Mercurial > repos > computational-metabolomics > mspurity_averagefragspectra

annotate spectralMatching.R @ 8:e98ae5c1f4e7 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
author computational-metabolomics
date Wed, 12 Jun 2024 16:01:28 +0000
parents 52d48bcd3608
children
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50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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1 library(msPurity)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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2 library(msPurityData)
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3 library(optparse)
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4 print(sessionInfo())
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5 # load in library spectra config
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6 source_local <- function(fname) {
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7 argv <- commandArgs(trailingOnly = FALSE)
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8 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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9 source(paste(base_dir, fname, sep = "/"))
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10 }
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11 source_local("dbconfig.R")
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13 option_list <- list(
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14 make_option(c("-o", "--outDir"), type = "character"),
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15 make_option("--q_dbPth", type = "character"),
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16 make_option("--l_dbPth", type = "character"),
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18 make_option("--q_dbType", type = "character", default = NA),
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19 make_option("--l_dbType", type = "character", default = NA),
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21 make_option("--q_msp", type = "character", default = NA),
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22 make_option("--l_msp", type = "character", default = NA),
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24 make_option("--q_defaultDb", action = "store_true"),
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25 make_option("--l_defaultDb", action = "store_true"),
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27 make_option("--q_ppmPrec", type = "double"),
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28 make_option("--l_ppmPrec", type = "double"),
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30 make_option("--q_ppmProd", type = "double"),
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31 make_option("--l_ppmProd", type = "double"),
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33 make_option("--q_raThres", type = "double", default = NA),
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34 make_option("--l_raThres", type = "double", default = NA),
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36 make_option("--q_polarity", type = "character", default = NA),
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37 make_option("--l_polarity", type = "character", default = NA),
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39 make_option("--q_purity", type = "double", default = NA),
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40 make_option("--l_purity", type = "double", default = NA),
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42 make_option("--q_xcmsGroups", type = "character", default = NA),
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43 make_option("--l_xcmsGroups", type = "character", default = NA),
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45 make_option("--q_pids", type = "character", default = NA),
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46 make_option("--l_pids", type = "character", default = NA),
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48 make_option("--q_rtrangeMin", type = "double", default = NA),
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49 make_option("--l_rtrangeMin", type = "double", default = NA),
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51 make_option("--q_rtrangeMax", type = "double", default = NA),
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52 make_option("--l_rtrangeMax", type = "double", default = NA),
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54 make_option("--q_accessions", type = "character", default = NA),
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55 make_option("--l_accessions", type = "character", default = NA),
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57 make_option("--q_sources", type = "character", default = NA),
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58 make_option("--l_sources", type = "character", default = NA),
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60 make_option("--q_sourcesUser", type = "character", default = NA),
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61 make_option("--l_sourcesUser", type = "character", default = NA),
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63 make_option("--q_instrumentTypes", type = "character", default = NA),
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64 make_option("--l_instrumentTypes", type = "character", default = NA),
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66 make_option("--q_instrumentTypesUser", type = "character", default = NA),
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67 make_option("--l_instrumentTypesUser", type = "character", default = NA),
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69 make_option("--q_instruments", type = "character", default = NA),
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70 make_option("--l_instruments", type = "character", default = NA),
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72 make_option("--q_spectraTypes", type = "character", default = NA),
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73 make_option("--l_spectraTypes", type = "character", default = NA),
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75 make_option("--q_spectraFilter", action = "store_true"),
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76 make_option("--l_spectraFilter", action = "store_true"),
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78 make_option("--usePrecursors", action = "store_true"),
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80 make_option("--mzW", type = "double"),
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81 make_option("--raW", type = "double"),
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83 make_option("--rttol", type = "double", default = NA),
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85 make_option("--updateDb", action = "store_true"),
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86 make_option("--copyDb", action = "store_true"),
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87 make_option("--cores", default = 1)
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88
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89
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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90 )
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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91
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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92 # store options
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93 opt <- parse_args(OptionParser(option_list = option_list))
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94
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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95 print(opt)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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96
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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97 # check if the sqlite databases have any spectra
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98 checkSPeakMeta <- function(dbPth, nme) {
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99 if (is.null(dbPth)) {
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100 return(TRUE)
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101 }else if ((file.exists(dbPth)) & (file.info(dbPth)$size > 0)) {
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102 con <- DBI::dbConnect(RSQLite::SQLite(), dbPth)
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103 if (DBI::dbExistsTable(con, "s_peak_meta")) {
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104 spm <- DBI::dbGetQuery(con, "SELECT * FROM s_peak_meta ORDER BY ROWID ASC LIMIT 1")
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105 return(TRUE)
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106 }else if (DBI::dbExistsTable(con, "library_spectra_meta")) {
