camera_combinexsannos: lib.r annotate

annotate lib.r @ 4:4c4945bce185 draft

"planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998"

author	workflow4metabolomics
date	Thu, 22 Apr 2021 10:27:58 +0000
parents	c4c13745e797
children	2443150161b4

rev	line source
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	1 # lib.r
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	2
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	3 #@author G. Le Corguille
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	4 # solve an issue with batch if arguments are logical TRUE/FALSE
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	5 parseCommandArgs <- function(...) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	6 args <- batch::parseCommandArgs(...)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	7 for (key in names(args)) {
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	8 if (args[key] %in% c("TRUE", "FALSE"))
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	9 args[key] <- as.logical(args[key])
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	10 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	11 return(args)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	12 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	13
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	14 #@author G. Le Corguille
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	15 # This function will
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	16 # - load the packages
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	17 # - display the sessionInfo
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	18 loadAndDisplayPackages <- function(pkgs) {
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	19 for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE)))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	20
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	21 sessioninfo <- sessionInfo()
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	22 cat(sessioninfo$R.version$version.string, "\n")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	23 cat("Main packages:\n")
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	24 for (pkg in names(sessioninfo$otherPkgs)) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	25 cat(paste(pkg, packageVersion(pkg)), "\t")
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	26 }
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	27 cat("\n")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	28 cat("Other loaded packages:\n")
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	29 for (pkg in names(sessioninfo$loadedOnly)) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	30 cat(paste(pkg, packageVersion(pkg)), "\t")
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	31 }
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	32 cat("\n")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	33 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	34
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	35 # This function retrieve a xset like object
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	36 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	37 getxcmsSetObject <- function(xobject) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	38 # XCMS 1.x
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	39 if (class(xobject) == "xcmsSet")
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	40 return(xobject)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	41 # XCMS 3.x
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	42 if (class(xobject) == "XCMSnExp") {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	43 # Get the legacy xcmsSet object
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	44 suppressWarnings(xset <- as(xobject, "xcmsSet"))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	45 if (is.null(xset@phenoData$sample_group))
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	46 sampclass(xset) <- "."
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	47 else
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	48 sampclass(xset) <- xset@phenoData$sample_group
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	49 if (!is.null(xset@phenoData$sample_name))
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	50 rownames(xset@phenoData) <- xset@phenoData$sample_name
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	51 return(xset)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	52 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	53 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	54
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	55 #@author G. Le Corguille
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	56 #The function create a pdf from the different png generated by diffreport
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	57 diffreport_png2pdf <- function(filebase) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	58 dir.create("pdf")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	59
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	60 pdfEicOutput <- paste0("pdf/", filebase, "-eic_pdf.pdf")
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	61 pdfBoxOutput <- paste0("pdf/", filebase, "-box_pdf.pdf")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	62
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	63 system(paste0("gm convert ", filebase, "_eic/*.png ", pdfEicOutput))
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	64 system(paste0("gm convert ", filebase, "_box/*.png ", pdfBoxOutput))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	65
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	66 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	67
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	68 #@author G. Le Corguille
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	69 #The function create a zip archive from the different png generated by diffreport
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	70 diffreport_png2zip <- function() {
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	71 zip("eic.zip", dir(pattern = "_eic"), zip = Sys.which("zip"))
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	72 zip("box.zip", dir(pattern = "_box"), zip = Sys.which("zip"))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	73 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	74
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	75 #The function create a zip archive from the different tabular generated by diffreport
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	76 diffreport_tabular2zip <- function() {
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	77 zip("tabular.zip", dir(pattern = "tabular/*"), zip = Sys.which("zip"))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	78 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	79
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	80 #@author G. Le Corguille
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	81 #This function convert if it is required the Retention Time in minutes
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	82 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	83 if (convertRTMinute) {
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	84 #converting the retention times (seconds) into minutes
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	85 print("converting the retention times into minutes in the variableMetadata")
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	86 variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	87 variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	88 variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	89 }
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	90 return(variableMetadata)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	91 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	92
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	93 #@author G. Le Corguille
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	94 #This function format ions identifiers
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	95 formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	96 splitDeco <- strsplit(as.character(variableMetadata$name), "_")
