#!/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())