annotate xcms_fillpeaks.r @ 21:05d322d6facb draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 8ed93601e09e1db2fbaef5af29d58464b639f2a8
author lecorguille
date Tue, 09 Apr 2019 12:23:16 -0400
parents 27fbe73c4279
children 3bc94c3abb28
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
13
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
1 #!/usr/bin/env Rscript
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
2
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
3 # ----- LOG FILE -----
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
4 log_file=file("log.txt", open = "wt")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
5 sink(log_file)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
6 sink(log_file, type = "output")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
7
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
8
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
9 # ----- PACKAGE -----
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
10 cat("\tSESSION INFO\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
11
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
12 #Import the different functions
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
13 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
14 source_local("lib.r")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
15
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
16 pkgs <- c("xcms","batch")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
17 loadAndDisplayPackages(pkgs)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
18 cat("\n\n");
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
19
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
20
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
21 # ----- ARGUMENTS -----
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
22 cat("\tARGUMENTS INFO\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
23 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
24 write.table(as.matrix(args), col.names=F, quote=F, sep='\t')
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
25
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
26 cat("\n\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
27
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
28 # ----- PROCESSING INFILE -----
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
29 cat("\tARGUMENTS PROCESSING INFO\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
30
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
31 #saving the specific parameters
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
32 method <- "FillChromPeaks"
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
33
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
34 if (!is.null(args$convertRTMinute)) convertRTMinute <- args$convertRTMinute
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
35 if (!is.null(args$numDigitsMZ)) numDigitsMZ <- args$numDigitsMZ
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
36 if (!is.null(args$numDigitsRT)) numDigitsRT <- args$numDigitsRT
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
37 if (!is.null(args$intval)) intval <- args$intval
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
38 if (!is.null(args$naTOzero)) naTOzero <- args$naTOzero
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
39
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
40 cat("\n\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
41
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
42
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
43 # ----- ARGUMENTS PROCESSING -----
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
44 cat("\tINFILE PROCESSING INFO\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
45
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
46 #image is an .RData file necessary to use xset variable given by previous tools
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
47 load(args$image)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
48 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
49
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
50 #Verification of a group step before doing the fillpeaks job.
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
51 if (!hasFeatures(xdata)) stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
52
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
53 # Handle infiles
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
54 if (!exists("singlefile")) singlefile <- NULL
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
55 if (!exists("zipfile")) zipfile <- NULL
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
56 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
57 zipfile <- rawFilePath$zipfile
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
58 singlefile <- rawFilePath$singlefile
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
59 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
60
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
61 # Check some character issues
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
62 md5sumList <- list("origin" = getMd5sum(directory))
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
63 checkXmlStructure(directory)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
64 checkFilesCompatibilityWithXcms(directory)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
65
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
66
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
67 cat("\n\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
68
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
69 # ----- MAIN PROCESSING INFO -----
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
70 cat("\tMAIN PROCESSING INFO\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
71
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
72
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
73 cat("\t\tCOMPUTE\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
74
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
75 cat("\t\t\tFilling missing peaks using default settings\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
76 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
77 args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))]
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
78
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
79 fillChromPeaksParam <- do.call(paste0(method,"Param"), args)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
80 print(fillChromPeaksParam)
18
27fbe73c4279 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
lecorguille
parents: 13
diff changeset
81
27fbe73c4279 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
lecorguille
parents: 13
diff changeset
82 # back compatibility between xcms-3.0.0 and xcms-3.5.2
27fbe73c4279 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
lecorguille
parents: 13
diff changeset
83 xdata <- updateObject(xdata)
27fbe73c4279 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
lecorguille
parents: 13
diff changeset
84
13
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
85 xdata <- fillChromPeaks(xdata, param=fillChromPeaksParam)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
86
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
87 if (exists("intval")) {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
88 getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
89 }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
90
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
91 cat("\n\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
92
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
93 # ----- EXPORT -----
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
94
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
95 cat("\tXCMSnExp OBJECT INFO\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
96 print(xdata)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
97 cat("\n\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
98
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
99 cat("\txcmsSet OBJECT INFO\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
100 # Get the legacy xcmsSet object
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
101 xset <- getxcmsSetObject(xdata)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
102 print(xset)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
103 cat("\n\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
104
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
105 #saving R data in .Rdata file to save the variables used in the present tool
21
05d322d6facb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 8ed93601e09e1db2fbaef5af29d58464b639f2a8
lecorguille
parents: 18
diff changeset
106 objects2save = c("xdata","zipfile","singlefile","md5sumList","sampleNamesList") #, "chromTIC", "chromBPI", "chromTIC_adjusted", "chromBPI_adjusted")
13
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
107 save(list=objects2save[objects2save %in% ls()], file="fillpeaks.RData")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
108
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
109 cat("\n\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
110
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
111
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
112 cat("\tDONE\n")