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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 07:45:02 -0500
parents f52287a06c02
children 2f71b3495221
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f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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1 library(msPurity)
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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2 library(optparse)
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3 print(sessionInfo())
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4 option_list <- list(
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5 make_option(c("-o", "--out_dir"), type="character", default=getwd(),
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6 help="Output folder for resulting files [default = %default]"
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7 ),
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8 make_option(c("-x", "--xset_path"), type="character", default=file.path(getwd(),"xset.rds"),
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9 help="The path to the xcmsSet object [default = %default]"
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10 ),
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11 make_option("--polarity", default=NA,
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12 help="polarity (just used for naming purpose for files being saved) [positive, negative, NA] [default %default]"
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13 ),
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14 make_option("--rsd_i_blank", default=100,
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15 help="RSD threshold for the blank [default = %default]"
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16 ),
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17 make_option("--minfrac_blank", default=0.5,
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18 help="minimum fraction of files for features needed for the blank [default = %default]"
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19 ),
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20 make_option("--rsd_rt_blank", default=100,
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21 help="RSD threshold for the RT of the blank [default = %default]"
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22 ),
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23
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24 make_option("--ithres_blank", default=0,
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25 help="Intensity threshold for the blank [default = %default]"
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26 ),
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27 make_option("--s2b", default=10,
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28 help="fold change (sample/blank) needed for sample peak to be allowed. e.g.
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29 if s2b set to 10 and the recorded sample 'intensity' value was 100 and blank was 10.
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30 1000/10 = 100, so sample has fold change higher than the threshold and the peak
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31 is not considered a blank [default = %default]"
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33 make_option("--blank_class", default='blank', type="character",
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34 help="A string representing the class that will be used for the blank.[default = %default]"
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35 ),
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36 make_option("--egauss_thr", default=NA,
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37 help="Threshold for filtering out non gaussian shaped peaks. Note this only works
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38 if the 'verbose columns' and 'fit gauss' was used with xcms
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39 [default = %default]"
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40 ),
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41 make_option("--rsd_i_sample", default=100,
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42 help="RSD threshold for the samples [default = %default]"
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43 ),
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44 make_option("--minfrac_sample", default=0.8,
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45 help="minimum fraction of files for features needed for the samples [default = %default]"
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46 ),
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47 make_option("--rsd_rt_sample", default=100,
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48 help="RSD threshold for the RT of the samples [default = %default]"
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49 ),
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50 make_option("--ithres_sample", default=5000,
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51 help="Intensity threshold for the sample [default = %default]"
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52 ),
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53 make_option("--grp_rm_ids", default=NA,
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54 help="vector of grouped_xcms peaks to remove (corresponds to the row from xcms::group output)
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55 [default = %default]"
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57 make_option("--remove_spectra", action="store_true",
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58 help=" TRUE if flagged spectra is to be removed [default = %default]"
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59 ),
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60 make_option("--minfrac_xcms", default=0.5,
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61 help="minfrac for xcms grouping [default = %default]"
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62 ),
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63 make_option("--mzwid", default=0.001,
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64 help="mzwid for xcms grouping [default = %default]"
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65 ),
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66 make_option("--bw", default=5,
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67 help="bw for xcms grouping [default = %default]"
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68 ),
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69
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70 make_option("--temp_save", action="store_true",
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71 help="Assign True if files for each step saved (for testing purposes) [default = %default]"
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72 ),
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74 make_option("--samplelist", type="character", help="Sample list to determine the blank class")
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80 )
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82 #make_option("--multilist", action="store_true"
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83 # help="NOT CURRENTLY IMPLEMENTED: If paired blank removal is to be performed a - multilist - sample list file has to be provided"
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84 #),
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86 # store options
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87 opt<- parse_args(OptionParser(option_list=option_list))
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88
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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89 opt <- replace(opt, opt == "NA", NA)
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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90
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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91
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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92
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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93
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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94 if (is.null(opt$temp_save)){
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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95 temp_save<-FALSE
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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96 }else{
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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97 temp_save<-TRUE
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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98 }
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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99
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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100 if (is.null(opt$remove_spectra)){
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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101 remove_spectra<-FALSE
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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102 }else{
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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103 remove_spectra<-TRUE
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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104 }
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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105
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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106
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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107 print(opt)
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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108
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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109 getxcmsSetObject <- function(xobject) {