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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107 spm <- DBI::dbGetQuery(con, "SELECT * FROM library_spectra_meta ORDER BY ROWID ASC LIMIT 1")
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108 return(TRUE)
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109 }else{
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110 print(paste("No spectra available for ", nme))
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111 return(FALSE)
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112 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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113 }else{
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114 print(paste("file empty or does not exist for", nme))
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115 return(FALSE)
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116 }
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117
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118
0
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119 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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120
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121
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122 addQueryNameColumn <- function(sm) {
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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123 if (is.null(sm$matchedResults) || length(sm$matchedResults) == 1 || nrow(sm$matchedResults) == 0) {
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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124 return(sm)
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125 }
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126
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127 con <- DBI::dbConnect(RSQLite::SQLite(), sm$q_dbPth)
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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128 if (DBI::dbExistsTable(con, "s_peak_meta")) {
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129 spm <- DBI::dbGetQuery(con, "SELECT pid, name AS query_entry_name FROM s_peak_meta")
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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130 }else if (DBI::dbExistsTable(con, "library_spectra_meta")) {
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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131 spm <- DBI::dbGetQuery(con, "SELECT id AS pid, name AS query_entry_name FROM library_spectra_meta")
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132 }
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133 print(sm$matchedResults)
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134 if ("pid" %in% colnames(sm$matchedResults)) {
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135 sm$matchedResults <- merge(sm$matchedResults, spm, by.x = "pid", by.y = "pid")
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136 }else{
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137 sm$matchedResults <- merge(sm$matchedResults, spm, by.x = "qpid", by.y = "pid")
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138 }
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139
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140 print(sm$xcmsMatchedResults)
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141 if (is.null(sm$xcmsMatchedResults) || length(sm$xcmsMatchedResults) == 1 || nrow(sm$xcmsMatchedResults) == 0) {
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142 return(sm)
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143 }else{
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144 if ("pid" %in% colnames(sm$xcmsMatchedResults)) {
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145 sm$xcmsMatchedResults <- merge(sm$xcmsMatchedResults, spm, by.x = "pid", by.y = "pid")
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146 }else{
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147 sm$xcmsMatchedResults <- merge(sm$xcmsMatchedResults, spm, by.x = "qpid", by.y = "pid")
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148 }
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149 }
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150
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151 return(sm)
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152
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153 }
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154
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155
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156 updateDbF <- function(q_con, l_con) {
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157 message("Adding extra details to database")
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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158 q_con <- DBI::dbConnect(RSQLite::SQLite(), sm$q_dbPth)
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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159 if (DBI::dbExistsTable(q_con, "l_s_peak_meta")) {
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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160 l_s_peak_meta <- DBI::dbGetQuery(q_con, "SELECT * FROM l_s_peak_meta")
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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161 colnames(l_s_peak_meta)[1] <- "pid"
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162 }
6
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163
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164 l_con <- DBI::dbConnect(RSQLite::SQLite(), l_dbPth)
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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165 if (DBI::dbExistsTable(l_con, "s_peaks")) {
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166 l_s_peaks <- DBI::dbGetQuery(q_con, sprintf("SELECT * FROM s_peaks WHERE pid in (%s)", paste(unique(l_s_peak_meta$pid), collapse = ",")))
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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167
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168 }else if (DBI::dbExistsTable(l_con, "library_spectra")) {
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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169 l_s_peaks <- DBI::dbGetQuery(l_con, sprintf("SELECT * FROM library_spectra
6
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170 WHERE library_spectra_meta_id in (%s)", paste(unique(l_s_peak_meta$pid), collapse = ",")))
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171 }else{
6
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172 l_s_peaks <- NULL
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173 }
6
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174
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175 if (DBI::dbExistsTable(l_con, "source")) {
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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176 l_source <- DBI::dbGetQuery(l_con, "SELECT * FROM source")
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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diff changeset
177 }else if (DBI::dbExistsTable(l_con, "library_spectra_source")) {
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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diff changeset
178 l_source <- DBI::dbGetQuery(l_con, "SELECT * FROM library_spectra_source")
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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179 }else{
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52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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180 l_source <- NULL
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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181 }
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52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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182
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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183 if (!is.null(l_s_peaks)) {
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
184 DBI::dbWriteTable(q_con, name = "l_s_peaks", value = l_s_peaks, row.names = FALSE, append = TRUE)
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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185 }
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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186
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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187 if (!is.null(l_source)) {
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
188 DBI::dbWriteTable(q_con, name = "l_source", value = l_source, row.names = FALSE, append = TRUE)
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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189 }
