Mercurial > repos > lecorguille > xcms_plot_chromatogram
comparison xcms_plot_chromatogram.r @ 14:8846a03995d3 draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
| author | workflow4metabolomics |
|---|---|
| date | Mon, 11 Sep 2023 09:18:38 +0000 |
| parents | 024974037c4e |
| children |
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| 13:024974037c4e | 14:8846a03995d3 |
|---|---|
| 4 # ----- PACKAGE ----- | 4 # ----- PACKAGE ----- |
| 5 cat("\tSESSION INFO\n") | 5 cat("\tSESSION INFO\n") |
| 6 | 6 |
| 7 #Import the different functions | 7 #Import the different functions |
| 8 source_local <- function(fname) { | 8 source_local <- function(fname) { |
| 9 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/")) | 9 argv <- commandArgs(trailingOnly = FALSE) |
| 10 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) | |
| 11 source(paste(base_dir, fname, sep = "/")) | |
| 10 } | 12 } |
| 11 source_local("lib.r") | 13 source_local("lib.r") |
| 12 | 14 |
| 13 pkgs <- c("xcms", "batch", "RColorBrewer") | 15 pkgs <- c("xcms", "batch", "RColorBrewer") |
| 14 loadAndDisplayPackages(pkgs) | 16 loadAndDisplayPackages(pkgs) |
| 15 cat("\n\n"); | 17 cat("\n\n") |
| 16 | 18 |
| 17 | 19 |
| 18 # ----- ARGUMENTS ----- | 20 # ----- ARGUMENTS ----- |
| 19 cat("\tARGUMENTS INFO\n") | 21 cat("\tARGUMENTS INFO\n") |
| 20 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects | 22 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects |
| 21 write.table(as.matrix(args), col.names = F, quote = F, sep = "\t") | 23 write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t") |
| 22 | 24 |
| 23 cat("\n\n") | 25 cat("\n\n") |
| 24 | 26 |
| 25 # ----- PROCESSING INFILE ----- | 27 # ----- PROCESSING INFILE ----- |
| 26 cat("\tARGUMENTS PROCESSING INFO\n") | 28 cat("\tARGUMENTS PROCESSING INFO\n") |
| 50 | 52 |
| 51 cat("\t\tDRAW GRAPHICS\n") | 53 cat("\t\tDRAW GRAPHICS\n") |
| 52 | 54 |
| 53 register(SerialParam()) | 55 register(SerialParam()) |
| 54 if (!exists("chromTIC") || is.null(chromTIC)) { | 56 if (!exists("chromTIC") || is.null(chromTIC)) { |
| 55 cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") | 57 cat("\t\t\tCompute TIC\n") |
| 58 chromTIC <- chromatogram(xdata, aggregationFun = "sum") | |
| 56 } | 59 } |
| 57 if (!exists("chromBPI") || is.null(chromBPI)) { | 60 if (!exists("chromBPI") || is.null(chromBPI)) { |
| 58 cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") | 61 cat("\t\t\tCompute BPI\n") |
| 62 chromBPI <- chromatogram(xdata, aggregationFun = "max") | |
| 59 } | 63 } |
| 60 | 64 |
| 61 if (!is.null(chromTIC_adjusted)) chromTIC <- chromTIC_adjusted | 65 if (!is.null(chromTIC_adjusted)) chromTIC <- chromTIC_adjusted |
| 62 if (!is.null(chromBPI_adjusted)) chromBPI <- chromBPI_adjusted | 66 if (!is.null(chromBPI_adjusted)) chromBPI <- chromBPI_adjusted |
| 63 | 67 |