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	97 idsDeco <- sapply(splitDeco, function(x) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	98 deco <- unlist(x)[2]; if (is.na(deco)) return("") else return(paste0("_", deco))
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	99 })
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	100 namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco))
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	101 variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))])
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	102 return(variableMetadata)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	103 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	104
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	105 #The function annotateDiffreport without the corr function which bugs
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	106 annotatediff <- function(xset = xset, args = args, variableMetadataOutput = "variableMetadata.tsv") {
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	107 # Resolve the bug with x11, with the function png
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	108 options(bitmapType = "cairo")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	109
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	110 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	111 res <- try(is.null(xset@filled))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	112
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	113 # ------ annot -------
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	114 args$calcCiS <- as.logical(args$calcCiS)
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	115 args$calcIso <- as.logical(args$calcIso)
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	116 args$calcCaS <- as.logical(args$calcCaS)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	117
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	118 # common parameters
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	119 args4annotate <- list(object = xset,
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	120 nSlaves = args$nSlaves, sigma = args$sigma, perfwhm = args$perfwhm,
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	121 maxcharge = args$maxcharge, maxiso = args$maxiso, minfrac = args$minfrac,
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	122 ppm = args$ppm, mzabs = args$mzabs, quick = args$quick,
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	123 polarity = args$polarity, max_peaks = args$max_peaks, intval = args$intval)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	124
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	125 if (args$quick == FALSE) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	126 args4annotate <- append(args4annotate,
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	127 list(graphMethod = args$graphMethod, cor_eic_th = args$cor_eic_th, pval = args$pval,
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	128 calcCiS = args$calcCiS, calcIso = args$calcIso, calcCaS = args$calcCaS))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	129 # no ruleset
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	130 if (!is.null(args$multiplier)) {
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	131 args4annotate <- append(args4annotate,
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	132 list(multiplier = args$multiplier))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	133 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	134 # ruleset
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	135 else {
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	136 rulset <- read.table(args$rules, h = T, sep = ";")
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	137 if (ncol(rulset) < 4) rulset <- read.table(args$rules, h = T, sep = "\t")
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	138 if (ncol(rulset) < 4) rulset <- read.table(args$rules, h = T, sep = ",")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	139 if (ncol(rulset) < 4) {
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	140 error_message <- "Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation"
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	141 print(error_message)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	142 stop(error_message)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	143 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	144
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	145 args4annotate <- append(args4annotate,
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	146 list(rules = rulset))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	147 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	148 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	149
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	150
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	151 # launch annotate
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	152 xa <- do.call("annotate", args4annotate)
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	153 peakList <- getPeaklist(xa, intval = args$intval)
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	154 peakList <- cbind(groupnames(xa@xcmsSet), peakList); colnames(peakList)[1] <- c("name");
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	155
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	156 # --- Multi condition : diffreport ---
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	157 diffrepOri <- NULL
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	158 if (!is.null(args$runDiffreport) & nlevels(sampclass(xset)) >= 2) {
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	159 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	160 res <- try(is.null(xset@filled))
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	161 classes <- levels(sampclass(xset))
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	162 x <- 1:(length(classes) - 1)
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	163 for (i in seq(along = x)) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	164 y <- 1:(length(classes))
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	165 for (n in seq(along = y)) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	166 if (i + n <= length(classes)) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	167 filebase <- paste(classes[i], class2 = classes[i + n], sep = "-vs-")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	168
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	169 diffrep <- diffreport(
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	170 object = xset, class1 = classes[i], class2 = classes[i + n],
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	171 filebase = filebase, eicmax = args$eicmax, eicwidth = args$eicwidth,
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	172 sortpval = TRUE, value = args$value, h = args$h, w = args$w, mzdec = args$mzdec, missing = 0)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	173
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	174 diffrepOri <- diffrep
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	175
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	176 # renamming of the column rtmed to rt to fit with camera peaklist function output
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	177 colnames(diffrep)[colnames(diffrep) == "rtmed"] <- "rt"
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	178 colnames(diffrep)[colnames(diffrep) == "mzmed"] <- "mz"
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	179
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	180 # combines results and reorder columns
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	181 diffrep <- merge(peakList, diffrep[, c("name", "fold", "tstat", "pvalue")], by.x = "name", by.y = "name", sort = F)
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	182 diffrep <- cbind(diffrep[, !(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))], diffrep[, (colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))])
