Mercurial > repos > workflow4metabolomics > xcms_refine

comparison xcms_refine.r @ 3:6c2798bce3eb draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
author workflow4metabolomics
date Mon, 03 Feb 2025 14:46:55 +0000
parents 20f8ebc3a391
children
comparison
equal deleted inserted replaced
2:090b33a9981c 3:6c2798bce3eb
1 #!/usr/bin/env Rscript 1 #!/usr/bin/env Rscript
2 2
3 # ----- LOG FILE ----- 3 # ----- LOG FILE -----
4 log_file <- file("log.txt", open = "wt") 4 log_file <- file("log.txt", open = "wt")
5 sink(log_file) 5 sink(log_file)
6 sink(log_file, type = "output") 6 sink(log_file, type = "output")
7 7
8 8
9 # ----- PACKAGE ----- 9 # ----- PACKAGE -----
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) { 13 source_local <- function(fname) {
14 argv <- commandArgs(trailingOnly = FALSE) 14 argv <- commandArgs(trailingOnly = FALSE)
15 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) 15 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
16 source(paste(base_dir, fname, sep = "/")) 16 source(paste(base_dir, fname, sep = "/"))
17 } 17 }
18 source_local("lib.r") 18 source_local("lib.r")
19 19
20 pkgs <- c("xcms", "batch", "RColorBrewer") 20 pkgs <- c("xcms", "batch", "RColorBrewer")
21 loadAndDisplayPackages(pkgs) 21 loadAndDisplayPackages(pkgs)
30 cat("\n\n") 30 cat("\n\n")
31 31
32 # ----- PROCESSING INFILE ----- 32 # ----- PROCESSING INFILE -----
33 cat("\tARGUMENTS PROCESSING INFO\n") 33 cat("\tARGUMENTS PROCESSING INFO\n")
34 34
35 #saving the specific parameters 35 # saving the specific parameters
36 args_method <- args$method 36 args_method <- args$method
37 args_image <- args$image 37 args_image <- args$image
38 args_msLevel <- args$msLevel 38 args_msLevel <- args$msLevel
39 param_args <- list() 39 param_args <- list()
40 40
41 if (args_method == "CleanPeaks") { 41 if (args_method == "CleanPeaks") {
42 param_args$maxPeakwidth <- args$maxPeakwidth 42 param_args$maxPeakwidth <- args$maxPeakwidth
43 } else if (args_method == "FilterIntensity") { 43 } else if (args_method == "FilterIntensity") {
44 param_args$threshold <- args$threshold 44 param_args$threshold <- args$threshold
45 param_args$value <- args$value 45 param_args$value <- args$value
46 param_args$nValues <- args$nValues 46 param_args$nValues <- args$nValues
47 } else if (args_method == "MergeNeighboringPeaks") { 47 } else if (args_method == "MergeNeighboringPeaks") {
48 param_args$expandRt <- args$expandRt 48 param_args$expandRt <- args$expandRt
49 param_args$expandMz <- args$expandMz 49 param_args$expandMz <- args$expandMz
50 param_args$ppm <- args$ppm 50 param_args$ppm <- args$ppm
51 param_args$minProp <- args$minProp 51 param_args$minProp <- args$minProp
52 } 52 }
53 53
54 cat("\n\n") 54 cat("\n\n")
55 55
56 56
57 # ----- ARGUMENTS PROCESSING ----- 57 # ----- ARGUMENTS PROCESSING -----
58 cat("\tINFILE PROCESSING INFO\n") 58 cat("\tINFILE PROCESSING INFO\n")
59 59
60 #image is an .RData file necessary to use xset variable given by previous tools 60 # image is an .RData file necessary to use xset variable given by previous tools
61 load(args_image) 61 load(args_image)
62 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. Such RData as this might have been created by an old version of XMCS 2.*") 62 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. Such RData as this might have been created by an old version of XMCS 2.*")
63 63
64 # Handle infiles 64 # Handle infiles
65 if (!exists("singlefile")) singlefile <- NULL 65 if (!exists("singlefile")) singlefile <- NULL
76 76
77 77
78 cat("\t\tPREPARE PARAMETERS\n\n") 78 cat("\t\tPREPARE PARAMETERS\n\n")
79 79
80 if (args_method == "CleanPeaks") { 80 if (args_method == "CleanPeaks") {
81 refineChromPeaksParam <- CleanPeaksParam(maxPeakwidth = param_args$maxPeakwidth) 81 refineChromPeaksParam <- CleanPeaksParam(maxPeakwidth = param_args$maxPeakwidth)
82 } else if (args_method == "FilterIntensity") { 82 } else if (args_method == "FilterIntensity") {
83 refineChromPeaksParam <- FilterIntensityParam( 83 refineChromPeaksParam <- FilterIntensityParam(
84 threshold = param_args$threshold, 84 threshold = param_args$threshold,
85 nValues = param_args$nValues, 85 nValues = param_args$nValues,
86 value = param_args$value 86 value = param_args$value
87 ) 87 )
88 } else if (args_method == "MergeNeighboringPeaks") { 88 } else if (args_method == "MergeNeighboringPeaks") {
89 refineChromPeaksParam <- MergeNeighboringPeaksParam( 89 refineChromPeaksParam <- MergeNeighboringPeaksParam(
90 expandRt = param_args$expandRt, 90 expandRt = param_args$expandRt,
91 expandMz = param_args$expandMz, 91 expandMz = param_args$expandMz,
92 ppm = param_args$ppm, 92 ppm = param_args$ppm,
93 minProp = param_args$minProp 93 minProp = param_args$minProp
94 ) 94 )
95 } 95 }
96 96
97 cat(str(refineChromPeaksParam)) 97 cat(str(refineChromPeaksParam))
98 98
99 cat("\n\n\t\tCOMPUTE\n") 99 cat("\n\n\t\tCOMPUTE\n")
114 # Get the legacy xcmsSet object 114 # Get the legacy xcmsSet object
115 xset <- getxcmsSetObject(xdata) 115 xset <- getxcmsSetObject(xdata)
116 print(xset) 116 print(xset)
117 cat("\n\n") 117 cat("\n\n")
118 118
119 #saving R data in .Rdata file to save the variables used in the present tool 119 # saving R data in .Rdata file to save the variables used in the present tool
120 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") 120 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
121 save(list = objects2save[objects2save %in% ls()], file = "xcmsSet.RData") 121 save(list = objects2save[objects2save %in% ls()], file = "xcmsSet.RData")
122 122
123 cat("\n\n") 123 cat("\n\n")
124 124