Mercurial > repos > computational-metabolomics > mspurity_dimspredictpuritysingle

annotate purityX.R @ 7:2ce66d2f6a24 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
author computational-metabolomics
date Tue, 08 Feb 2022 13:59:55 +0000
parents 090775983be7
children 75b761fbacc0
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e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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diff changeset
1 library(msPurity)
e96082a25ff0 "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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5 option_list <- list(
6
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6 make_option(c("--xset_path"), type = "character"),
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7 make_option(c("-o", "--out_dir"), type = "character"),
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8 make_option(c("--mzML_path"), type = "character"),
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9 make_option("--minOffset", default = 0.5),
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10 make_option("--maxOffset", default = 0.5),
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11 make_option("--ilim", default = 0.05),
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12 make_option("--iwNorm", default = "none", type = "character"),
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13 make_option("--exclude_isotopes", action = "store_true"),
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14 make_option("--isotope_matrix", type = "character"),
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15 make_option("--purityType", default = "purityFWHMmedian"),
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16 make_option("--singleFile", default = 0),
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17 make_option("--cores", default = 4),
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18 make_option("--xgroups", type = "character"),
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19 make_option("--rdata_name", default = "xset"),
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20 make_option("--camera_xcms", default = "xset"),
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21 make_option("--files", type = "character"),
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22 make_option("--galaxy_files", type = "character"),
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23 make_option("--choose_class", type = "character"),
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24 make_option("--ignore_files", type = "character"),
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25 make_option("--rtraw_columns", action = "store_true")
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26 )
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29 opt <- parse_args(OptionParser(option_list = option_list))
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30 print(opt)
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33 if (!is.null(opt$xgroups)) {
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34 xgroups <- as.numeric(strsplit(opt$xgroups, ",")[[1]])
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35 }else{
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36 xgroups <- NULL
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37 }
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40 print(xgroups)
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41
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42 if (!is.null(opt$remove_nas)) {
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43 df <- df[!is.na(df$mz), ]
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44 }
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46 if (is.null(opt$isotope_matrix)) {
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47 im <- NULL
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48 }else{
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49 im <- read.table(opt$isotope_matrix,
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50 header = TRUE, sep = "\t", stringsAsFactors = FALSE)
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51 }
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53 if (is.null(opt$exclude_isotopes)) {
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54 isotopes <- FALSE
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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55 }else{
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56 isotopes <- TRUE
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57 }
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59 if (is.null(opt$rtraw_columns)) {
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60 rtraw_columns <- FALSE
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61 }else{
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62 rtraw_columns <- TRUE
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63 }
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64
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65 loadRData <- function(rdata_path, xset_name) {
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66 #loads an RData file, and returns the named xset object if it is there
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67 load(rdata_path)
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68 return(get(ls()[ls() == xset_name]))
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69 }
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71 target_obj <- loadRData(opt$xset_path, opt$rdata_name)
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73 if (opt$camera_xcms == "camera") {
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74 xset <- target_obj@xcmsSet
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75 }else{
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76 xset <- target_obj
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77 }
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79 print(xset)
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81 minOffset <- as.numeric(opt$minOffset)
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82 maxOffset <- as.numeric(opt$maxOffset)
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84 if (opt$iwNorm == "none") {
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85 iwNorm <- FALSE
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86 iwNormFun <- NULL
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87 }else if (opt$iwNorm == "gauss") {
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88 iwNorm <- TRUE
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89 iwNormFun <- msPurity::iwNormGauss(minOff = -minOffset, maxOff = maxOffset)
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90 }else if (opt$iwNorm == "rcosine") {
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91 iwNorm <- TRUE
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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92 iwNormFun <- msPurity::iwNormRcosine(minOff = -minOffset, maxOff = maxOffset)
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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93 }else if (opt$iwNorm == "QE5") {
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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94 iwNorm <- TRUE
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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95 iwNormFun <- msPurity::iwNormQE.5()
0
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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96 }
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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97
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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98 print(xset@filepaths)
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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99
6
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computational-metabolomics
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100 if (!is.null(opt$files)) {
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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101 updated_filepaths <- trimws(strsplit(opt$files, ",")[[1]])
0
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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102 updated_filepaths <- updated_filepaths[updated_filepaths != ""]
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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103 print(updated_filepaths)
6
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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104 updated_filenames <- basename(updated_filepaths)
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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105 original_filenames <- basename(xset@filepaths)
