Mercurial > repos > computational-metabolomics > mspurity_spectralmatching
diff purityA.R @ 8:77706396e7bd draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
author | computational-metabolomics |
---|---|
date | Wed, 12 Jun 2024 16:03:14 +0000 |
parents | fecfe8c80e25 |
children |
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--- a/purityA.R Tue Feb 08 14:03:00 2022 +0000 +++ b/purityA.R Wed Jun 12 16:03:14 2024 +0000 @@ -3,20 +3,20 @@ print(sessionInfo()) option_list <- list( - make_option(c("-o", "--out_dir"), type = "character"), - make_option("--mzML_files", type = "character"), - make_option("--galaxy_names", type = "character"), - make_option("--minOffset", type = "numeric"), - make_option("--maxOffset", type = "numeric"), - make_option("--ilim", type = "numeric"), - make_option("--iwNorm", default = "none", type = "character"), - make_option("--exclude_isotopes", action = "store_true"), - make_option("--isotope_matrix", type = "character"), - make_option("--mostIntense", action = "store_true"), - make_option("--plotP", action = "store_true"), - make_option("--nearest", action = "store_true"), - make_option("--cores", default = 4), - make_option("--ppmInterp", default = 7) + make_option(c("-o", "--out_dir"), type = "character"), + make_option("--mzML_files", type = "character"), + make_option("--galaxy_names", type = "character"), + make_option("--minOffset", type = "numeric"), + make_option("--maxOffset", type = "numeric"), + make_option("--ilim", type = "numeric"), + make_option("--iwNorm", default = "none", type = "character"), + make_option("--exclude_isotopes", action = "store_true"), + make_option("--isotope_matrix", type = "character"), + make_option("--mostIntense", action = "store_true"), + make_option("--plotP", action = "store_true"), + make_option("--nearest", action = "store_true"), + make_option("--cores", default = 4), + make_option("--ppmInterp", default = 7) ) opt <- parse_args(OptionParser(option_list = option_list)) @@ -25,23 +25,27 @@ if (opt$iwNorm == "none") { iwNorm <- FALSE iwNormFun <- NULL -}else if (opt$iwNorm == "gauss") { +} else if (opt$iwNorm == "gauss") { iwNorm <- TRUE if (is.null(opt$minOffset) || is.null(opt$maxOffset)) { - print("User has to define offsets if using Gaussian normalisation") - }else{ - iwNormFun <- msPurity::iwNormGauss(minOff = -as.numeric(opt$minOffset), - maxOff = as.numeric(opt$maxOffset)) + print("User has to define offsets if using Gaussian normalisation") + } else { + iwNormFun <- msPurity::iwNormGauss( + minOff = -as.numeric(opt$minOffset), + maxOff = as.numeric(opt$maxOffset) + ) } -}else if (opt$iwNorm == "rcosine") { +} else if (opt$iwNorm == "rcosine") { iwNorm <- TRUE if (is.null(opt$minOffset) || is.null(opt$maxOffset)) { - print("User has to define offsets if using R-cosine normalisation") - }else{ - iwNormFun <- msPurity::iwNormRcosine(minOff = -as.numeric(opt$minOffset), - maxOff = as.numeric(opt$maxOffset)) + print("User has to define offsets if using R-cosine normalisation") + } else { + iwNormFun <- msPurity::iwNormRcosine( + minOff = -as.numeric(opt$minOffset), + maxOff = as.numeric(opt$maxOffset) + ) } -}else if (opt$iwNorm == "QE5") { +} else if (opt$iwNorm == "QE5") { iwNorm <- TRUE iwNormFun <- msPurity::iwNormQE.5() } @@ -53,27 +57,27 @@ if (is.null(opt$minOffset) || is.null(opt$maxOffset)) { offsets <- NA -}else{ +} else { offsets <- as.numeric(c(opt$minOffset, opt$maxOffset)) } if (is.null(opt$mostIntense)) { mostIntense <- FALSE -}else{ +} else { mostIntense <- TRUE } if (is.null(opt$nearest)) { nearest <- FALSE -}else{ +} else { nearest <- TRUE } if (is.null(opt$plotP)) { plotP <- FALSE plotdir <- NULL -}else{ +} else { plotP <- TRUE plotdir <- opt$out_dir } @@ -81,32 +85,34 @@ if (is.null(opt$isotope_matrix)) { im <- NULL -}else{ +} else { im <- read.table(opt$isotope_matrix, - header = TRUE, sep = "\t", stringsAsFactors = FALSE) + header = TRUE, sep = "\t", stringsAsFactors = FALSE + ) } if (is.null(opt$exclude_isotopes)) { isotopes <- FALSE -}else{ +} else { isotopes <- TRUE } pa <- msPurity::purityA(filepaths, - cores = opt$cores, - mostIntense = mostIntense, - nearest = nearest, - offsets = offsets, - plotP = plotP, - plotdir = plotdir, - interpol = "linear", - iwNorm = iwNorm, - iwNormFun = iwNormFun, - ilim = opt$ilim, - mzRback = "pwiz", - isotopes = isotopes, - im = im, - ppmInterp = opt$ppmInterp) + cores = opt$cores, + mostIntense = mostIntense, + nearest = nearest, + offsets = offsets, + plotP = plotP, + plotdir = plotdir, + interpol = "linear", + iwNorm = iwNorm, + iwNormFun = iwNormFun, + ilim = opt$ilim, + mzRback = "pwiz", + isotopes = isotopes, + im = im, + ppmInterp = opt$ppmInterp +) if (!is.null(opt$galaxy_names)) {