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annotate createMSP.R @ 3:d2373ced0ded draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
author computational-metabolomics
date Thu, 09 Apr 2020 14:13:16 -0400
parents 5d0461edc7fd
children a67b129cd78e
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
1 library(optparse)
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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2 library(msPurity)
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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3 print(sessionInfo())
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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5 # Get the parameter
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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6 option_list <- list(
5d0461edc7fd "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"),
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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8 make_option("--method",type="character"),
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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9 make_option("--metadata",type="character"),
5d0461edc7fd "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"),
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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11 make_option("--metadata_cols_filter",type="character"),
5d0461edc7fd "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"),
5d0461edc7fd "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"),
5d0461edc7fd "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"),
5d0461edc7fd "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"),
5d0461edc7fd "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"),
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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17 make_option("--msp_schema",type="character"),
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d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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18 make_option("--include_adducts_custom",type="character", default=""),
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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19 make_option("--out_dir",type="character", default=".")
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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20 )
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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21 opt <- parse_args(OptionParser(option_list=option_list))
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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23 print(opt)
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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25 load(opt$rdata_input)
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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27 if (is.null(opt$metadata)){
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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28 metadata <- NULL
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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29 }else{
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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30 metadata <- read.table(opt$metadata, header = TRUE, sep='\t', stringsAsFactors = FALSE, check.names = FALSE)
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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32 if(!opt$metadata_cols_filter==''){
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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33 metadata_cols_filter <- strsplit(opt$metadata_cols_filter, ',')[[1]]
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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35 metadata <- metadata[,metadata_cols_filter, drop=FALSE]
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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36 print(metadata)
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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38 if (!"grpid" %in% colnames(metadata)){
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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39 metadata$grpid <- 1:nrow(metadata)
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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40 }
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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42 print(metadata)
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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44 }
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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46 }
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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50 if (is.null(opt$metadata_cols) || opt$metadata_cols==''){
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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51 metadata_cols <- NULL
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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52 }else{
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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53 metadata_cols <- opt$metadata_cols
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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55 }
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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58 if(is.null(opt$adduct_split)){
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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59 adduct_split <- FALSE
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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60 }else{
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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61 adduct_split <- TRUE
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62 }
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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64 if (is.null(opt$xcms_groupids)){
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65 xcms_groupids <- NULL
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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66 }else{
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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67 xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ',')[[1]])
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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68 }
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74 if (is.null(opt$include_adducts_custom)){
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75 include_adducts_custom <- ''
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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76 }else{
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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77 include_adducts_custom <- opt$include_adducts_custom
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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78 }
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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81 if (opt$include_adducts=='None'){
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82 include_adducts <- ''
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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83 }else{
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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84 include_adducts <- opt$include_adducts
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85 }
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87 include_adducts_all <- paste(include_adducts_custom, ',', include_adducts, sep="")
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89 include_adducts_all <- gsub("^,", "", include_adducts_all)
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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90 include_adducts_all <- gsub(",$", "", include_adducts_all)
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91
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92 include_adducts_all <- gsub("__ob__", "[", include_adducts_all)
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93 include_adducts_all <- gsub("__cb__", "]", include_adducts_all)
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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94 include_adducts_all <- trimws(include_adducts_all)
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95 include_adducts_all <- gsub(",", " ", include_adducts_all)
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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96
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98
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99 if(is.null(opt$filter)){
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100 filter <- FALSE
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101 }else{
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102 filter <- TRUE
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103 }
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104
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105
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106
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107 msPurity::createMSP(pa,
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108 msp_file_pth = file.path(opt$out_dir, 'lcmsms_spectra.msp'),
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109 metadata = metadata,
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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110 metadata_cols = metadata_cols,
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111 method = opt$method,
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112 adduct_split = adduct_split,
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113 xcms_groupids = xcms_groupids,
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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114 filter = filter,
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115 intensity_ra=opt$intensity_ra,
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116 include_adducts=include_adducts_all,
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117 msp_schema=opt$msp_schema)
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118
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119 print('msp created')