Mercurial > repos > computational-metabolomics > mspurity_combineannotations

annotate createDatabase.R @ 1:cf62d2c0104e draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
author computational-metabolomics
date Thu, 05 Dec 2019 07:47:31 -0500
parents 7f3183988100
children d4376a743f7b
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7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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1 library(msPurity)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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2 library(optparse)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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3 library(xcms)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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4 library(CAMERA)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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5 print(sessionInfo())
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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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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7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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10 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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11 # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
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12 # needs to be done due to Galaxy moving the files around and screwing up any links to files
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7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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14 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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15 filepaths <- filepaths[filepaths != ""]
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16 new_names <- basename(filepaths)
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18 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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19 galaxy_names <- galaxy_names[galaxy_names != ""]
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21 nsave <- names(pa@fileList)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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22 old_filenames <- basename(pa@fileList)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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23 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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24 names(pa@fileList) <- nsave
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26 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
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27 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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28 }
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31 if(!all(basename(pa@fileList)==basename(xset@filepaths))){
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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32 if(!all(names(pa@fileList)==basename(xset@filepaths))){
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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33 print('FILELISTS DO NOT MATCH')
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34 message('FILELISTS DO NOT MATCH')
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35 quit(status = 1)
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36 }else{
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37 xset@filepaths <- unname(pa@fileList)
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38 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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39 }
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41 print(xset@phenoData)
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42 print(xset@filepaths)
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44 return(list(pa, xset))
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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45 }
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50 option_list <- list(
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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51 make_option(c("-o", "--outDir"), type="character"),
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52 make_option("--pa", type="character"),
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53 make_option("--xset_xa", type="character"),
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54 make_option("--xcms_camera_option", type="character"),
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55 make_option("--eic", action="store_true"),
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56 make_option("--cores", default=4),
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57 make_option("--mzML_files", type="character"),
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58 make_option("--galaxy_names", type="character"),
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59 make_option("--grpPeaklist", type="character")
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60 )
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63 # store options
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64 opt<- parse_args(OptionParser(option_list=option_list))
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65 print(opt)
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66
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67 loadRData <- function(rdata_path, name){
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68 #loads an RData file, and returns the named xset object if it is there
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69 load(rdata_path)
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70 return(get(ls()[ls() %in% name]))
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71 }
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73 getxcmsSetObject <- function(xobject) {
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74 # XCMS 1.x
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75 if (class(xobject) == "xcmsSet")
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76 return (xobject)
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77 # XCMS 3.x
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78 if (class(xobject) == "XCMSnExp") {
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79 # Get the legacy xcmsSet object
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80 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
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81 sampclass(xset) <- xset@phenoData$sample_group
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82 return (xset)
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83 }
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84 }
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85
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86
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87 print(paste('pa', opt$pa))
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88 print(opt$xset)
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89
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90 print(opt$xcms_camera_option)
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91 # Requires
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92 pa <- loadRData(opt$pa, 'pa')
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93
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94
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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95 print(pa@fileList)
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96
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97
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98
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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99 if (opt$xcms_camera_option=='xcms'){
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100
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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101 xset <- loadRData(opt$xset, c('xset','xdata'))
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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102 xset <- getxcmsSetObject(xset)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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103 fix <- xset_pa_filename_fix(opt, pa, xset)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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104 pa <- fix[[1]]
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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105 xset <- fix[[2]]
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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106 xa <- NULL
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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107 }else{
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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108
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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109 xa <- loadRData(opt$xset, 'xa')
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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110 fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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111 pa <- fix[[1]]
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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112 xa@xcmsSet <- fix[[2]]
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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113 xset <- NULL
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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114 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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115
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116
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117
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118 if(is.null(opt$grp_peaklist)){
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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119 grpPeaklist = NA
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120 }else{
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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121 grpPeaklist = opt$grp_peaklist
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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122 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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123
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124
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125
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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126 dbPth <- msPurity::createDatabase(pa,
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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127 xset=xset,
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128 xsa=xa,
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129 outDir=opt$outDir,
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130 grpPeaklist=grpPeaklist,
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131 dbName='createDatabase_output.sqlite'
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132 )
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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133
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134
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135
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136
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137
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138 if (!is.null(opt$eic)){
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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139
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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140 if (is.null(xset)){
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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141 xset <- xa@xcmsSet
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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142 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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143 # previous check should have matched filelists together
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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144 xset@filepaths <- unname(pa@fileList)
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145
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146 convert2Raw <- function(x, xset){
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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147 sid <- unique(x$sample)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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148 # for each file get list of peaks
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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149 x$rt_raw <- xset@rt$raw[[sid]][match(x$rt, xset@rt$corrected[[sid]])]
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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150 x$rtmin_raw <- xset@rt$raw[[sid]][match(x$rtmin, xset@rt$corrected[[sid]])]
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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151 x$rtmax_raw <- xset@rt$raw[[sid]][match(x$rtmax, xset@rt$corrected[[sid]])]
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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152 return(x)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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153
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154 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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155
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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156 xset@peaks <- as.matrix(plyr::ddply(data.frame(xset@peaks), ~ sample, convert2Raw, xset=xset))
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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157
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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158 # Saves the EICS into the previously created database
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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159 px <- msPurity::purityX(xset,
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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160 saveEIC = TRUE,
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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161 cores=1,
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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162 sqlitePth=dbPth,
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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163 rtrawColumns = TRUE)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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164
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165 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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166
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167 closeAllConnections()