Mercurial > repos > computational-metabolomics > mspurity_spectralmatching

annotate createMSP.R @ 1:4db043151468 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
author computational-metabolomics
date Thu, 05 Dec 2019 07:34:21 -0500
parents 5ff9d40c7a42
children 15e3df50be3c
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5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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1 library(optparse)
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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2 library(msPurity)
5ff9d40c7a42 "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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4
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5 # Get the parameter
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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6 option_list <- list(
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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7 make_option("--rdata_input",type="character"),
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8 make_option("--method",type="character"),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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9 make_option("--metadata",type="character"),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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10 make_option("--metadata_cols",type="character"),
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11 make_option("--metadata_cols_filter",type="character"),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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12 make_option("--adduct_split", action="store_true"),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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13 make_option("--xcms_groupids",type="character"),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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14 make_option("--filter",action="store_true"),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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15 make_option("--intensity_ra",type="character"),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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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("--out_dir",type="character", default=".")
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19 )
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20 opt <- parse_args(OptionParser(option_list=option_list))
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22 print(opt)
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24 load(opt$rdata_input)
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26 if (is.null(opt$metadata)){
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27 metadata <- NULL
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28 }else{
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29 metadata <- read.table(opt$metadata, header = TRUE, sep='\t', stringsAsFactors = FALSE, check.names = FALSE)
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31 if(!opt$metadata_cols_filter==''){
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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32 metadata_cols_filter <- strsplit(opt$metadata_cols_filter, ',')[[1]]
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34 metadata <- metadata[,metadata_cols_filter, drop=FALSE]
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35 print(metadata)
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37 if (!"grpid" %in% colnames(metadata)){
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38 metadata$grpid <- 1:nrow(metadata)
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39 }
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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41 print(metadata)
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43 }
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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45 }
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49 if (is.null(opt$metadata_cols) || opt$metadata_cols==''){
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50 metadata_cols <- NULL
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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51 }else{
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52 metadata_cols <- opt$metadata_cols
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54 }
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57 if(is.null(opt$adduct_split)){
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58 adduct_split <- FALSE
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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59 }else{
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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60 adduct_split <- TRUE
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61 }
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63 if (is.null(opt$xcms_groupids)){
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64 xcms_groupids <- NULL
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65 }else{
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66 xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ',')[[1]])
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67 }
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69 if (opt$include_adducts=='None'){
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70 include_adducts <- ''
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71 }else{
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72 include_adducts <- opt$include_adducts
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73 include_adducts <- gsub("__ob__", "[", include_adducts)
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74 include_adducts <- gsub("__cb__", "]", include_adducts)
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75 include_adducts <- trimws(include_adducts)
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77 include_adducts <- gsub(",", " ", include_adducts)
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79 }
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82 if(is.null(opt$filter)){
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83 filter <- FALSE
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84 }else{
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85 filter <- TRUE
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86 }
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89
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
90 msPurity::createMSP(pa,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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91 msp_file_pth = file.path(opt$out_dir, 'lcmsms_spectra.msp'),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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92 metadata = metadata,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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93 metadata_cols = metadata_cols,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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94 method = opt$method,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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95 adduct_split = adduct_split,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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96 xcms_groupids = xcms_groupids,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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97 filter = filter,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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98 intensity_ra=opt$intensity_ra,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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99 include_adducts=include_adducts,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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100 msp_schema=opt$msp_schema)
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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101
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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102 print('msp created')