mspurity_purityx: createDatabase.R annotate

annotate createDatabase.R @ 9:374022b7b469 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f

author	computational-metabolomics
date	Thu, 13 Jun 2024 11:36:53 +0000
parents	b16952cc06d2
children

rev	line source
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	1 library(msPurity)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	2 library(optparse)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	3 library(xcms)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	4 library(CAMERA)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	5 print(sessionInfo())
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	6 print("CREATING DATABASE")
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	7
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	8 xset_pa_filename_fix <- function(opt, pa, xset) {
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	9 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)) {
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	10 # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	11 # needs to be done due to Galaxy moving the files around and screwing up any links to files
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	12
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	13 filepaths <- trimws(strsplit(opt$mzML_files, ",")[[1]])
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	14 filepaths <- filepaths[filepaths != ""]
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	15
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	16 galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]])
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	17 galaxy_names <- galaxy_names[galaxy_names != ""]
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	18
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	19 nsave <- names(pa@fileList)
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	20 old_filenames <- basename(pa@fileList)
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	21 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	22 names(pa@fileList) <- nsave
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	23
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	24 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	25 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	26 }
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	27
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	28
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	29 if (!all(basename(pa@fileList) == basename(xset@filepaths))) {
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	30 if (!all(names(pa@fileList) == basename(xset@filepaths))) {
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	31 print("FILELISTS DO NOT MATCH")
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	32 message("FILELISTS DO NOT MATCH")
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	33 quit(status = 1)
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	34 } else {
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	35 xset@filepaths <- unname(pa@fileList)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	36 }
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	37 }
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	38
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	39 print(xset@phenoData)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	40 print(xset@filepaths)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	41
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	42 return(list(pa, xset))
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	43 }
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	44
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	45
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	46
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	47
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	48 option_list <- list(
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	49 make_option(c("-o", "--outDir"), type = "character"),
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	50 make_option("--pa", type = "character"),
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	51 make_option("--xset_xa", type = "character"),
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	52 make_option("--xcms_camera_option", type = "character"),
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	53 make_option("--eic", action = "store_true"),
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	54 make_option("--cores", default = 4),
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	55 make_option("--mzML_files", type = "character"),
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	56 make_option("--galaxy_names", type = "character"),
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	57 make_option("--grpPeaklist", type = "character")
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	58 )
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	59
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	60
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	61 # store options
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	62 opt <- parse_args(OptionParser(option_list = option_list))
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	63 print(opt)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	64
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	65 loadRData <- function(rdata_path, name) {
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	66 # loads an RData file, and returns the named xset object if it is there
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	67 load(rdata_path)
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	68 return(get(ls()[ls() %in% name]))
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	69 }
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	70
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	71 getxcmsSetObject <- function(xobject) {
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	72 # XCMS 1.x
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	73 if (class(xobject) == "xcmsSet") {
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	74 return(xobject)
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	75 }
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	76 # XCMS 3.x
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	77 if (class(xobject) == "XCMSnExp") {
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	78 # Get the legacy xcmsSet object
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	79 suppressWarnings(xset <- as(xobject, "xcmsSet"))
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	80 xcms::sampclass(xset) <- xset@phenoData$sample_group
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	81 return(xset)
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	82 }
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	83 }
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	84
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	85
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	86 print(paste("pa", opt$pa))
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	87 print(opt$xset)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	88
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	89 print(opt$xcms_camera_option)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	90 # Requires
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	91 pa <- loadRData(opt$pa, "pa")
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	92
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	93
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	94 print(pa@fileList)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	95
4 7856fc53df1d "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950" computational-metabolomics parents: 2 diff changeset	96 # Missing list element causes failures (should be updated
7856fc53df1d "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950" computational-metabolomics parents: 2 diff changeset	97 # in msPurity R package for future releases)
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	98 if (!exists("allfrag", where = pa@filter_frag_params)) {
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	99 pa@filter_frag_params$allfrag <- FALSE
4 7856fc53df1d "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950" computational-metabolomics parents: 2 diff changeset	100 }
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	101
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	102 if (opt$xcms_camera_option == "xcms") {
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	103 xset <- loadRData(opt$xset, c("xset", "xdata"))
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	104 xset <- getxcmsSetObject(xset)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	105 fix <- xset_pa_filename_fix(opt, pa, xset)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	106 pa <- fix[[1]]
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	107 xset <- fix[[2]]
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	108 xa <- NULL
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	109 } else {
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	110 xa <- loadRData(opt$xset, "xa")
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	111 fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	112 pa <- fix[[1]]
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	113 xa@xcmsSet <- fix[[2]]
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	114 xset <- NULL
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	115 }
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	116
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	117
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	118 if (is.null(opt$grpPeaklist)) {
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	119 grpPeaklist <- NA
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	120 } else {
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	121 grpPeaklist <- opt$grpPeaklist
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	122 }
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	123
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	124 dbPth <- msPurity::createDatabase(pa,
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	125 xset = xset,
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	126 xsa = xa,
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	127 outDir = opt$outDir,
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	128 grpPeaklist = grpPeaklist,
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	129 dbName = "createDatabase_output.sqlite"
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	130 )
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	131
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	132
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	133
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	134
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	135
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	136 if (!is.null(opt$eic)) {
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	137 if (is.null(xset)) {
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	138 xset <- xa@xcmsSet
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	139 }
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	140 # previous check should have matched filelists together
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	141 xset@filepaths <- unname(pa@fileList)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	142
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	143 convert2Raw <- function(x, xset) {
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	144 sid <- unique(x$sample)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	145 # for each file get list of peaks
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	146 x$rt_raw <- xset@rt$raw[[sid]][match(x$rt, xset@rt$corrected[[sid]])]
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	147 x$rtmin_raw <- xset@rt$raw[[sid]][match(x$rtmin, xset@rt$corrected[[sid]])]
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	148 x$rtmax_raw <- xset@rt$raw[[sid]][match(x$rtmax, xset@rt$corrected[[sid]])]
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	149 return(x)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	150 }
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	151
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 4 diff changeset	152 xset@peaks <- as.matrix(
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	153 plyr::ddply(data.frame(xset@peaks), ~sample, convert2Raw, xset = xset)
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	154 )
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	155
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	156 # Saves the EICS into the previously created database
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	157 px <- msPurity::purityX(xset,
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	158 saveEIC = TRUE,
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	159 cores = 1,
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	160 sqlitePth = dbPth,
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	161 rtrawColumns = TRUE
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	162 )
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	163 }
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	164
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	165 closeAllConnections()

Mercurial > repos > computational-metabolomics > mspurity_purityx

annotate createDatabase.R @ 9:374022b7b469 draft