mspurity_purityx: frag4feature.R annotate

annotate frag4feature.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(optparse)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	2 library(msPurity)
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 print(sessionInfo())
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	5
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	6 xset_pa_filename_fix <- function(opt, pa, xset = NULL) {
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	7 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)) {
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	8 # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	9 # needs to be done due to Galaxy moving the files around and screwing up any links to files
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	10
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	11 filepaths <- trimws(strsplit(opt$mzML_files, ",")[[1]]) # nolint
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	12
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	13 filepaths <- filepaths[filepaths != ""]
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	14
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	15 galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]])
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	16 galaxy_names <- galaxy_names[galaxy_names != ""]
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	17
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	18 nsave <- names(pa@fileList)
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	19 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	20
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	21 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	22 names(pa@fileList) <- nsave
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	23
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	24 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	25 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	26 }
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	27 print(pa@fileList)
0 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 (!is.null(xset)) {
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	30 print(xset@filepaths)
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	31
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	32 if (!all(basename(pa@fileList) == basename(xset@filepaths))) {
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	33 if (!all(names(pa@fileList) == basename(xset@filepaths))) {
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	34 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	35 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	36 quit(status = 1)
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	37 } else {
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	38 xset@filepaths <- unname(pa@fileList)
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	39 }
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	40 }
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	41 }
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	42
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	43 return(list(pa, xset))
0 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 option_list <- list(
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	48 make_option(c("-o", "--out_dir"), type = "character"),
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	49 make_option("--pa", type = "character"),
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	50 make_option("--xset", type = "character"),
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	51 make_option("--ppm", default = 10),
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	52 make_option("--plim", default = 0.0),
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	53 make_option("--convert2RawRT", action = "store_true"),
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	54 make_option("--intense", action = "store_true"),
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	55 make_option("--createDB", action = "store_true"),
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	56 make_option("--cores", default = 4),
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	57 make_option("--mzML_files", type = "character"),
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	58 make_option("--galaxy_names", type = "character"),
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	59 make_option("--grp_peaklist", type = "character"),
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	60 make_option("--useGroup", action = "store_true")
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	61 )
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	62
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	63 # store options
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	64 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	65 print(opt)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	66
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	67 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	68 # loads an RData file, and returns the named xset object if it is there
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	69 load(rdata_path)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	70 return(get(ls()[ls() %in% name]))
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	71 }
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	72
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	73 # This function retrieve a xset like object
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	74 # @author Gildas Le Corguille lecorguille@sb-roscoff.fr
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	75 getxcmsSetObject <- function(xobject) {
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	76 # XCMS 1.x
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	77 if (class(xobject) == "xcmsSet") {
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	78 return(xobject)
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	79 }
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	80 # XCMS 3.x
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	81 if (class(xobject) == "XCMSnExp") {
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	82 # Get the legacy xcmsSet object
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	83 suppressWarnings(xset <- as(xobject, "xcmsSet"))
9 374022b7b469 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f computational-metabolomics parents: 8 diff changeset	84 if (!is.null(xset@phenoData$sample_group)) {
374022b7b469 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f computational-metabolomics parents: 8 diff changeset	85 xcms::sampclass(xset) <- xset@phenoData$sample_group
374022b7b469 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f computational-metabolomics parents: 8 diff changeset	86 } else {
374022b7b469 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f computational-metabolomics parents: 8 diff changeset	87 xcms::sampclass(xset) <- "."
374022b7b469 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f computational-metabolomics parents: 8 diff changeset	88 }
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	89 return(xset)
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	90 }
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	91 }
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 # Requires
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	94 pa <- loadRData(opt$pa, "pa")
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	95 xset <- loadRData(opt$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	96 xset <- getxcmsSetObject(xset)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	97
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	98 pa@cores <- opt$cores
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	99
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	100 print(pa@fileList)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	101 print(xset@filepaths)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	102
9 374022b7b469 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f computational-metabolomics parents: 8 diff changeset	103
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	104 if (is.null(opt$intense)) {
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	105 intense <- FALSE
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	106 } else {
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	107 intense <- TRUE
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	108 }
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	109
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	110 if (is.null(opt$convert2RawRT)) {
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	111 convert2RawRT <- FALSE
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	112 } else {
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	113 convert2RawRT <- TRUE
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	114 }
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	115
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	116 if (is.null(opt$createDB)) {
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	117 createDB <- FALSE
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	118 } else {
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	119 createDB <- TRUE
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	120 }
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	121
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	122 if (is.null(opt$useGroup)) {
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	123 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	124 pa <- fix[[1]]
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	125 xset <- fix[[2]]
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	126 useGroup <- FALSE
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	127 } else {
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	128 # if are only aligning to the group not eah file we do not need to align the files between the xset and pa object
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	129 print("useGroup")
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	130 fix <- xset_pa_filename_fix(opt, pa)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	131 pa <- fix[[1]]
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	132 useGroup <- TRUE
0 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: 0 diff changeset	136 if (is.null(opt$grp_peaklist)) {
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	137 grp_peaklist <- NA
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	138 } else {
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	139 grp_peaklist <- opt$grp_peaklist
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	140 }
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	141 print(useGroup)
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	142
8 b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	143 pa <- msPurity::frag4feature(
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	144 pa = pa,
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	145 xset = xset,
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	146 ppm = opt$ppm,
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	147 plim = opt$plim,
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	148 intense = intense,
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	149 convert2RawRT = convert2RawRT,
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	150 db_name = "alldata.sqlite",
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	151 out_dir = opt$out_dir,
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	152 grp_peaklist = grp_peaklist,
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	153 create_db = createDB,
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	154 use_group = useGroup
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3 computational-metabolomics parents: 6 diff changeset	155 )
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	156 print(pa)
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	157 save(pa, file = file.path(opt$out_dir, "frag4feature_output.RData"))
0 a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	158
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	159 pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)])
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	160
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" computational-metabolomics parents: diff changeset	161 print(head(pa@grped_df))
6 6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: 0 diff changeset	162 write.table(pa@grped_df, file.path(opt$out_dir, "frag4feature_output.tsv"), row.names = FALSE, sep = "\t")

Mercurial > repos > computational-metabolomics > mspurity_purityx

annotate frag4feature.R @ 9:374022b7b469 draft