Mercurial > repos > computational-metabolomics > mspurity_frag4feature

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 94f746247c464fb270358421399810d8a9fb9e8a
author computational-metabolomics
date Fri, 13 Sep 2024 13:37:23 +0000
parents cb4aeec93d49
children
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ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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1 library(msPurity)
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2 library(optparse)
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3 library(xcms)
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4 library(CAMERA)
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5 print(sessionInfo())
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6 print("CREATING DATABASE")
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8 xset_pa_filename_fix <- function(opt, pa, xset) {
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9 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)) {
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10 # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
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11 # needs to be done due to Galaxy moving the files around and screwing up any links to files
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13 filepaths <- trimws(strsplit(opt$mzML_files, ",")[[1]])
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14 filepaths <- filepaths[filepaths != ""]
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16 galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]])
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17 galaxy_names <- galaxy_names[galaxy_names != ""]
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19 nsave <- names(pa@fileList)
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20 old_filenames <- basename(pa@fileList)
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21 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
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22 names(pa@fileList) <- nsave
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24 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
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25 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
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26 }
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29 if (!all(basename(pa@fileList) == basename(xset@filepaths))) {
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30 if (!all(names(pa@fileList) == basename(xset@filepaths))) {
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31 print("FILELISTS DO NOT MATCH")
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32 message("FILELISTS DO NOT MATCH")
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33 quit(status = 1)
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34 } else {
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35 xset@filepaths <- unname(pa@fileList)
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36 }
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37 }
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39 print(xset@phenoData)
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40 print(xset@filepaths)
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42 return(list(pa, xset))
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43 }
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48 option_list <- list(
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49 make_option(c("-o", "--outDir"), type = "character"),
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50 make_option("--pa", type = "character"),
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51 make_option("--xset_xa", type = "character"),
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52 make_option("--xcms_camera_option", type = "character"),
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53 make_option("--eic", action = "store_true"),
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54 make_option("--cores", default = 4),
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55 make_option("--mzML_files", type = "character"),
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56 make_option("--galaxy_names", type = "character"),
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57 make_option("--grpPeaklist", type = "character")
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58 )
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61 # store options
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62 opt <- parse_args(OptionParser(option_list = option_list))
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63 print(opt)
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64
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65 loadRData <- function(rdata_path, name) {
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66 # loads an RData file, and returns the named xset object if it is there
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67 load(rdata_path)
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68 return(get(ls()[ls() %in% name]))
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69 }
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71 getxcmsSetObject <- function(xobject) {
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72 # XCMS 1.x
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73 if (class(xobject) == "xcmsSet") {
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74 return(xobject)
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75 }
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76 # XCMS 3.x
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77 if (class(xobject) == "XCMSnExp") {
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78 # Get the legacy xcmsSet object
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79 suppressWarnings(xset <- as(xobject, "xcmsSet"))
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80 xcms::sampclass(xset) <- xset@phenoData$sample_group
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81 return(xset)
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82 }
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83 }
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86 print(paste("pa", opt$pa))
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87 print(opt$xset)
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89 print(opt$xcms_camera_option)
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90 # Requires
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91 pa <- loadRData(opt$pa, "pa")
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92
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93
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94 print(pa@fileList)
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95
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96 # Missing list element causes failures (should be updated
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97 # in msPurity R package for future releases)
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98 if (!exists("allfrag", where = pa@filter_frag_params)) {
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99 pa@filter_frag_params$allfrag <- FALSE
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100 }
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101
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102 if (opt$xcms_camera_option == "xcms") {
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103 xset <- loadRData(opt$xset, c("xset", "xdata"))
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104 xset <- getxcmsSetObject(xset)
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105 fix <- xset_pa_filename_fix(opt, pa, xset)
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106 pa <- fix[[1]]
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107 xset <- fix[[2]]
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108 xa <- NULL
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109 } else {
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110 xa <- loadRData(opt$xset, "xa")
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111 fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet)
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112 pa <- fix[[1]]
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113 xa@xcmsSet <- fix[[2]]
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114 xset <- NULL
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115 }
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116
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117
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118 if (is.null(opt$grpPeaklist)) {
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119 grpPeaklist <- NA
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120 } else {
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121 grpPeaklist <- opt$grpPeaklist
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122 }
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123
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124 dbPth <- msPurity::createDatabase(pa,
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125 xset = xset,
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126 xsa = xa,
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127 outDir = opt$outDir,
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128 grpPeaklist = grpPeaklist,
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129 dbName = "createDatabase_output.sqlite"
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130 )
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131
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132
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133
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134
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135
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136 if (!is.null(opt$eic)) {
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137 if (is.null(xset)) {
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138 xset <- xa@xcmsSet
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139 }
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140 # previous check should have matched filelists together
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141 xset@filepaths <- unname(pa@fileList)
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142
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143 convert2Raw <- function(x, xset) {
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144 sid <- unique(x$sample)
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145 # for each file get list of peaks
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146 x$rt_raw <- xset@rt$raw[[sid]][match(x$rt, xset@rt$corrected[[sid]])]
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147 x$rtmin_raw <- xset@rt$raw[[sid]][match(x$rtmin, xset@rt$corrected[[sid]])]
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148 x$rtmax_raw <- xset@rt$raw[[sid]][match(x$rtmax, xset@rt$corrected[[sid]])]
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149 return(x)
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150 }
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151
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152 xset@peaks <- as.matrix(
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153 plyr::ddply(data.frame(xset@peaks), ~sample, convert2Raw, xset = xset)
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154 )
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155
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156 # Saves the EICS into the previously created database
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157 px <- msPurity::purityX(xset,
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158 saveEIC = TRUE,
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159 cores = 1,
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160 sqlitePth = dbPth,
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161 rtrawColumns = TRUE
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162 )
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163 }
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164
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165 closeAllConnections()