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annotate createMSP.R @ 9:174a523cb1da draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
author computational-metabolomics
date Thu, 13 Jun 2024 11:42:28 +0000
parents cb4aeec93d49
children
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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(optparse)
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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2 library(msPurity)
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3 print(sessionInfo())
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5 # Get the parameter
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6 option_list <- list(
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7 make_option("--rdata_input", type = "character"),
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8 make_option("--method", type = "character"),
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9 make_option("--metadata", type = "character"),
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10 make_option("--metadata_cols", type = "character"),
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11 make_option("--metadata_cols_filter", type = "character"),
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12 make_option("--adduct_split", action = "store_true"),
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13 make_option("--xcms_groupids", type = "character"),
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14 make_option("--filter", action = "store_true"),
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15 make_option("--intensity_ra", type = "character"),
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16 make_option("--include_adducts", type = "character"),
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17 make_option("--msp_schema", type = "character"),
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18 make_option("--include_adducts_custom", type = "character", default = ""),
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19 make_option("--out_dir", type = "character", default = ".")
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20 )
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21 opt <- parse_args(OptionParser(option_list = option_list))
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23 print(opt)
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25 load(opt$rdata_input)
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27 if (is.null(opt$metadata)) {
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28 metadata <- NULL
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29 } else {
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30 metadata <- read.table(opt$metadata,
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31 header = TRUE, sep = "\t",
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32 stringsAsFactors = FALSE, check.names = FALSE
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33 )
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35 if (!opt$metadata_cols_filter == "") {
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36 metadata_cols_filter <- strsplit(opt$metadata_cols_filter, ",")[[1]]
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38 metadata <- metadata[, metadata_cols_filter, drop = FALSE]
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39 print(metadata)
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41 if (!"grpid" %in% colnames(metadata)) {
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42 metadata$grpid <- seq_len(nrow(metadata))
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43 }
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45 print(metadata)
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46 }
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47 }
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51 if (is.null(opt$metadata_cols) || opt$metadata_cols == "") {
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52 metadata_cols <- NULL
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53 } else {
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54 metadata_cols <- opt$metadata_cols
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55 }
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58 if (is.null(opt$adduct_split)) {
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59 adduct_split <- FALSE
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60 } else {
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61 adduct_split <- TRUE
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62 }
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64 if (is.null(opt$xcms_groupids)) {
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65 xcms_groupids <- NULL
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66 } else {
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67 xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ",")[[1]])
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68 }
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71 if (is.null(opt$include_adducts_custom)) {
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72 include_adducts_custom <- ""
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73 } else {
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74 include_adducts_custom <- opt$include_adducts_custom
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75 }
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78 if (opt$include_adducts == "None") {
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79 include_adducts <- ""
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80 } else {
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81 include_adducts <- opt$include_adducts
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82 }
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84 include_adducts_all <- paste(include_adducts_custom, ",", include_adducts, sep = "")
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86 include_adducts_all <- gsub("^,", "", include_adducts_all)
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87 include_adducts_all <- gsub(",$", "", include_adducts_all)
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89 include_adducts_all <- gsub("__ob__", "[", include_adducts_all)
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90 include_adducts_all <- gsub("__cb__", "]", include_adducts_all)
309dcd558030 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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91 include_adducts_all <- trimws(include_adducts_all)
309dcd558030 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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92 include_adducts_all <- gsub(",", " ", include_adducts_all)
309dcd558030 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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93
0
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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94
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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95
6
d4a17be5429a "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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96 if (is.null(opt$filter)) {
0
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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97 filter <- FALSE
8
cb4aeec93d49 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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98 } else {
0
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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99 filter <- TRUE
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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100 }
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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101
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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102
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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103
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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104 msPurity::createMSP(pa,
8
cb4aeec93d49 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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105 msp_file_pth = file.path(opt$out_dir, "lcmsms_spectra.msp"),
cb4aeec93d49 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
106 metadata = metadata,
cb4aeec93d49 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
107 metadata_cols = metadata_cols,
cb4aeec93d49 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
108 method = opt$method,
cb4aeec93d49 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
109 adduct_split = adduct_split,
cb4aeec93d49 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
110 xcms_groupids = xcms_groupids,
cb4aeec93d49 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
111 filter = filter,
cb4aeec93d49 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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112 intensity_ra = opt$intensity_ra,
cb4aeec93d49 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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113 include_adducts = include_adducts_all,
cb4aeec93d49 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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114 msp_schema = opt$msp_schema
cb4aeec93d49 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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115 )
0
ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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116
8
cb4aeec93d49 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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117 print("msp created")