Mercurial > repos > computational-metabolomics > mspurity_purityx

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author computational-metabolomics
date Thu, 04 Mar 2021 12:11:29 +0000
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3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
1 library(optparse)
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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2 library(msPurity)
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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3 print(sessionInfo())
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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4
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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5 # Get the parameter
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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6 option_list <- list(
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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7 make_option("--rdata_input", type = "character"),
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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8 make_option("--method", type = "character"),
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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9 make_option("--metadata", type = "character"),
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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10 make_option("--metadata_cols", type = "character"),
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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11 make_option("--metadata_cols_filter", type = "character"),
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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12 make_option("--adduct_split", action = "store_true"),
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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13 make_option("--xcms_groupids", type = "character"),
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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14 make_option("--filter", action = "store_true"),
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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15 make_option("--intensity_ra", type = "character"),
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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16 make_option("--include_adducts", type = "character"),
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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17 make_option("--msp_schema", type = "character"),
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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18 make_option("--include_adducts_custom", type = "character", default = ""),
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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19 make_option("--out_dir", type = "character", default = ".")
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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20 )
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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21 opt <- parse_args(OptionParser(option_list = option_list))
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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23 print(opt)
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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25 load(opt$rdata_input)
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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27 if (is.null(opt$metadata)) {
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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28 metadata <- NULL
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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29 }else{
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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30 metadata <- read.table(opt$metadata, header = TRUE, sep = "\t",
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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31 stringsAsFactors = FALSE, check.names = FALSE)
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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32
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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33 if (!opt$metadata_cols_filter == "") {
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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34 metadata_cols_filter <- strsplit(opt$metadata_cols_filter, ",")[[1]]
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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36 metadata <- metadata[, metadata_cols_filter, drop = FALSE]
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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37 print(metadata)
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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38
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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39 if (!"grpid" %in% colnames(metadata)) {
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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40 metadata$grpid <- seq_len(nrow(metadata))
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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41 }
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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43 print(metadata)
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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45 }
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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47 }
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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51 if (is.null(opt$metadata_cols) || opt$metadata_cols == "") {
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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52 metadata_cols <- NULL
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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53 }else{
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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54 metadata_cols <- opt$metadata_cols
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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56 }
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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57
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58
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59 if (is.null(opt$adduct_split)) {
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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60 adduct_split <- FALSE
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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61 }else{
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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62 adduct_split <- TRUE
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63 }
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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64
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65 if (is.null(opt$xcms_groupids)) {
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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66 xcms_groupids <- NULL
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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67 }else{
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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68 xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ",")[[1]])
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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69 }
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72 if (is.null(opt$include_adducts_custom)) {
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73 include_adducts_custom <- ""
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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74 }else{
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75 include_adducts_custom <- opt$include_adducts_custom
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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76 }
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79 if (opt$include_adducts == "None") {
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80 include_adducts <- ""
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81 }else{
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82 include_adducts <- opt$include_adducts
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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83 }
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85 include_adducts_all <- paste(include_adducts_custom, ",", include_adducts, sep = "")
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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87 include_adducts_all <- gsub("^,", "", include_adducts_all)
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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88 include_adducts_all <- gsub(",$", "", include_adducts_all)
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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89
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90 include_adducts_all <- gsub("__ob__", "[", include_adducts_all)
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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91 include_adducts_all <- gsub("__cb__", "]", include_adducts_all)
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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92 include_adducts_all <- trimws(include_adducts_all)
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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93 include_adducts_all <- gsub(",", " ", include_adducts_all)
3db32ffd33b0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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94
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95
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96
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97 if (is.null(opt$filter)) {
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98 filter <- FALSE
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99 }else{
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100 filter <- TRUE
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101 }
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102
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103
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104
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105 msPurity::createMSP(pa,
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106 msp_file_pth = file.path(opt$out_dir, "lcmsms_spectra.msp"),
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107 metadata = metadata,
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108 metadata_cols = metadata_cols,
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109 method = opt$method,
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110 adduct_split = adduct_split,
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111 xcms_groupids = xcms_groupids,
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112 filter = filter,
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113 intensity_ra = opt$intensity_ra,
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114 include_adducts = include_adducts_all,
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115 msp_schema = opt$msp_schema)
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116
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117 print("msp created")