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52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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190
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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191 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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192
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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193
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52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
194 extractMultiple <- function(optParam) {
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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195 if (!is.na(optParam)) {
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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196 param <- trimws(strsplit(optParam, ",")[[1]])
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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197 param <- param[param != ""]
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52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
198 }else {
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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199 param <- NA
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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200 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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201 return(param)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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202
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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203 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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204
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52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
205 if (!is.null(opt$q_defaultDb)) {
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
206 q_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package = "msPurityData")
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
207 q_dbType <- "sqlite"
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
208 }else if (!opt$q_dbType == "local_config") {
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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209 q_dbType <- opt$q_dbType
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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210 q_dbPth <- opt$q_dbPth
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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211 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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212
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diff changeset
213 if (!is.null(opt$l_defaultDb)) {
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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214 l_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package = "msPurityData")
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
215 l_dbType <- "sqlite"
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
216 }else if (!opt$l_dbType == "local_config") {
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
217 l_dbType <- opt$l_dbType
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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218 l_dbPth <- opt$l_dbPth
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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219 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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220
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
221 q_spectraTypes <- extractMultiple(opt$q_spectraTypes)
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
222 l_spectraTypes <- extractMultiple(opt$l_spectraTypes)
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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223
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
224 q_polarity <- extractMultiple(opt$q_polarity)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
225 l_polarity <- extractMultiple(opt$l_polarity)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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226
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
227 q_xcmsGroups <- extractMultiple(opt$q_xcmsGroups)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
228 l_xcmsGroups <- extractMultiple(opt$l_xcmsGroups)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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229
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
230 q_pids <- extractMultiple(opt$q_pids)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
231 l_pids <- extractMultiple(opt$l_pids)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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232
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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233 q_sources <- extractMultiple(opt$q_sources)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
234 l_sources <- extractMultiple(opt$l_sources)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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235
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
236 q_sourcesUser <- extractMultiple(opt$q_sourcesUser)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
237 l_sourcesUser <- extractMultiple(opt$l_sourcesUser)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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238
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
239 q_sources <- c(q_sources, q_sourcesUser)
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
240 l_sources <- c(l_sources, l_sourcesUser)
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
241
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
242 q_instrumentTypes <- extractMultiple(opt$q_instrumentTypes)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
243 l_instrumentTypes <- extractMultiple(opt$l_instrumentTypes)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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244
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52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
245 q_instrumentTypes <- c(q_instrumentTypes, q_instrumentTypes)
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
246 l_instrumentTypes <- c(l_instrumentTypes, l_instrumentTypes)
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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247
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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248
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52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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diff changeset
249 if (!is.null(opt$l_spectraFilter)) {
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
250 l_spectraFilter <- TRUE
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
251 }else{
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
252 l_spectraFilter <- FALSE
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
253 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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254
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52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
255 if (!is.null(opt$q_spectraFilter)) {
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
256 q_spectraFilter <- TRUE
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
257 }else{
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
258 q_spectraFilter <- FALSE
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
259 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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260
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52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
261 if (!is.null(opt$updateDb)) {
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
262 updateDb <- TRUE
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
263 }else{
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
264 updateDb <- FALSE
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
265 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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266
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52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
267 if (!is.null(opt$copyDb)) {
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
268 copyDb <- TRUE
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
269 }else{
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
270 copyDb <- FALSE
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
271 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
272
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
273 if (!is.null(opt$l_rtrangeMax)) {
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
