400
@@ -0,0 +1,107 @@
+#!/usr/bin/env Rscript
+
+library(batch) ## parseCommandArgs
+
+source_local <- function(fname){
+    argv <- commandArgs(trailingOnly = FALSE)
+    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+    source(paste(base_dir, fname, sep="/"))
+}
+
+source_local("checkformat_script.R")
+
+argVc <- unlist(parseCommandArgs(evaluate = FALSE))
+
+
+##------------------------------
+## Initializing
+##------------------------------
+
+## options
+##--------
+
+strAsFacL <- options()$stringsAsFactors
+options(stringsAsFactors = FALSE)
+
+## constants
+##----------
+
+modNamC <- "Check Format" ## module name
+
+## log file
+##---------
+
+sink(argVc["information"])
+
+cat("\nStart of the '", modNamC, "' Galaxy module call: ",
+    format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
+
+
+##------------------------------
+## Computation
+##------------------------------
+
+
+resLs <- readAndCheckF(argVc["dataMatrix_in"],
+                       argVc["sampleMetadata_in"],
+                       argVc["variableMetadata_in"])
+chkL <- resLs[["chkL"]]
+
+
+##------------------------------
+## Ending
+##------------------------------
+
+
+if(chkL) {
+
+    cat("\nTable formats are OK; enjoy your analyses!\n", sep="")
+
+    cat("\nEnd of the '", modNamC, "' Galaxy module call: ",
+        format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
+
+    cat("\n\n\n============================================================================")
+    cat("\nAdditional information about the call:\n")
+    cat("\n1) Parameters:\n")
+    print(cbind(value = argVc))
+    
+    cat("\n2) Session Info:\n")
+    sessioninfo <- sessionInfo()
+    cat(sessioninfo$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$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
+    
+    cat("============================================================================\n")
+    
+    sink()
+    
+} else {
+    
+    cat("\n\n\n============================================================================")
+    cat("\nAdditional information about the call:\n")
+    cat("\n1) Parameters:\n")
+    print(cbind(value = argVc))
+    
+    cat("\n2) Session Info:\n")
+    sessioninfo <- sessionInfo()
+    cat(sessioninfo$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()
+    stop("Please check the generated 'information' file")
+
+}
+
+## closing
+##--------
+
+options(stringsAsFactors = strAsFacL)
+
+rm(list = ls())