Mercurial > repos > computational-metabolomics > mspurity_combineannotations

annotate dimsPredictPuritySingle.R @ 8:94a2b6571758 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
author computational-metabolomics
date Wed, 12 Jun 2024 16:06:42 +0000
parents 18c0038dde9c
children
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7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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diff changeset
1 library(msPurity)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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2 library(optparse)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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3 print(sessionInfo())
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5 option_list <- list(
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94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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6 make_option(c("--mzML_file"), type = "character"),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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7 make_option(c("--mzML_files"), type = "character"),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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8 make_option(c("--mzML_filename"), type = "character", default = ""),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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9 make_option(c("--mzML_galaxy_names"), type = "character", default = ""),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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10 make_option(c("--peaks_file"), type = "character"),
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11 make_option(c("-o", "--out_dir"), type = "character"),
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12 make_option("--minoffset", default = 0.5),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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13 make_option("--maxoffset", default = 0.5),
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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14 make_option("--ilim", default = 0.05),
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15 make_option("--ppm", default = 4),
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16 make_option("--dimspy", action = "store_true"),
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17 make_option("--sim", action = "store_true"),
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18 make_option("--remove_nas", action = "store_true"),
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19 make_option("--iwNorm", default = "none", type = "character"),
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20 make_option("--file_num_dimspy", default = 1),
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21 make_option("--exclude_isotopes", action = "store_true"),
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22 make_option("--isotope_matrix", type = "character")
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23 )
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25 # store options
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26 opt <- parse_args(OptionParser(option_list = option_list))
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28 print(sessionInfo())
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29 print(opt)
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31 print(opt$mzML_files)
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32 print(opt$mzML_galaxy_names)
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34 str_to_vec <- function(x) {
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35 print(x)
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36 x <- trimws(strsplit(x, ",")[[1]])
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37 return(x[x != ""])
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38 }
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39
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40 find_mzml_file <- function(mzML_files, galaxy_names, mzML_filename) {
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41 mzML_filename <- trimws(mzML_filename)
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42 mzML_files <- str_to_vec(mzML_files)
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43 galaxy_names <- str_to_vec(galaxy_names)
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44 if (mzML_filename %in% galaxy_names) {
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45 return(mzML_files[galaxy_names == mzML_filename])
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46 } else {
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47 stop(paste("mzML file not found - ", mzML_filename))
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48 }
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49 }
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51
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52 if (is.null(opt$dimspy)) {
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53 df <- read.table(opt$peaks_file, header = TRUE, sep = "\t")
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54 if (file.exists(opt$mzML_file)) {
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55 mzML_file <- opt$mzML_file
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56 } else if (!is.null(opt$mzML_files)) {
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57 mzML_file <- find_mzml_file(
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58 opt$mzML_files, opt$mzML_galaxy_names,
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59 opt$mzML_filename
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60 )
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61 } else {
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62 mzML_file <- file.path(opt$mzML_file, filename)
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63 }
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64 } else {
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65 indf <- read.table(opt$peaks_file,
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66 header = TRUE, sep = "\t", stringsAsFactors = FALSE
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67 )
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68
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69 filename <- colnames(indf)[8:ncol(indf)][opt$file_num_dimspy]
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70 print(filename)
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71 # check if the data file is mzML or RAW (can only use mzML currently) so
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72 # we expect an mzML file of the same name in the same folder
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73 indf$i <- indf[, colnames(indf) == filename]
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74 indf[, colnames(indf) == filename] <- as.numeric(indf[, colnames(indf) == filename])
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76 filename <- sub("raw", "mzML", filename, ignore.case = TRUE)
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77 print(filename)
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79 if (file.exists(opt$mzML_file)) {
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80 mzML_file <- opt$mzML_file
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81 } else if (!is.null(opt$mzML_files)) {
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82 mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names, filename)
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83 } else {
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84 mzML_file <- file.path(opt$mzML_file, filename)
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85 }
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87 # Update the dimspy output with the correct information
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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88 df <- indf[4:nrow(indf), ]
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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89 if ("blank_flag" %in% colnames(df)) {
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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90 df <- df[df$blank_flag == 1, ]
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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91 }
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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92 colnames(df)[colnames(df) == "m.z"] <- "mz"
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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93
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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94 if ("nan" %in% df$mz) {
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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95 df[df$mz == "nan", ]$mz <- NA
0
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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96 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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97 df$mz <- as.numeric(df$mz)
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98 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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99
6
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100 if (!is.null(opt$remove_nas)) {
8
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101 df <- df[!is.na(df$mz), ]
0
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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102 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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103
6
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104 if (is.null(opt$isotope_matrix)) {
0
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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105 im <- NULL
8
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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106 } else {
0
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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107 im <- read.table(opt$isotope_matrix,
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94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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108 header = TRUE, sep = "\t", stringsAsFactors = FALSE
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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109 )
0
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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110 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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111
6
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112 if (is.null(opt$exclude_isotopes)) {
0
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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113 isotopes <- FALSE
8
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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114 } else {
0
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115 isotopes <- TRUE
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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116 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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117
6
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118 if (is.null(opt$sim)) {
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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119 sim <- FALSE
8
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120 } else {
6
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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121 sim <- TRUE
0
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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122 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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123
6
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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124 minOffset <- as.numeric(opt$minoffset)
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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125 maxOffset <- as.numeric(opt$maxoffset)
0
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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126
6
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127 if (opt$iwNorm == "none") {
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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128 iwNorm <- FALSE
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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129 iwNormFun <- NULL
8
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130 } else if (opt$iwNorm == "gauss") {
6
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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131 iwNorm <- TRUE
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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132 iwNormFun <- msPurity::iwNormGauss(minOff = -minOffset, maxOff = maxOffset)
8
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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133 } else if (opt$iwNorm == "rcosine") {
6
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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134 iwNorm <- TRUE
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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135 iwNormFun <- msPurity::iwNormRcosine(minOff = -minOffset, maxOff = maxOffset)
8
94a2b6571758 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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136 } else if (opt$iwNorm == "QE5") {
6
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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137 iwNorm <- TRUE
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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138 iwNormFun <- msPurity::iwNormQE.5()
0
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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139 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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140
6
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141 print("FIRST ROWS OF PEAK FILE")
0
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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142 print(head(df))
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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143 print(mzML_file)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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144 predicted <- msPurity::dimsPredictPuritySingle(df$mz,
8
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145 filepth = mzML_file,
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146 minOffset = minOffset,
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computational-metabolomics
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147 maxOffset = maxOffset,
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148 ppm = opt$ppm,
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149 mzML = TRUE,
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150 sim = sim,
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151 ilim = opt$ilim,
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152 isotopes = isotopes,
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153 im = im,
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154 iwNorm = iwNorm,
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155 iwNormFun = iwNormFun
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156 )
0
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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157 predicted <- cbind(df, predicted)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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158
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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159 print(head(predicted))
6
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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160 print(file.path(opt$out_dir, "dimsPredictPuritySingle_output.tsv"))
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161
6
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162 write.table(predicted,
8
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163 file.path(opt$out_dir, "dimsPredictPuritySingle_output.tsv"),
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164 row.names = FALSE, sep = "\t"
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165 )