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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110 # XCMS 1.x
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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111 if (class(xobject) == "xcmsSet")
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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112 return (xobject)
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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113 # XCMS 3.x
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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114 if (class(xobject) == "XCMSnExp") {
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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115 # Get the legacy xcmsSet object
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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116 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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117 sampclass(xset) <- xset@phenoData$sample_group
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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118 return (xset)
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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119 }
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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120 }
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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121
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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122
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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123 loadRData <- function(rdata_path, name){
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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124 #loads an RData file, and returns the named xset object if it is there
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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125 load(rdata_path)
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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126 return(get(ls()[ls() %in% name]))
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computational-metabolomics
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127 }
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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128
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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129 xset <- getxcmsSetObject(loadRData(opt$xset_path, c('xset','xdata')))
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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130
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131 print(xset)
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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132 if (is.null(opt$samplelist)){
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computational-metabolomics
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133 blank_class <- opt$blank_class
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computational-metabolomics
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134 }else{
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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135 samplelist <- read.table(opt$samplelist, sep='\t', header=TRUE)
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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136 samplelist_blank <- unique(samplelist$sample_class[samplelist$blank=='yes'])
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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137
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computational-metabolomics
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138 chosen_blank <- samplelist_blank[samplelist_blank %in% xset@phenoData$class]
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
139 if (length(chosen_blank)>1){
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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140 print('ERROR: only 1 blank is currently allowed to be used with this tool')
1
600a866a510c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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141 quit()
0
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142 }
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computational-metabolomics
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143 blank_class <- as.character(chosen_blank)
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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144 print(blank_class)
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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145 }
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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146
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147
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diff changeset
148 if (is.null(opt$multilist)){
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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149 ffrm_out <- flag_remove(xset,
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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150 pol=opt$polarity,
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computational-metabolomics
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151 rsd_i_blank=opt$rsd_i_blank,
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computational-metabolomics
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152 minfrac_blank=opt$minfrac_blank,
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computational-metabolomics
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153 rsd_rt_blank=opt$rsd_rt_blank,
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
154 ithres_blank=opt$ithres_blank,
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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155 s2b=opt$s2b,
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
156 ref.class=blank_class,
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
157 egauss_thr=opt$egauss_thr,
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
158 rsd_i_sample=opt$rsd_i_sample,
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
159 minfrac_sample=opt$minfrac_sample,
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
160 rsd_rt_sample=opt$rsd_rt_sample,
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
161 ithres_sample=opt$ithres_sample,
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
162 minfrac_xcms=opt$minfrac_xcms,
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
163 mzwid=opt$mzwid,
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
164 bw=opt$bw,
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
165 out_dir=opt$out_dir,
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
166 temp_save=temp_save,
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
167 remove_spectra=remove_spectra,
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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168 grp_rm_ids=unlist(strsplit(as.character(opt$grp_rm_ids), split=", "))[[1]])
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
169 print('flag remove finished')
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
170 xset <- ffrm_out[[1]]
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
171 grp_peaklist <- ffrm_out[[2]]
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
172 removed_peaks <- ffrm_out[[3]]
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
173
1
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computational-metabolomics
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diff changeset
174 save.image(file=file.path(opt$out_dir, 'xset_filtered.RData'), version=2)
0
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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175
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
176 # grpid needed for mspurity ID needed for deconrank... (will clean up at some up)
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
177 peak_pth <- file.path(opt$out_dir, 'peaklist_filtered.tsv')
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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178 print(peak_pth)
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179 write.table(data.frame('grpid'=rownames(grp_peaklist), 'ID'=rownames(grp_peaklist), grp_peaklist),
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180 peak_pth, row.names=FALSE, sep='\t')
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181
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182 removed_peaks <- data.frame(removed_peaks)
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183 write.table(data.frame('ID'=rownames(removed_peaks),removed_peaks),
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184 file.path(opt$out_dir, 'removed_peaks.tsv'), row.names=FALSE, sep='\t')
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185
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186 }else{
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187
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188
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189 # TODO
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190 #xsets <- split(xset, multilist_df$multlist)
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191 #
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192 #mult_grps <- unique(multilist_df$multlist)
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193 #
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194 #for (mgrp in mult_grps){
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195 # xset_i <- xsets[mgrp]
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196 # xcms::group(xset_i,
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197 #
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198 # }
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199
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200
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201
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202 }
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203
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204