Mercurial > repos > computational-metabolomics > mspurity_createmsp
annotate dimsPredictPuritySingle.R @ 5:50409aeeeac5 draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit b1b879e29d5d6c97fdc3636aa6e900ad03695f9e"
author | computational-metabolomics |
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date | Fri, 13 Nov 2020 10:10:53 +0000 |
parents | 35898942bfbb |
children | d25273689e04 |
rev | line source |
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0
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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1 library(msPurity) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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2 library(optparse) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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3 print(sessionInfo()) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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4 |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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5 option_list <- list( |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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6 make_option(c("--mzML_file"), type="character"), |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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7 make_option(c("--mzML_files"), type="character"), |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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8 make_option(c("--mzML_filename"), type="character", default=''), |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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9 make_option(c("--mzML_galaxy_names"), type="character", default=''), |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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10 make_option(c("--peaks_file"), type="character"), |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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11 make_option(c("-o", "--out_dir"), type="character"), |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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12 make_option("--minoffset", default=0.5), |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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13 make_option("--maxoffset", default=0.5), |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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14 make_option("--ilim", default=0.05), |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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15 make_option("--ppm", default=4), |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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16 make_option("--dimspy", action="store_true"), |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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17 make_option("--sim", action="store_true"), |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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18 make_option("--remove_nas", action="store_true"), |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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19 make_option("--iwNorm", default="none", type="character"), |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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20 make_option("--file_num_dimspy", default=1), |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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21 make_option("--exclude_isotopes", action="store_true"), |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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22 make_option("--isotope_matrix", type="character") |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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23 ) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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24 |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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25 # store options |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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26 opt<- parse_args(OptionParser(option_list=option_list)) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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27 |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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28 print(sessionInfo()) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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29 print(opt) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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30 |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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31 print(opt$mzML_files) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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32 print(opt$mzML_galaxy_names) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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33 |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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34 str_to_vec <- function(x){ |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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35 print(x) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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36 x <- trimws(strsplit(x, ',')[[1]]) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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37 return(x[x != ""]) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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38 } |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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39 |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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40 find_mzml_file <- function(mzML_files, galaxy_names, mzML_filename){ |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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41 mzML_filename <- trimws(mzML_filename) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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42 mzML_files <- str_to_vec(mzML_files) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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43 galaxy_names <- str_to_vec(galaxy_names) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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44 if (mzML_filename %in% galaxy_names){ |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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45 return(mzML_files[galaxy_names==mzML_filename]) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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46 }else{ |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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47 stop(paste("mzML file not found - ", mzML_filename)) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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48 } |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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49 } |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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50 |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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51 |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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52 if (is.null(opt$dimspy)){ |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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53 df <- read.table(opt$peaks_file, header = TRUE, sep='\t') |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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54 if (file.exists(opt$mzML_file)){ |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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55 mzML_file <- opt$mzML_file |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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56 }else if (!is.null(opt$mzML_files)){ |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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57 mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names, |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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58 opt$mzML_filename) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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59 }else{ |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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60 mzML_file <- file.path(opt$mzML_file, filename) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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61 } |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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62 }else{ |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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63 indf <- read.table(opt$peaks_file, |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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64 header = TRUE, sep='\t', stringsAsFactors = FALSE) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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65 |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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66 filename <- colnames(indf)[8:ncol(indf)][opt$file_num_dimspy] |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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67 print(filename) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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68 # check if the data file is mzML or RAW (can only use mzML currently) so |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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69 # we expect an mzML file of the same name in the same folder |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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70 indf$i <- indf[,colnames(indf)==filename] |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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71 indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename]) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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72 |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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73 filename = sub("raw", "mzML", filename, ignore.case = TRUE) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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74 print(filename) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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75 |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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76 |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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77 if (file.exists(opt$mzML_file)){ |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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78 mzML_file <- opt$mzML_file |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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79 }else if (!is.null(opt$mzML_files)){ |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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80 mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names, filename) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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81 }else{ |
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82 mzML_file <- file.path(opt$mzML_file, filename) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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83 } |
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84 |
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85 # Update the dimspy output with the correct information |
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86 df <- indf[4:nrow(indf),] |
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87 if ('blank_flag' %in% colnames(df)){ |
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88 df <- df[df$blank_flag==1,] |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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89 } |
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90 colnames(df)[colnames(df)=='m.z'] <- 'mz' |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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91 |
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92 if ('nan' %in% df$mz){ |
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93 df[df$mz=='nan',]$mz <- NA |
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94 } |
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95 df$mz <- as.numeric(df$mz) |
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96 } |
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97 |
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98 if (!is.null(opt$remove_nas)){ |
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99 df <- df[!is.na(df$mz),] |
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100 } |
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101 |
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102 if (is.null(opt$isotope_matrix)){ |
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103 im <- NULL |
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104 }else{ |
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105 im <- read.table(opt$isotope_matrix, |
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106 header = TRUE, sep='\t', stringsAsFactors = FALSE) |
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107 } |
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108 |
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109 if (is.null(opt$exclude_isotopes)){ |
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110 isotopes <- FALSE |
35898942bfbb
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111 }else{ |
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112 isotopes <- TRUE |
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113 } |
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114 |
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115 if (is.null(opt$sim)){ |
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116 sim=FALSE |
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117 }else{ |
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118 sim=TRUE |
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119 } |
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120 |
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121 minOffset = as.numeric(opt$minoffset) |
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122 maxOffset = as.numeric(opt$maxoffset) |
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123 |
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124 if (opt$iwNorm=='none'){ |
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125 iwNorm = FALSE |
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126 iwNormFun = NULL |
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127 }else if (opt$iwNorm=='gauss'){ |
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128 iwNorm = TRUE |
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129 iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset) |
35898942bfbb
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130 }else if (opt$iwNorm=='rcosine'){ |
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131 iwNorm = TRUE |
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132 iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset) |
35898942bfbb
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133 }else if (opt$iwNorm=='QE5'){ |
35898942bfbb
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134 iwNorm = TRUE |
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135 iwNormFun = msPurity::iwNormQE.5() |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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136 } |
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137 |
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138 print('FIRST ROWS OF PEAK FILE') |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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139 print(head(df)) |
35898942bfbb
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140 print(mzML_file) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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141 predicted <- msPurity::dimsPredictPuritySingle(df$mz, |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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142 filepth=mzML_file, |
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143 minOffset=minOffset, |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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144 maxOffset=maxOffset, |
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145 ppm=opt$ppm, |
35898942bfbb
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146 mzML=TRUE, |
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147 sim = sim, |
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148 ilim = opt$ilim, |
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149 isotopes = isotopes, |
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150 im = im, |
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151 iwNorm = iwNorm, |
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152 iwNormFun = iwNormFun |
35898942bfbb
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153 ) |
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154 predicted <- cbind(df, predicted) |
35898942bfbb
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155 |
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156 print(head(predicted)) |
35898942bfbb
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157 print(file.path(opt$out_dir, 'dimsPredictPuritySingle_output.tsv')) |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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158 |
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159 write.table(predicted, |
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160 file.path(opt$out_dir, 'dimsPredictPuritySingle_output.tsv'), |
35898942bfbb
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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161 row.names=FALSE, sep='\t') |
35898942bfbb
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162 |
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163 |