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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106 update_idx <- match(updated_filenames, original_filenames)
0
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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107
6
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computational-metabolomics
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108 if (!is.null(opt$galaxy_files)) {
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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109 galaxy_files <- trimws(strsplit(opt$galaxy_files, ",")[[1]])
0
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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110 galaxy_files <- galaxy_files[galaxy_files != ""]
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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111 xset@filepaths <- galaxy_files[update_idx]
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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112 }else{
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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113 xset@filepaths <- updated_filepaths[update_idx]
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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114 }
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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115 }
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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116
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117 if (!is.null(opt$choose_class)) {
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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118 classes <- trimws(strsplit(opt$choose_class, ",")[[1]])
0
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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119
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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120 ignore_files_class <- which(!as.character(xset@phenoData$class) %in% classes)
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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121
6
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122 print("choose class")
0
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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123 print(ignore_files_class)
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 ignore_files_class <- NA
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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126 }
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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127
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128 if (!is.null(opt$ignore_files)) {
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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129 ignore_files_string <- trimws(strsplit(opt$ignore_files, ",")[[1]])
0
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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130 filenames <- rownames(xset@phenoData)
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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131 ignore_files <- which(filenames %in% ignore_files_string)
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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132
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133 ignore_files <- unique(c(ignore_files, ignore_files_class))
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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134 ignore_files <- ignore_files[ignore_files != ""]
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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135 }else{
6
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136 if (anyNA(ignore_files_class)) {
0
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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137 ignore_files <- NULL
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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138 }else{
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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139 ignore_files <- ignore_files_class
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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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
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142 }
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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143
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144 print("ignore_files")
0
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145 print(ignore_files)
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146
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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147
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148 ppLCMS <- msPurity::purityX(xset = xset,
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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149 offsets = c(minOffset, maxOffset),
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
150 cores = opt$cores,
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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151 xgroups = xgroups,
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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152 purityType = opt$purityType,
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
153 ilim = opt$ilim,
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
154 isotopes = isotopes,
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
155 im = im,
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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156 iwNorm = iwNorm,
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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157 iwNormFun = iwNormFun,
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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158 singleFile = opt$singleFile,
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
159 fileignore = ignore_files,
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
160 rtrawColumns = rtraw_columns)
0
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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161
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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162 dfp <- ppLCMS@predictions
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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163
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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164 # to make compatable with deconrank
6
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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165 colnames(dfp)[colnames(dfp) == "grpid"] <- "peakID"
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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166 colnames(dfp)[colnames(dfp) == "median"] <- "medianPurity"
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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167 colnames(dfp)[colnames(dfp) == "mean"] <- "meanPurity"
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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168 colnames(dfp)[colnames(dfp) == "sd"] <- "sdPurity"
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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169 colnames(dfp)[colnames(dfp) == "stde"] <- "sdePurity"
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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170 colnames(dfp)[colnames(dfp) == "RSD"] <- "cvPurity"
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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171 colnames(dfp)[colnames(dfp) == "pknm"] <- "pknmPurity"
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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172
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173 if (sum(is.na(dfp$medianPurity)) > 0) {
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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174 dfp[is.na(dfp$medianPurity), ]$medianPurity <- 0
0
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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175 }
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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176
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177 print(head(dfp))
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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178 write.table(dfp, file.path(opt$out_dir, "purityX_output.tsv"), row.names = FALSE, sep = "\t")
0
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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179
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180 save.image(file.path(opt$out_dir, "purityX_output.RData"))