Mercurial > repos > ethevenot > transformation
view transformation_wrapper.R @ 3:cc0e9eff0de2 draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 60ebb3e8919c09c18f89a5362750ae45ca84d0c2
author | ethevenot |
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date | Wed, 28 Feb 2018 09:15:47 -0500 |
parents | 0ccfc3e15710 |
children |
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#!/usr/bin/env Rscript library(batch) ## parseCommandArgs # Constants argv <- commandArgs(trailingOnly = FALSE) script.path <- sub("--file=","",argv[grep("--file=",argv)]) prog.name <- basename(script.path) # Print help if (length(grep('-h', argv)) >0) { cat("Usage:", prog.name, "dataMatrix_in myDataMatrixInput.tsv", "method log2|log10|sqrt", "dataMatrix_out myDataMatrixOutput.tsv", "information information.txt", "\n") quit(status = 0) } 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("transformation_script.R") argVc <- unlist(parseCommandArgs(evaluate=FALSE)) ##------------------------------ ## Initializing ##------------------------------ ## options ##-------- strAsFacL <- options()[["stringsAsFactors"]] options(stringsAsFactors=FALSE) ## constants ##---------- modNamC <- "Transformation" ## module name ## log file ##--------- sink(argVc[["information"]]) cat("\nStart of the '", modNamC, "' module: ", format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="") ## loading ##-------- datMN <- t(as.matrix(read.table(argVc[["dataMatrix_in"]], check.names = FALSE, header = TRUE, row.names = 1, sep = "\t"))) metC <- argVc[["method"]] ##------------------------------ ## Computation ##------------------------------ datMN <- transformF(datMN = datMN, ## dataMatrix metC = metC) ## transformation method ##------------------------------ ## Ending ##------------------------------ ## saving ##------- datDF <- cbind.data.frame(dataMatrix = colnames(datMN), as.data.frame(t(datMN))) write.table(datDF, file = argVc[["dataMatrix_out"]], quote = FALSE, row.names = FALSE, sep = "\t") ## ending ##------- 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() options(stringsAsFactors = strAsFacL) rm(list = ls())