Mercurial > repos > lecorguille > xcms_fillpeaks

comparison xcms_fillpeaks.r @ 18:27fbe73c4279 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
author lecorguille
date Mon, 11 Feb 2019 06:11:33 -0500
parents 91c71f3808f3
children 05d322d6facb
comparison
equal deleted inserted replaced
17:b6b62413936f 18:27fbe73c4279
10 cat("\tSESSION INFO\n") 10 cat("\tSESSION INFO\n")
11 11
12 #Import the different functions 12 #Import the different functions
13 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } 13 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
14 source_local("lib.r") 14 source_local("lib.r")
15 source_local("lib-xcms3.x.x.r")
16 15
17 pkgs <- c("xcms","batch") 16 pkgs <- c("xcms","batch")
18 loadAndDisplayPackages(pkgs) 17 loadAndDisplayPackages(pkgs)
19 cat("\n\n"); 18 cat("\n\n");
20 19
65 checkFilesCompatibilityWithXcms(directory) 64 checkFilesCompatibilityWithXcms(directory)
66 65
67 66
68 cat("\n\n") 67 cat("\n\n")
69 68
70
71 # ----- MAIN PROCESSING INFO ----- 69 # ----- MAIN PROCESSING INFO -----
72 cat("\tMAIN PROCESSING INFO\n") 70 cat("\tMAIN PROCESSING INFO\n")
73 71
74 72
75 cat("\t\tCOMPUTE\n") 73 cat("\t\tCOMPUTE\n")
78 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ... 76 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
79 args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))] 77 args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))]
80 78
81 fillChromPeaksParam <- do.call(paste0(method,"Param"), args) 79 fillChromPeaksParam <- do.call(paste0(method,"Param"), args)
82 print(fillChromPeaksParam) 80 print(fillChromPeaksParam)
81
82 # back compatibility between xcms-3.0.0 and xcms-3.5.2
83 xdata <- updateObject(xdata)
84
83 xdata <- fillChromPeaks(xdata, param=fillChromPeaksParam) 85 xdata <- fillChromPeaks(xdata, param=fillChromPeaksParam)
84 86
85 if (exists("intval")) { 87 if (exists("intval")) {
86 getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv") 88 getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv")
87 } 89 }