274 l_rtrangeMax <- opt$l_rtrangeMax
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
275 }else{
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
276 l_rtrangeMax <- NA
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
277 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
278
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
279 if (!is.null(opt$q_rtrangeMax)) {
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
280 q_rtrangeMax <- opt$q_rtrangeMax
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
281 }else{
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
282 q_rtrangeMax <- NA
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
283 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
284
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
285 if (!is.null(opt$l_rtrangeMin)) {
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
286 l_rtrangeMin <- opt$l_rtrangeMin
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
287 }else{
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
288 l_rtrangeMin <- NA
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
289 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
290
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
291 if (!is.null(opt$q_rtrangeMin)) {
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
292 q_rtrangeMin <- opt$q_rtrangeMin
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
293 }else{
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
294 q_rtrangeMin <- NA
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
295 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
296
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
297 q_check <- checkSPeakMeta(opt$q_dbPth, "query")
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
298 l_check <- checkSPeakMeta(opt$l_dbPth, "library")
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
299
4
8442dd3d2136 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
computational-metabolomics
parents: 0
diff changeset
300
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
301 if (q_check && l_check) {
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
302 sm <- msPurity::spectralMatching(
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
303 q_purity = opt$q_purity,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
304 l_purity = opt$l_purity,
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
305
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
306 q_ppmProd = opt$q_ppmProd,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
307 l_ppmProd = opt$l_ppmProd,
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
308
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
309 q_ppmPrec = opt$q_ppmPrec,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
310 l_ppmPrec = opt$l_ppmPrec,
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
311
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
312 q_raThres = opt$q_raThres,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
313 l_raThres = opt$l_raThres,
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
314
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
315 q_pol = q_polarity,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
316 l_pol = l_polarity,
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
317
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
318 q_spectraFilter = q_spectraFilter,
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
319 l_spectraFilter = l_spectraFilter,
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
320
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
321 q_xcmsGroups = q_xcmsGroups,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
322 l_xcmsGroups = l_xcmsGroups,
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
323
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
324 q_pids = q_pids,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
325 l_pids = l_pids,
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
326
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
327 q_sources = q_sources,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
328 l_sources = l_sources,
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
329
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
330 q_instrumentTypes = q_instrumentTypes,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
331 l_instrumentTypes = l_instrumentTypes,
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
332
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
333 q_spectraTypes = q_spectraTypes,
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
334 l_spectraTypes = l_spectraTypes,
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
335
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
336 l_rtrange = c(l_rtrangeMin, l_rtrangeMax),
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
337 q_rtrange = c(q_rtrangeMin, q_rtrangeMax),
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
338
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
339 q_accessions = opt$q_accessions,
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
340 l_accessions = opt$l_accessions,
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
341
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
342 raW = opt$raW,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
343 mzW = opt$mzW,
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
344 rttol = opt$rttol,
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
345 cores = opt$cores,
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
346
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
347 copyDb = copyDb,
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
348 updateDb = updateDb,
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
349 outPth = "db_with_spectral_matching.sqlite",
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
350
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
351 q_dbPth = q_dbPth,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
352 q_dbType = q_dbType,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
353 q_dbName = q_dbName,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
354 q_dbHost = q_dbHost,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
355 q_dbUser = q_dbUser,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
356 q_dbPass = q_dbPass,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
357 q_dbPort = q_dbPort,
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 4
diff changeset
358
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
359 l_dbPth = l_dbPth,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
360 l_dbType = l_dbType,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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361 l_dbName = l_dbName,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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362 l_dbHost = l_dbHost,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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363 l_dbUser = l_dbUser,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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364 l_dbPass = l_dbPass,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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365 l_dbPort = l_dbPort
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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366
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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367 )
6
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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368
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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369 sm <- addQueryNameColumn(sm)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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370 # Get name of the query results (and merged with the data frames)
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52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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371 write.table(sm$matchedResults, "matched_results.tsv", sep = "\t", row.names = FALSE, col.names = TRUE)
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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372 write.table(sm$xcmsMatchedResults, "xcms_matched_results.tsv", sep = "\t", row.names = FALSE, col.names = TRUE)
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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373
52d48bcd3608 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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374 if (updateDb) {
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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375 updateDbF(q_con, l_con)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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376 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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377 }