camera_combinexsannos: lib.r annotate

annotate lib.r @ 7:e461f344226c draft default tip

planemo upload commit 24d44ee26b7c23380c2b42fae2f7f6e58472100d

author	workflow4metabolomics
date	Sun, 24 Nov 2024 21:28:22 +0000
parents	2443150161b4
children

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
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	3 # @author G. Le Corguille
0 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(...) {
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	6 args <- batch::parseCommandArgs(...)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	7 for (key in names(args)) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	8 if (args[key] %in% c("TRUE", "FALSE")) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	9 args[key] <- as.logical(args[key])
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	10 }
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	11 }
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	12 return(args)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	13 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	14
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	15 # @author G. Le Corguille
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	16 # This function will
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	17 # - load the packages
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	18 # - display the sessionInfo
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	19 loadAndDisplayPackages <- function(pkgs) {
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	20 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	21
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	22 sessioninfo <- sessionInfo()
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	23 cat(sessioninfo$R.version$version.string, "\n")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	24 cat("Main packages:\n")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	25 for (pkg in names(sessioninfo$otherPkgs)) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	26 cat(paste(pkg, packageVersion(pkg)), "\t")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	27 }
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	28 cat("\n")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	29 cat("Other loaded packages:\n")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	30 for (pkg in names(sessioninfo$loadedOnly)) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	31 cat(paste(pkg, packageVersion(pkg)), "\t")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	32 }
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	33 cat("\n")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	34 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	35
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	36 # This function retrieve a xset like object
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	37 # @author Gildas Le Corguille lecorguille@sb-roscoff.fr
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	38 getxcmsSetObject <- function(xobject) {
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	39 # XCMS 1.x
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	40 if (class(xobject) == "xcmsSet") {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	41 return(xobject)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	42 }
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	43 # XCMS 3.x
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	44 if (class(xobject) == "XCMSnExp") {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	45 # Get the legacy xcmsSet object
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	46 suppressWarnings(xset <- as(xobject, "xcmsSet"))
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	47 if (is.null(xset@phenoData$sample_group)) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	48 sampclass(xset) <- "."
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	49 } else {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	50 sampclass(xset) <- xset@phenoData$sample_group
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	51 }
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	52 if (!is.null(xset@phenoData$sample_name)) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	53 rownames(xset@phenoData) <- xset@phenoData$sample_name
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	54 }
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	55 return(xset)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	56 }
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	57 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	58
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	59 # @author G. Le Corguille
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	60 # The function create a pdf from the different png generated by diffreport
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	61 diffreport_png2pdf <- function(filebase) {
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	62 dir.create("pdf")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	63
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	64 pdfEicOutput <- paste0("pdf/", filebase, "-eic_pdf.pdf")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	65 pdfBoxOutput <- paste0("pdf/", filebase, "-box_pdf.pdf")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	66
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	67 system(paste0("gm convert ", filebase, "_eic/*.png ", pdfEicOutput))
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	68 system(paste0("gm convert ", filebase, "_box/*.png ", pdfBoxOutput))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	69 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	70
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	71 # @author G. Le Corguille
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	72 # The function create a zip archive from the different png generated by diffreport
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	73 diffreport_png2zip <- function() {
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	74 zip("eic.zip", dir(pattern = "_eic"), zip = Sys.which("zip"))
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	75 zip("box.zip", dir(pattern = "_box"), zip = Sys.which("zip"))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	76 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	77
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	78 # The function create a zip archive from the different tabular generated by diffreport
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	79 diffreport_tabular2zip <- function() {
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	80 zip("tabular.zip", dir(pattern = "tabular/*"), zip = Sys.which("zip"))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	81 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	82
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	83 # @author G. Le Corguille
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	84 # This function convert if it is required the Retention Time in minutes
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	85 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	86 if (convertRTMinute) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	87 # converting the retention times (seconds) into minutes
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	88 print("converting the retention times into minutes in the variableMetadata")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	89 variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	90 variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	91 variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	92 }
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	93 return(variableMetadata)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	94 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	95
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	96 # @author G. Le Corguille
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	97 # This function format ions identifiers
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	98 formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) {
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	99 splitDeco <- strsplit(as.character(variableMetadata$name), "_")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	100 idsDeco <- sapply(splitDeco, function(x) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	101 deco <- unlist(x)[2]
