Mercurial > repos > computational-metabolomics > mspurity_filterfragspectra
view createDatabase.R @ 6:cc0f8ddad4a8 draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author | computational-metabolomics |
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date | Thu, 04 Mar 2021 12:28:18 +0000 |
parents | 448363111457 |
children | a46824d13914 |
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library(msPurity) library(optparse) library(xcms) library(CAMERA) print(sessionInfo()) print("CREATING DATABASE") xset_pa_filename_fix <- function(opt, pa, xset) { if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)) { # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables # needs to be done due to Galaxy moving the files around and screwing up any links to files filepaths <- trimws(strsplit(opt$mzML_files, ",")[[1]]) filepaths <- filepaths[filepaths != ""] galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]]) galaxy_names <- galaxy_names[galaxy_names != ""] nsave <- names(pa@fileList) old_filenames <- basename(pa@fileList) pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)] names(pa@fileList) <- nsave pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)]) pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)]) } if (!all(basename(pa@fileList) == basename(xset@filepaths))) { if (!all(names(pa@fileList) == basename(xset@filepaths))) { print("FILELISTS DO NOT MATCH") message("FILELISTS DO NOT MATCH") quit(status = 1) }else{ xset@filepaths <- unname(pa@fileList) } } print(xset@phenoData) print(xset@filepaths) return(list(pa, xset)) } option_list <- list( make_option(c("-o", "--outDir"), type = "character"), make_option("--pa", type = "character"), make_option("--xset_xa", type = "character"), make_option("--xcms_camera_option", type = "character"), make_option("--eic", action = "store_true"), make_option("--cores", default = 4), make_option("--mzML_files", type = "character"), make_option("--galaxy_names", type = "character"), make_option("--grpPeaklist", type = "character") ) # store options opt <- parse_args(OptionParser(option_list = option_list)) print(opt) loadRData <- function(rdata_path, name) { #loads an RData file, and returns the named xset object if it is there load(rdata_path) return(get(ls()[ls() %in% name])) } getxcmsSetObject <- function(xobject) { # XCMS 1.x if (class(xobject) == "xcmsSet") return(xobject) # XCMS 3.x if (class(xobject) == "XCMSnExp") { # Get the legacy xcmsSet object suppressWarnings(xset <- as(xobject, "xcmsSet")) xcms::sampclass(xset) <- xset@phenoData$sample_group return(xset) } } print(paste("pa", opt$pa)) print(opt$xset) print(opt$xcms_camera_option) # Requires pa <- loadRData(opt$pa, "pa") print(pa@fileList) # Missing list element causes failures (should be updated # in msPurity R package for future releases) if (!exists("allfrag", where = pa@filter_frag_params)) { pa@filter_frag_params$allfrag <- FALSE } if (opt$xcms_camera_option == "xcms") { xset <- loadRData(opt$xset, c("xset", "xdata")) xset <- getxcmsSetObject(xset) fix <- xset_pa_filename_fix(opt, pa, xset) pa <- fix[[1]] xset <- fix[[2]] xa <- NULL }else{ xa <- loadRData(opt$xset, "xa") fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet) pa <- fix[[1]] xa@xcmsSet <- fix[[2]] xset <- NULL } if (is.null(opt$grpPeaklist)) { grpPeaklist <- NA }else{ grpPeaklist <- opt$grpPeaklist } dbPth <- msPurity::createDatabase(pa, xset = xset, xsa = xa, outDir = opt$outDir, grpPeaklist = grpPeaklist, dbName = "createDatabase_output.sqlite" ) if (!is.null(opt$eic)) { if (is.null(xset)) { xset <- xa@xcmsSet } # previous check should have matched filelists together xset@filepaths <- unname(pa@fileList) convert2Raw <- function(x, xset) { sid <- unique(x$sample) # for each file get list of peaks x$rt_raw <- xset@rt$raw[[sid]][match(x$rt, xset@rt$corrected[[sid]])] x$rtmin_raw <- xset@rt$raw[[sid]][match(x$rtmin, xset@rt$corrected[[sid]])] x$rtmax_raw <- xset@rt$raw[[sid]][match(x$rtmax, xset@rt$corrected[[sid]])] return(x) } xset@peaks <- as.matrix( plyr::ddply(data.frame(xset@peaks), ~ sample, convert2Raw, xset = xset)) # Saves the EICS into the previously created database px <- msPurity::purityX(xset, saveEIC = TRUE, cores = 1, sqlitePth = dbPth, rtrawColumns = TRUE) } closeAllConnections()