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	183
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	184 diffrep <- RTSecondToMinute(diffrep, args$convertRTMinute)
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	185 diffrep <- formatIonIdentifiers(diffrep, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	186
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	187 if (args$sortpval) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	188 diffrep <- diffrep[order(diffrep$pvalue), ]
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	189 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	190
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	191 dir.create("tabular", showWarnings = FALSE)
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	192 write.table(diffrep, sep = "\t", quote = FALSE, row.names = FALSE, file = paste("tabular/", filebase, "_tsv.tabular", sep = ""))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	193
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	194 if (args$eicmax != 0) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	195 if (args$png2 == "pdf")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	196 diffreport_png2pdf(filebase)
2 c4c13745e797 "planemo upload commit f978cc0a7aa81c244591e560f44970f0d61bf74e" workflow4metabolomics parents: 1 diff changeset	197 if (args$png2 == "zip")
c4c13745e797 "planemo upload commit f978cc0a7aa81c244591e560f44970f0d61bf74e" workflow4metabolomics parents: 1 diff changeset	198 diffreport_png2zip()
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	199 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	200 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	201 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	202 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	203 if (args$tabular2 == "zip")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	204 diffreport_tabular2zip()
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	205 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	206
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	207 # --- variableMetadata ---
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	208 variableMetadata <- peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	209 variableMetadata <- RTSecondToMinute(variableMetadata, args$convertRTMinute)
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	210 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	211 # if we have 2 conditions, we keep stat of diffrep
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	212 if (!is.null(args$runDiffreport) & nlevels(sampclass(xset)) == 2) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	213 variableMetadata <- merge(variableMetadata, diffrep[, c("name", "fold", "tstat", "pvalue")], by.x = "name", by.y = "name", sort = F)
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	214 if (exists("args[[\"sortpval\"]]")) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	215 variableMetadata <- variableMetadata[order(variableMetadata$pvalue), ]
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	216 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	217 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	218
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	219 variableMetadataOri <- variableMetadata
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	220 write.table(variableMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = variableMetadataOutput)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	221
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	222 return(list("xa" = xa, "diffrep" = diffrepOri, "variableMetadata" = variableMetadataOri));
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	223
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	224 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	225
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	226
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	227 combinexsAnnos_function <- function(xaP, xaN, diffrepP = NULL, diffrepN = NULL,
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	228 pos = TRUE, tol = 2, ruleset = NULL, keep_meta = TRUE, convertRTMinute = F, numDigitsMZ = 0,
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	229 numDigitsRT = 0, variableMetadataOutput = "variableMetadata.tsv") {
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	230
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	231 #Load the two Rdata to extract the xset objects from positive and negative mode
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	232 cat("\tObject xset from positive mode\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	233 print(xaP)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	234 cat("\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	235
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	236 cat("\tObject xset from negative mode\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	237 print(xaN)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	238 cat("\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	239
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	240 cat("\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	241 cat("\tCombining...\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	242 #Convert the string to numeric for creating matrix
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	243 row <- as.numeric(strsplit(ruleset, ",")[[1]][1])
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	244 column <- as.numeric(strsplit(ruleset, ",")[[1]][2])
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	245 ruleset <- cbind(row, column)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	246 #Test if the file comes from an older version tool
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	247 if ((!is.null(xaP)) & (!is.null(xaN))) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	248 #Launch the combinexsannos function from CAMERA
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	249 cAnnot <- combinexsAnnos(xaP, xaN, pos = pos, tol = tol, ruleset = ruleset)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	250 } else {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	251 stop("You must relauch the CAMERA.annotate step with the lastest version.")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	252 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	253
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	254 if (pos) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	255 xa <- xaP
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	256 mode <- "neg. Mode"
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	257 } else {
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	258 xa <- xaN
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	259 mode <- "pos. Mode"
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	260 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	261
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	262 peakList <- getPeaklist(xa)
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	263 peakList <- cbind(groupnames(xa@xcmsSet), peakList); colnames(peakList)[1] <- c("name");
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	264 variableMetadata <- cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup", mode)]);
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	265 variableMetadata <- variableMetadata[, !(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	266
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	267 #Test if there are more than two classes (conditions)
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	268 if (nlevels(sampclass(xaP@xcmsSet)) == 2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	269 diffrepP <- diffrepP[, c("name", "fold", "tstat", "pvalue")]; colnames(diffrepP) <- paste("P.", colnames(diffrepP), sep = "")
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	270 diffrepN <- diffrepN[, c("name", "fold", "tstat", "pvalue")]; colnames(diffrepN) <- paste("N.", colnames(diffrepN), sep = "")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	271
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	272 variableMetadata <- merge(variableMetadata, diffrepP, by.x = "name", by.y = "P.name")
