diff xcms_fillpeaks.r @ 26:bb9ee352fce0 draft

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e

--- a/xcms_fillpeaks.r	Wed Apr 07 10:34:07 2021 +0000
+++ b/xcms_fillpeaks.r	Mon Sep 11 09:15:33 2023 +0000
@@ -11,19 +11,21 @@
 
 #Import the different functions
 source_local <- function(fname) {
-  argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/"))
+  argv <- commandArgs(trailingOnly = FALSE)
+  base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+  source(paste(base_dir, fname, sep = "/"))
 }
 source_local("lib.r")
 
 pkgs <- c("xcms", "batch")
 loadAndDisplayPackages(pkgs)
-cat("\n\n");
+cat("\n\n")
 
 
 # ----- ARGUMENTS -----
 cat("\tARGUMENTS INFO\n")
 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
-write.table(as.matrix(args), col.names = F, quote = F, sep = "\t")
+write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
 
 cat("\n\n")
 
@@ -81,7 +83,7 @@
 xdata <- fillChromPeaks(xdata, param = fillChromPeaksParam)
 
 if (exists("intval")) {
-    getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv")
+  getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv")
 }
 
 cat("\n\n")