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	102 if (is.na(deco)) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	103 return("")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	104 } else {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	105 return(paste0("_", deco))
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	106 }
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	107 })
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	108 namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco))
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	109 variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))])
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	110 return(variableMetadata)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	111 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	112
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	113 # The function annotateDiffreport without the corr function which bugs
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	114 annotatediff <- function(xset = xset, args = args, variableMetadataOutput = "variableMetadata.tsv") {
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	115 # Resolve the bug with x11, with the function png
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	116 options(bitmapType = "cairo")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	117
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	118 # Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	119 res <- try(is.null(xset@filled))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	120
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	121 # ------ annot -------
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	122 args$calcCiS <- as.logical(args$calcCiS)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	123 args$calcIso <- as.logical(args$calcIso)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	124 args$calcCaS <- as.logical(args$calcCaS)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	125
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	126 # common parameters
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	127 args4annotate <- list(
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	128 object = xset,
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	129 nSlaves = args$nSlaves, sigma = args$sigma, perfwhm = args$perfwhm,
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	130 maxcharge = args$maxcharge, maxiso = args$maxiso, minfrac = args$minfrac,
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	131 ppm = args$ppm, mzabs = args$mzabs, quick = args$quick,
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	132 polarity = args$polarity, max_peaks = args$max_peaks, intval = args$intval
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	133 )
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	134
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	135 if (args$quick == FALSE) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	136 args4annotate <- append(
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	137 args4annotate,
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	138 list(
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	139 graphMethod = args$graphMethod, cor_eic_th = args$cor_eic_th, pval = args$pval,
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	140 calcCiS = args$calcCiS, calcIso = args$calcIso, calcCaS = args$calcCaS
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	141 )
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	142 )
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	143 # no ruleset
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	144 if (!is.null(args$multiplier)) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	145 args4annotate <- append(
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	146 args4annotate,
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	147 list(multiplier = args$multiplier)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	148 )
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	149 } else { # ruleset
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	150 rulset <- read.table(args$rules, h = TRUE, sep = ";")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	151 if (ncol(rulset) < 4) rulset <- read.table(args$rules, h = TRUE, sep = "\t")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	152 if (ncol(rulset) < 4) rulset <- read.table(args$rules, h = TRUE, sep = ",")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	153 if (ncol(rulset) < 4) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	154 error_message <- "Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation"
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	155 print(error_message)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	156 stop(error_message)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	157 }
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	158
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	159 args4annotate <- append(
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	160 args4annotate,
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	161 list(rules = rulset)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	162 )
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	163 }
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	164 }
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	165
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	166
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	167 # launch annotate
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	168 xa <- do.call("annotate", args4annotate)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	169 peakList <- getPeaklist(xa, intval = args$intval)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	170 peakList <- cbind(groupnames(xa@xcmsSet), peakList)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	171 colnames(peakList)[1] <- c("name")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	172
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	173 # --- Multi condition : diffreport ---
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	174 diffrepOri <- NULL
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	175 if (!is.null(args$runDiffreport) && nlevels(sampclass(xset)) >= 2) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	176 # Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	177 res <- try(is.null(xset@filled))
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	178 classes <- levels(sampclass(xset))
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	179 for (i in seq_len(length(classes) - 1)) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	180 for (n in seq_len(length(classes))) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	181 if (i + n <= length(classes)) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	182 filebase <- paste(classes[i], class2 = classes[i + n], sep = "-vs-")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	183
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	184 diffrep <- diffreport(
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	185 object = xset, class1 = classes[i], class2 = classes[i + n],
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	186 filebase = filebase, eicmax = args$eicmax, eicwidth = args$eicwidth,
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	187 sortpval = TRUE, value = args$value, h = args$h, w = args$w, mzdec = args$mzdec, missing = 0
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	188 )
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	189
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	190 diffrepOri <- diffrep
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	191
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	192 # renamming of the column rtmed to rt to fit with camera peaklist function output
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	193 colnames(diffrep)[colnames(diffrep) == "rtmed"] <- "rt"
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	194 colnames(diffrep)[colnames(diffrep) == "mzmed"] <- "mz"
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	195
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	196 # combines results and reorder columns
