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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 07:43:58 -0500
parents e96082a25ff0
children 090775983be7
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e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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1 library(optparse)
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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2 library(msPurity)
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3 library(xcms)
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4 print(sessionInfo())
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6 xset_pa_filename_fix <- function(opt, pa, xset=NULL){
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e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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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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e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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13 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
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14 filepaths <- filepaths[filepaths != ""]
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15 new_names <- basename(filepaths)
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17 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
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18 galaxy_names <- galaxy_names[galaxy_names != ""]
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20 nsave <- names(pa@fileList)
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21 old_filenames <- basename(pa@fileList)
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23 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
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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)])
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28 }
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29 print(pa@fileList)
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31 if(!is.null(xset)){
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33 print(xset@filepaths)
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35 if(!all(basename(pa@fileList)==basename(xset@filepaths))){
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36 if(!all(names(pa@fileList)==basename(xset@filepaths))){
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37 print('FILELISTS DO NOT MATCH')
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38 message('FILELISTS DO NOT MATCH')
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39 quit(status = 1)
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40 }else{
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41 xset@filepaths <- unname(pa@fileList)
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42 }
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43 }
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44 }
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46 return(list(pa, xset))
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47 }
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48
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49
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50 option_list <- list(
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51 make_option(c("-o", "--out_dir"), type="character"),
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52 make_option("--pa", type="character"),
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53 make_option("--xset", type="character"),
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54 make_option("--ppm", default=10),
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55 make_option("--plim", default=0.0),
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56 make_option("--convert2RawRT", action="store_true"),
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57 make_option("--intense", action="store_true"),
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58 make_option("--createDB", action="store_true"),
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59 make_option("--cores", default=4),
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60 make_option("--mzML_files", type="character"),
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61 make_option("--galaxy_names", type="character"),
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62 make_option("--grp_peaklist", type="character"),
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63 make_option("--useGroup", action="store_true")
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64 )
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65
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66 # store options
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67 opt<- parse_args(OptionParser(option_list=option_list))
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68 print(opt)
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69
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70 loadRData <- function(rdata_path, name){
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71 #loads an RData file, and returns the named xset object if it is there
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72 load(rdata_path)
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73 return(get(ls()[ls() %in% name]))
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74 }
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75
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76 # This function retrieve a xset like object
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77 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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78 getxcmsSetObject <- function(xobject) {
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79 # XCMS 1.x
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80 if (class(xobject) == "xcmsSet")
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81 return (xobject)
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82 # XCMS 3.x
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83 if (class(xobject) == "XCMSnExp") {
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84 # Get the legacy xcmsSet object
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85 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
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86 sampclass(xset) <- xset@phenoData$sample_group
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87 return (xset)
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88 }
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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89 }
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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90
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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91 # Requires
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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92 pa <- loadRData(opt$pa, 'pa')
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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93 xset <- loadRData(opt$xset, c('xset','xdata'))
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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94 xset <- getxcmsSetObject(xset)
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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95
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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96 pa@cores <- opt$cores
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97
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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98 print(pa@fileList)
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99 print(xset@filepaths)
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100
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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101 if(is.null(opt$intense)){
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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102 intense = FALSE
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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103 }else{
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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104 intense = TRUE
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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105 }
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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106
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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107 if(is.null(opt$convert2RawRT)){
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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108 convert2RawRT = FALSE
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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109 }else{
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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110 convert2RawRT= TRUE
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111 }
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112
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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113 if(is.null(opt$createDB)){
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114 createDB = FALSE
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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115 }else{
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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116 createDB = TRUE
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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117 }
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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118
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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119 if(is.null(opt$useGroup)){
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120 fix <- xset_pa_filename_fix(opt, pa, xset)
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121 pa <- fix[[1]]
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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122 xset <- fix[[2]]
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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123 useGroup=FALSE
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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124 }else{
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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125 # if are only aligning to the group not eah file we do not need to align the files between the xset and pa object
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126 print('useGroup')
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127 fix <- xset_pa_filename_fix(opt, pa)
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128 pa <- fix[[1]]
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129 useGroup=TRUE
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130 }
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131
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132
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133 if(is.null(opt$grp_peaklist)){
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134 grp_peaklist = NA
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135 }else{
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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136 grp_peaklist = opt$grp_peaklist
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137 }
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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138 print(useGroup)
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139
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140
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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141
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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142 pa <- msPurity::frag4feature(pa=pa,
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143 xset=xset,
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144 ppm=opt$ppm,
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145 plim=opt$plim,
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146 intense=intense,
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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147 convert2RawRT=convert2RawRT,
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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148 db_name='alldata.sqlite',
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149 out_dir=opt$out_dir,
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computational-metabolomics
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150 grp_peaklist=grp_peaklist,
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151 create_db=createDB,
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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152 use_group=useGroup)
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153
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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154 print(pa)
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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155 save(pa, file=file.path(opt$out_dir, 'frag4feature_output.RData'))
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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156
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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157 pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)])
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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158
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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159 print(head(pa@grped_df))
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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160 write.table(pa@grped_df, file.path(opt$out_dir, 'frag4feature_output.tsv'), row.names=FALSE, sep='\t')