Mercurial > repos > lecorguille > xcms_fillpeaks
comparison xcms_fillpeaks.r @ 25:26d77e9ceb49 draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author | workflow4metabolomics |
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date | Wed, 07 Apr 2021 10:34:07 +0000 |
parents | 999f9db0ca2c |
children | bb9ee352fce0 |
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24:999f9db0ca2c | 25:26d77e9ceb49 |
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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){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } | 13 source_local <- function(fname) { |
14 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/")) | |
15 } | |
14 source_local("lib.r") | 16 source_local("lib.r") |
15 | 17 |
16 pkgs <- c("xcms","batch") | 18 pkgs <- c("xcms", "batch") |
17 loadAndDisplayPackages(pkgs) | 19 loadAndDisplayPackages(pkgs) |
18 cat("\n\n"); | 20 cat("\n\n"); |
19 | 21 |
20 | 22 |
21 # ----- ARGUMENTS ----- | 23 # ----- ARGUMENTS ----- |
22 cat("\tARGUMENTS INFO\n") | 24 cat("\tARGUMENTS INFO\n") |
23 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects | 25 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects |
24 write.table(as.matrix(args), col.names=F, quote=F, sep='\t') | 26 write.table(as.matrix(args), col.names = F, quote = F, sep = "\t") |
25 | 27 |
26 cat("\n\n") | 28 cat("\n\n") |
27 | 29 |
28 # ----- PROCESSING INFILE ----- | 30 # ----- PROCESSING INFILE ----- |
29 cat("\tARGUMENTS PROCESSING INFO\n") | 31 cat("\tARGUMENTS PROCESSING INFO\n") |
51 if (!hasFeatures(xdata)) stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step") | 53 if (!hasFeatures(xdata)) stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step") |
52 | 54 |
53 # Handle infiles | 55 # Handle infiles |
54 if (!exists("singlefile")) singlefile <- NULL | 56 if (!exists("singlefile")) singlefile <- NULL |
55 if (!exists("zipfile")) zipfile <- NULL | 57 if (!exists("zipfile")) zipfile <- NULL |
56 rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args) | 58 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args) |
57 zipfile <- rawFilePath$zipfile | 59 zipfile <- rawFilePath$zipfile |
58 singlefile <- rawFilePath$singlefile | 60 singlefile <- rawFilePath$singlefile |
59 | 61 |
60 | 62 |
61 cat("\n\n") | 63 cat("\n\n") |
66 | 68 |
67 cat("\t\tCOMPUTE\n") | 69 cat("\t\tCOMPUTE\n") |
68 | 70 |
69 cat("\t\t\tFilling missing peaks using default settings\n") | 71 cat("\t\t\tFilling missing peaks using default settings\n") |
70 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ... | 72 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ... |
71 args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))] | 73 args <- args[names(args) %in% slotNames(do.call(paste0(method, "Param"), list()))] |
72 | 74 |
73 fillChromPeaksParam <- do.call(paste0(method,"Param"), args) | 75 fillChromPeaksParam <- do.call(paste0(method, "Param"), args) |
74 print(fillChromPeaksParam) | 76 print(fillChromPeaksParam) |
75 | 77 |
76 # back compatibility between xcms-3.0.0 and xcms-3.5.2 | 78 # back compatibility between xcms-3.0.0 and xcms-3.5.2 |
77 xdata <- updateObject(xdata) | 79 xdata <- updateObject(xdata) |
78 register(SerialParam()) | 80 register(SerialParam()) |
79 xdata <- fillChromPeaks(xdata, param=fillChromPeaksParam) | 81 xdata <- fillChromPeaks(xdata, param = fillChromPeaksParam) |
80 | 82 |
81 if (exists("intval")) { | 83 if (exists("intval")) { |
82 getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv") | 84 getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv") |
83 } | 85 } |
84 | 86 |
95 xset <- getxcmsSetObject(xdata) | 97 xset <- getxcmsSetObject(xdata) |
96 print(xset) | 98 print(xset) |
97 cat("\n\n") | 99 cat("\n\n") |
98 | 100 |
99 #saving R data in .Rdata file to save the variables used in the present tool | 101 #saving R data in .Rdata file to save the variables used in the present tool |
100 objects2save = c("xdata","zipfile","singlefile","md5sumList","sampleNamesList") #, "chromTIC", "chromBPI", "chromTIC_adjusted", "chromBPI_adjusted") | 102 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI", "chromTIC_adjusted", "chromBPI_adjusted") |
101 save(list=objects2save[objects2save %in% ls()], file="fillpeaks.RData") | 103 save(list = objects2save[objects2save %in% ls()], file = "fillpeaks.RData") |
102 | 104 |
103 cat("\n\n") | 105 cat("\n\n") |
104 | 106 |
105 | 107 |
106 cat("\tDONE\n") | 108 cat("\tDONE\n") |