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	197 diffrep <- merge(peakList, diffrep[, c("name", "fold", "tstat", "pvalue")], by.x = "name", by.y = "name", sort = FALSE)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	198 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	199
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	200 diffrep <- RTSecondToMinute(diffrep, args$convertRTMinute)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	201 diffrep <- formatIonIdentifiers(diffrep, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	202
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	203 if (args$sortpval) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	204 diffrep <- diffrep[order(diffrep$pvalue), ]
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	205 }
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	206
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	207 dir.create("tabular", showWarnings = FALSE)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	208 write.table(diffrep, sep = "\t", quote = FALSE, row.names = FALSE, file = paste("tabular/", filebase, "_tsv.tabular", sep = ""))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	209
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	210 if (args$eicmax != 0) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	211 if (args$png2 == "pdf") {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	212 diffreport_png2pdf(filebase)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	213 }
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	214 if (args$png2 == "zip") {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	215 diffreport_png2zip()
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	216 }
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	217 }
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	218 }
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	219 }
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	220 }
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	221 if (args$tabular2 == "zip") {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	222 diffreport_tabular2zip()
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	223 }
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	224 }
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	225
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	226 # --- variableMetadata ---
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	227 variableMetadata <- peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	228 variableMetadata <- RTSecondToMinute(variableMetadata, args$convertRTMinute)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	229 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	230 # if we have 2 conditions, we keep stat of diffrep
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	231 if (!is.null(args$runDiffreport) && nlevels(sampclass(xset)) == 2) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	232 variableMetadata <- merge(variableMetadata, diffrep[, c("name", "fold", "tstat", "pvalue")], by.x = "name", by.y = "name", sort = FALSE)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	233 if (exists("args[[\"sortpval\"]]")) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	234 variableMetadata <- variableMetadata[order(variableMetadata$pvalue), ]
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	235 }
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	236 }
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	237
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	238 variableMetadataOri <- variableMetadata
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	239 write.table(variableMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = variableMetadataOutput)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	240
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	241 return(list("xa" = xa, "diffrep" = diffrepOri, "variableMetadata" = variableMetadataOri))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	242 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	243
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	244
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	245 combinexsAnnos_function <- function(
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	246 xaP, xaN, diffrepP = NULL, diffrepN = NULL,
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	247 pos = TRUE, tol = 2, ruleset = NULL, keep_meta = TRUE, convertRTMinute = FALSE, numDigitsMZ = 0,
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	248 numDigitsRT = 0, variableMetadataOutput = "variableMetadata.tsv") {
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	249 # Load the two Rdata to extract the xset objects from positive and negative mode
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	250 cat("\tObject xset from positive mode\n")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	251 print(xaP)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	252 cat("\n")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	253
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	254 cat("\tObject xset from negative mode\n")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	255 print(xaN)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	256 cat("\n")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	257
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	258 cat("\n")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	259 cat("\tCombining...\n")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	260 # Convert the string to numeric for creating matrix
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	261 row <- as.numeric(strsplit(ruleset, ",")[[1]][1])
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	262 column <- as.numeric(strsplit(ruleset, ",")[[1]][2])
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	263 ruleset <- cbind(row, column)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	264 # Test if the file comes from an older version tool
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	265 if ((!is.null(xaP)) && (!is.null(xaN))) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	266 # Launch the combinexsannos function from CAMERA
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	267 cAnnot <- combinexsAnnos(xaP, xaN, pos = pos, tol = tol, ruleset = ruleset)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	268 } else {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	269 stop("You must relauch the CAMERA.annotate step with the lastest version.")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	270 }
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	271
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	272 if (pos) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	273 xa <- xaP
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	274 mode <- "neg. Mode"
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	275 } else {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	276 xa <- xaN
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	277 mode <- "pos. Mode"
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	278 }
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	279
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	280 peakList <- getPeaklist(xa)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	281 peakList <- cbind(groupnames(xa@xcmsSet), peakList)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	282 colnames(peakList)[1] <- c("name")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	283 variableMetadata <- cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup", mode)])
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	284 variableMetadata <- variableMetadata[, !(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	285
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	286 # Test if there are more than two classes (conditions)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	287 if (nlevels(sampclass(xaP@xcmsSet)) == 2 && (!is.null(diffrepN)) && (!is.null(diffrepP))) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	288 diffrepP <- diffrepP[, c("name", "fold", "tstat", "pvalue")]
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	289 colnames(diffrepP) <- paste("P.", colnames(diffrepP), sep = "")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	290 diffrepN <- diffrepN[, c("name", "fold", "tstat", "pvalue")]
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	291 colnames(diffrepN) <- paste("N.", colnames(diffrepN), sep = "")
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	292
