Mercurial > repos > eschen42 > xcms_refine

comparison xcms_refine.r @ 0:ae9ef9219aae draft default tip

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 2f3f29dbaaa8568b40818d3476159c384f1a21d6-dirty"
author eschen42
date Fri, 12 Feb 2021 18:05:29 +0000
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-1:000000000000 0:ae9ef9219aae
1 #!/usr/bin/env Rscript
2
3 # ----- LOG FILE -----
4 log_file=file("log.txt", open = "wt")
5 sink(log_file)
6 sink(log_file, type = "output")
7
8
9 # ----- PACKAGE -----
10 cat("\tSESSION INFO\n")
11
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="/")) }
14 source_local("lib.r")
15
16 pkgs <- c("xcms","batch","RColorBrewer")
17 loadAndDisplayPackages(pkgs)
18 cat("\n\n");
19
20 # ----- EXPLORE NAMESPACE -----
21 # cat("\tXCMS NAMESPACE INFO\n")
22 # ls(asNamespace("xcms"))
23
24 # ----- ARGUMENTS -----
25 cat("\tARGUMENTS INFO\n")
26 args <- parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
27 write.table(as.matrix(args), col.names=F, quote=F, sep='\t')
28
29 cat("\n\n")
30
31 # ----- PROCESSING INFILE -----
32 cat("\tARGUMENTS PROCESSING INFO\n")
33
34 #saving the specific parameters
35 args_method <- args$method
36 args_image <- args$image
37 args_msLevel <- args$msLevel
38 #args[c('method','image','msLevel')] <- NULL
39 param_args <- list()
40
41 if ( args_method == "CleanPeaks" ) {
42 param_args$maxPeakwidth <- as.numeric(args$maxPeakwidth)
43 if (is.na(as.numeric(param_args$maxPeakwidth))) stop("\n\nERROR: The maxPeakwidth argument cannot be coerced to a numeric value.")
44 } else if ( args_method == "FilterIntensity" ) {
45 param_args$threshold <- as.numeric(args$threshold)
46 if (is.na(as.numeric(param_args$threshold))) stop("\n\nERROR: The threshold argument cannot be coerced to a numeric value.")
47 param_args$nValues <- as.numeric(args$nValues)
48 if (is.na(as.numeric(param_args$nValues))) stop("\n\nERROR: The nValues argument cannot be coerced to a numeric value.")
49 if (as.integer(param_args$nValues) != param_args$nValues) stop("\n\nERROR: The nValues argument is not an integer value.")
50 param_args$value <- args$value
51 } else if ( args_method == "MergeNeighboringPeaks" ) {
52 if (is.na(as.numeric(args$expandRt))) stop("\n\nERROR: The expandRt argument cannot be coerced to a numeric value.")
53 if (is.na(as.numeric(args$expandMz))) stop("\n\nERROR: The expandMz argument cannot be coerced to a numeric value.")
54 if (is.na(as.numeric(args$ppm))) stop("\n\nERROR: The ppm argument cannot be coerced to a numeric value.")
55 if (is.na(as.numeric(args$minProp))) stop("\n\nERROR: The minProp argument cannot be coerced to a numeric value.")
56 param_args$expandRt <- args$expandRt
57 param_args$expandMz <- args$expandMz
58 param_args$ppm <- args$ppm
59 param_args$minProp <- args$minProp
60 }
61
62 cat("\n\n")
63
64
65 # ----- ARGUMENTS PROCESSING -----
66 cat("\tINFILE PROCESSING INFO\n")
67
68 #image is an .RData file necessary to use xset variable given by previous tools
69 load(args_image)
70 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.*")
71
72 # Handle infiles
73 if (!exists("singlefile")) singlefile <- NULL
74 if (!exists("zipfile")) zipfile <- NULL
75 rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args)
76 zipfile <- rawFilePath$zipfile
77 singlefile <- rawFilePath$singlefile
78
79 cat("\n\n")
80
81
82 # ----- MAIN PROCESSING INFO -----
83 cat("\tMAIN PROCESSING INFO\n")
84
85
86 cat("\t\tPREPARE PARAMETERS\n\n")
87
88 if ( args_method == "CleanPeaks" ) {
89 refineChromPeaksParam <- CleanPeaksParam(maxPeakwidth = param_args$maxPeakwidth)
90 } else if ( args_method == "FilterIntensity" ) {
91 refineChromPeaksParam <- FilterIntensityParam(
92 threshold = param_args$threshold,
93 nValues = param_args$nValues,
94 value = param_args$value
95 )
96 } else if ( args_method == "MergeNeighboringPeaks" ) {
97 refineChromPeaksParam <- MergeNeighboringPeaksParam(
98 expandRt = param_args$expandRt,
99 expandMz = param_args$expandMz,
100 ppm = param_args$ppm,
101 minProp = param_args$minProp
102 )
103 }
104
105 cat(str(refineChromPeaksParam))
106
107 cat("\n\n\t\tCOMPUTE\n")
108
109 # cat("\t\t\tACE DEBUG show the xdata\n")
110 # cat(str(xdata))
111 # cat("\n\t\t\tACE DEBUG (end show the xdata)\n")
112
113 # cat("\t\t\tACE DEBUG show updateObject(xdata)\n")
114 xdata <- updateObject(xdata)
115 # cat(str(xdata))
116 # cat("\n\t\t\tACE DEBUG (end show updateObject(xdata))\n")
117 #
118 # cat("\t\t\tACE DEBUG show the param_args\n")
119 # cat(str(param_args))
120 # cat("\n\t\t\tACE DEBUG (end show the param_args)\n")
121 #
122 # cat("\t\t\tACE DEBUG show the refineChromPeaksParam\n")
123 # cat(str(refineChromPeaksParam))
124 # cat("\n\t\t\tACE DEBUG (end show the refineChromPeaksParam)\n")
125 #
126 # cat("\t\t\tACE DEBUG show the slotNames\n")
127 # cat(str(slotNames(refineChromPeaksParam)))
128 # cat("\n\t\t\tACE DEBUG (end show the slotNames)\n")
129
130 # # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or args_method ...
131 # param_args <- param_args[names(param_args) %in% slotNames(do.call(paste0(args_method,"Param"), param_args))]
132 #
133 # refineChromPeaksParam <- do.call(paste0(args_method,"Param"), param_args)
134 # print(refineChromPeaksParam)
135
136 # cat("\t\t\tACE DEBUG invoke refineChromPeaks\n")
137 xdata <- refineChromPeaks(xdata, param = refineChromPeaksParam)
138 # cat("\t\t\tACE DEBUG returned from refineChromPeaks\n")
139 #
140 #
141 # cat("\t\tDRAW GRAPHICS\n")
142 # getPlotChromPeakDensity(xdata, param = groupChromPeaksParam)
143 #
144 # if (exists("intval")) {
145 # getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv")
146 # }
147 #
148 cat("\n\n")
149
150 # ----- EXPORT -----
151
152 cat("\tXCMSnExp OBJECT INFO\n")
153 print(xdata)
154 cat("\n\n")
155
156 cat("\txcmsSet OBJECT INFO\n")
157 # Get the legacy xcmsSet object
158 xset <- getxcmsSetObject(xdata)
159 print(xset)
160 cat("\n\n")
161
162 #saving R data in .Rdata file to save the variables used in the present tool
163 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
164 save(list=objects2save[objects2save %in% ls()], file="xcmsSet.RData")
165
166 cat("\n\n")
167
168
169 cat("\tDONE\n")