Mercurial > repos > computational-metabolomics > mspurity_combineannotations

annotate createDatabase.R @ 5:03b45dceb134 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit b1b879e29d5d6c97fdc3636aa6e900ad03695f9e"
author computational-metabolomics
date Fri, 13 Nov 2020 09:57:42 +0000
parents 20768ba7f0b4
children 18c0038dde9c
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7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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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)){
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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$mzML_files, ',')[[1]])
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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15 filepaths <- filepaths[filepaths != ""]
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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16 new_names <- basename(filepaths)
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18 galaxy_names <- trimws(strsplit(opt$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)])
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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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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7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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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')
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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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 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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41 print(xset@phenoData)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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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$pa, 'pa')
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93
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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94
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95 print(pa@fileList)
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96
4
20768ba7f0b4 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
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97 # Missing list element causes failures (should be updated
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98 # in msPurity R package for future releases)
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99 if (!exists('allfrag', where=pa@filter_frag_params)){
20768ba7f0b4 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
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100 pa@filter_frag_params$allfrag <- FALSE
20768ba7f0b4 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
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101 }
0
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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102
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103 if (opt$xcms_camera_option=='xcms'){
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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104
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105 xset <- loadRData(opt$xset, c('xset','xdata'))
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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106 xset <- getxcmsSetObject(xset)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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107 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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108 pa <- fix[[1]]
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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109 xset <- fix[[2]]
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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110 xa <- NULL
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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111 }else{
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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112
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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113 xa <- loadRData(opt$xset, 'xa')
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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114 fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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115 pa <- fix[[1]]
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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116 xa@xcmsSet <- fix[[2]]
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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117 xset <- NULL
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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118 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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119
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120
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121
2
d4376a743f7b "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 242de155f13acd6cb88946e89b5196ac55578aa8"
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122 if(is.null(opt$grpPeaklist)){
0
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123 grpPeaklist = NA
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124 }else{
2
d4376a743f7b "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 242de155f13acd6cb88946e89b5196ac55578aa8"
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125 grpPeaklist = opt$grpPeaklist
0
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126 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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127
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128
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129
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130 dbPth <- msPurity::createDatabase(pa,
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131 xset=xset,
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132 xsa=xa,
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133 outDir=opt$outDir,
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134 grpPeaklist=grpPeaklist,
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135 dbName='createDatabase_output.sqlite'
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136 )
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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137
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138
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139
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140
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141
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142 if (!is.null(opt$eic)){
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143
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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144 if (is.null(xset)){
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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145 xset <- xa@xcmsSet
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146 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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147 # previous check should have matched filelists together
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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148 xset@filepaths <- unname(pa@fileList)
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149
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150 convert2Raw <- function(x, xset){
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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151 sid <- unique(x$sample)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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152 # 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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153 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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154 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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155 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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156 return(x)
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 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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159
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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160 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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161
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162 # 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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163 px <- msPurity::purityX(xset,
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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164 saveEIC = TRUE,
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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165 cores=1,
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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166 sqlitePth=dbPth,
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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167 rtrawColumns = TRUE)
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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168
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169 }
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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170
7f3183988100 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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171 closeAllConnections()