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	293 variableMetadata <- merge(variableMetadata, diffrepP, by.x = "name", by.y = "P.name")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	294 variableMetadata <- merge(variableMetadata, diffrepN, by.x = "name", by.y = "N.name")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	295 }
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	296
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	297 rownames(variableMetadata) <- NULL
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	298 # TODO: checker colnames(variableMetadata)[1:2] = c("name", "mz/rt");
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	299
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	300 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	301 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	302
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	303 # If the user want to keep only the metabolites which match a difference
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	304 if (keep_meta) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	305 variableMetadata <- variableMetadata[variableMetadata[, c(mode)] != "", ]
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	306 }
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	307
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	308 # Write the output into a tsv file
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	309 write.table(variableMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = variableMetadataOutput)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	310 return(variableMetadata)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	311 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	312
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	313 # This function get the raw file path from the arguments
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	314 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	315 if (!is.null(args$zipfile)) zipfile <- args$zipfile
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	316 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	317 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	318
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	319 if (!is.null(args$singlefile_galaxyPath)) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	320 singlefile_galaxyPaths <- args$singlefile_galaxyPath
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	321 singlefile_sampleNames <- args$singlefile_sampleName
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	322 }
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	323 if (!is.null(args$singlefile_galaxyPathPositive)) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	324 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	325 singlefile_sampleNames <- args$singlefile_sampleNamePositive
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	326 }
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	327 if (!is.null(args$singlefile_galaxyPathNegative)) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	328 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	329 singlefile_sampleNames <- args$singlefile_sampleNameNegative
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	330 }
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	331 if (exists("singlefile_galaxyPaths")) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	332 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths, ","))
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	333 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames, ","))
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	334
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	335 singlefile <- NULL
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	336 for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	337 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	338 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	339 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	340 }
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	341 }
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	342 for (argument in c(
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	343 "zipfile", "zipfilePositive", "zipfileNegative",
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	344 "singlefile_galaxyPath", "singlefile_sampleName",
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	345 "singlefile_galaxyPathPositive", "singlefile_sampleNamePositive",
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	346 "singlefile_galaxyPathNegative", "singlefile_sampleNameNegative"
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	347 )) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	348 args[[argument]] <- NULL
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	349 }
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	350 return(list(zipfile = zipfile, singlefile = singlefile, args = args))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	351 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	352
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	353
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	354 # This function retrieve the raw file in the working directory
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	355 # - if zipfile: unzip the file with its directory tree
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	356 # - if singlefiles: set symlink with the good filename
4 4c4945bce185 "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998" workflow4metabolomics parents: 2 diff changeset	357 retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile) {
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	358 if (!is.null(singlefile) && (length("singlefile") > 0)) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	359 for (singlefile_sampleName in names(singlefile)) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	360 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	361 if (!file.exists(singlefile_galaxyPath)) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	362 error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	363 print(error_message)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	364 stop(error_message)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	365 }
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	366
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	367 file.symlink(singlefile_galaxyPath, singlefile_sampleName)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	368 }
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	369 directory <- "."
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	370 }
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	371 if (!is.null(zipfile) && (zipfile != "")) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	372 if (!file.exists(zipfile)) {
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	373 error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	374 print(error_message)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	375 stop(error_message)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	376 }
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	377
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	378 # unzip
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	379 suppressWarnings(unzip(zipfile, unzip = "unzip"))
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	380
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	381 # get the directory name
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	382 filesInZip <- unzip(zipfile, list = TRUE)
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	383 directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	384 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	385 directory <- "."
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	386 if (length(directories) == 1) directory <- directories
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	387
6 2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	388 cat("files_root_directory\t", directory, "\n")
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	389 }
2443150161b4 planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58 workflow4metabolomics parents: 4 diff changeset	390 return(directory)
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	391 }

Mercurial > repos > workflow4metabolomics > camera_combinexsannos

annotate lib.r @ 7:e461f344226c draft default tip