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	273 variableMetadata <- merge(variableMetadata, diffrepN, by.x = "name", by.y = "N.name")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	274 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	275
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	276 rownames(variableMetadata) <- NULL
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	277 #TODO: checker colnames(variableMetadata)[1:2] = c("name", "mz/rt");
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	278
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	279 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	280 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	281
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	282 #If the user want to keep only the metabolites which match a difference
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	283 if (keep_meta) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	284 variableMetadata <- variableMetadata[variableMetadata[, c(mode)] != "", ]
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	285 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	286
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	287 #Write the output into a tsv file
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	288 write.table(variableMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = variableMetadataOutput)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	289 return(variableMetadata);
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	290
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	291 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	292
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	293 # This function get the raw file path from the arguments
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	294 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	295 if (!is.null(args$zipfile)) zipfile <- args$zipfile
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	296 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	297 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	298
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	299 if (!is.null(args$singlefile_galaxyPath)) {
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	300 singlefile_galaxyPaths <- args$singlefile_galaxyPath;
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	301 singlefile_sampleNames <- args$singlefile_sampleName
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	302 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	303 if (!is.null(args$singlefile_galaxyPathPositive)) {
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	304 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	305 singlefile_sampleNames <- args$singlefile_sampleNamePositive
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	306 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	307 if (!is.null(args$singlefile_galaxyPathNegative)) {
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	308 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	309 singlefile_sampleNames <- args$singlefile_sampleNameNegative
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	310 }
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	311 if (exists("singlefile_galaxyPaths")) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	312 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths, ","))
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	313 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames, ","))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	314
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	315 singlefile <- NULL
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	316 for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	317 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	318 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	319 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	320 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	321 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	322 for (argument in c("zipfile", "zipfilePositive", "zipfileNegative",
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	323 "singlefile_galaxyPath", "singlefile_sampleName",
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	324 "singlefile_galaxyPathPositive", "singlefile_sampleNamePositive",
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	325 "singlefile_galaxyPathNegative", "singlefile_sampleNameNegative")) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	326 args[[argument]] <- NULL
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	327 }
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	328 return(list(zipfile = zipfile, singlefile = singlefile, args = args))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	329 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	330
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	331
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	332 # This function retrieve the raw file in the working directory
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	333 # - if zipfile: unzip the file with its directory tree
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	334 # - if singlefiles: set symlink with the good filename
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	335 retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	336 if (!is.null(singlefile) && (length("singlefile") > 0)) {
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	337 for (singlefile_sampleName in names(singlefile)) {
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	338 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	339 if (!file.exists(singlefile_galaxyPath)) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	340 error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	341 print(error_message); stop(error_message)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	342 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	343
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	344 file.symlink(singlefile_galaxyPath, singlefile_sampleName)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	345 }
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	346 directory <- "."
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	347
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	348 }
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	349 if (!is.null(zipfile) && (zipfile != "")) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	350 if (!file.exists(zipfile)) {
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	351 error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	352 print(error_message)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	353 stop(error_message)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	354 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	355
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	356 #unzip
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	357 suppressWarnings(unzip(zipfile, unzip = "unzip"))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	358
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	359 #get the directory name
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	360 filesInZip <- unzip(zipfile, list = T);
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	361 directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])));
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	362 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	363 directory <- "."
4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	364 if (length(directories) == 1) directory <- directories
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	365
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	366 cat("files_root_directory\t", directory, "\n")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	367
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	368 }
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	369 return(directory)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	370 }

Mercurial > repos > workflow4metabolomics > camera_combinexsannos

annotate lib.r @ 4:4c4945bce185 draft