Mercurial > repos > computational-metabolomics > mspurity_frag4feature

annotate dimsPredictPuritySingle.R @ 7:e9fbb65451f6 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
author computational-metabolomics
date Tue, 08 Feb 2022 14:04:07 +0000
parents d4a17be5429a
children cb4aeec93d49
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ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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1 library(msPurity)
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2 library(optparse)
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3 print(sessionInfo())
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5 option_list <- list(
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6 make_option(c("--mzML_file"), type = "character"),
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7 make_option(c("--mzML_files"), type = "character"),
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8 make_option(c("--mzML_filename"), type = "character", default = ""),
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9 make_option(c("--mzML_galaxy_names"), type = "character", default = ""),
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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),
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13 make_option("--maxoffset", default = 0.5),
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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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33
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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$mzML_files)) {
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57 mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names,
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58 opt$mzML_filename)
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59 }else{
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60 mzML_file <- file.path(opt$mzML_file, filename)
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61 }
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62 }else{
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63 indf <- read.table(opt$peaks_file,
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64 header = TRUE, sep = "\t", stringsAsFactors = FALSE)
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65
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66 filename <- colnames(indf)[8:ncol(indf)][opt$file_num_dimspy]
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67 print(filename)
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68 # check if the data file is mzML or RAW (can only use mzML currently) so
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69 # we expect an mzML file of the same name in the same folder
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70 indf$i <- indf[, colnames(indf) == filename]
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71 indf[, colnames(indf) == filename] <- as.numeric(indf[, colnames(indf) == filename])
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73 filename <- sub("raw", "mzML", filename, ignore.case = TRUE)
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74 print(filename)
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76 if (file.exists(opt$mzML_file)) {
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77 mzML_file <- opt$mzML_file
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78 }else if (!is.null(opt$mzML_files)) {
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79 mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names, filename)
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80 }else{
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81 mzML_file <- file.path(opt$mzML_file, filename)
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82 }
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83
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84 # Update the dimspy output with the correct information
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85 df <- indf[4:nrow(indf), ]
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86 if ("blank_flag" %in% colnames(df)) {
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87 df <- df[df$blank_flag == 1, ]
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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88 }
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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89 colnames(df)[colnames(df) == "m.z"] <- "mz"
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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90
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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91 if ("nan" %in% df$mz) {
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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92 df[df$mz == "nan", ]$mz <- NA
0
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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93 }
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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94 df$mz <- as.numeric(df$mz)
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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95 }
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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96
6
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computational-metabolomics
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97 if (!is.null(opt$remove_nas)) {
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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98 df <- df[!is.na(df$mz), ]
0
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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99 }
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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100
6
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101 if (is.null(opt$isotope_matrix)) {
0
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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102 im <- NULL
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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103 }else{
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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104 im <- read.table(opt$isotope_matrix,
6
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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105 header = TRUE, sep = "\t", stringsAsFactors = FALSE)
0
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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106 }
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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107
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108 if (is.null(opt$exclude_isotopes)) {
0
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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109 isotopes <- FALSE
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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110 }else{
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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111 isotopes <- TRUE
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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112 }
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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113
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114 if (is.null(opt$sim)) {
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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115 sim <- FALSE
0
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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116 }else{
6
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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117 sim <- TRUE
0
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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118 }
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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119
6
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120 minOffset <- as.numeric(opt$minoffset)
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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121 maxOffset <- as.numeric(opt$maxoffset)
0
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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122
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123 if (opt$iwNorm == "none") {
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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124 iwNorm <- FALSE
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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125 iwNormFun <- NULL
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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126 }else if (opt$iwNorm == "gauss") {
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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127 iwNorm <- TRUE
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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128 iwNormFun <- msPurity::iwNormGauss(minOff = -minOffset, maxOff = maxOffset)
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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129 }else if (opt$iwNorm == "rcosine") {
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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130 iwNorm <- TRUE
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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131 iwNormFun <- msPurity::iwNormRcosine(minOff = -minOffset, maxOff = maxOffset)
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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132 }else if (opt$iwNorm == "QE5") {
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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133 iwNorm <- TRUE
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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134 iwNormFun <- msPurity::iwNormQE.5()
0
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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135 }
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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136
6
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137 print("FIRST ROWS OF PEAK FILE")
0
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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138 print(head(df))
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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139 print(mzML_file)
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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140 predicted <- msPurity::dimsPredictPuritySingle(df$mz,
6
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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141 filepth = mzML_file,
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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142 minOffset = minOffset,
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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143 maxOffset = maxOffset,
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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144 ppm = opt$ppm,
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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145 mzML = TRUE,
0
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146 sim = sim,
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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147 ilim = opt$ilim,
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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148 isotopes = isotopes,
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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149 im = im,
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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150 iwNorm = iwNorm,
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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151 iwNormFun = iwNormFun
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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152 )
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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153 predicted <- cbind(df, predicted)
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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154
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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155 print(head(predicted))
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d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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156 print(file.path(opt$out_dir, "dimsPredictPuritySingle_output.tsv"))
0
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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157
6
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158 write.table(predicted,
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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diff changeset
159 file.path(opt$out_dir, "dimsPredictPuritySingle_output.tsv"),
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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diff changeset
160 row.names = FALSE, sep = "\t")