Mercurial > repos > tomnl > assess_purity_msms

annotate anticipated_purity_lcms.R @ 23:c5ba85825284 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 04023134d8f28e85927ca293373c506484149ead-dirty
author tomnl
date Fri, 01 Jun 2018 15:28:32 -0400
parents faba6cd56875
children
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b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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1 library(msPurity)
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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2 library(optparse)
2
146699c00d38 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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3 print(sessionInfo())
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4
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5 option_list <- list(
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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6 make_option(c("--xset_path"), type="character"),
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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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"),
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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13 make_option("--exclude_isotopes", action="store_true"),
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14 make_option("--isotope_matrix", type="character"),
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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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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27
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28 # store options
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29 opt<- parse_args(OptionParser(option_list=option_list))
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30
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31 print(sessionInfo())
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32 print(opt)
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33
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34 if (!is.null(opt$xgroups)){
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35 xgroups = as.numeric(strsplit(opt$xgroups, ',')[[1]])
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36 }else{
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37 xgroups = NULL
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38 }
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39
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40
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42 print(xgroups)
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43
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44 if (!is.null(opt$remove_nas)){
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45 df <- df[!is.na(df$mz),]
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46 }
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47
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48 if (is.null(opt$isotope_matrix)){
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49 im <- NULL
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50 }else{
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51 im <- read.table(opt$isotope_matrix,
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52 header = TRUE, sep='\t', stringsAsFactors = FALSE)
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53 }
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54
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55 if (is.null(opt$exclude_isotopes)){
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56 isotopes <- FALSE
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57 }else{
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58 isotopes <- TRUE
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59 }
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60
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61 if (is.null(opt$rtraw_columns)){
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62 rtraw_columns <- FALSE
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63 }else{
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64 rtraw_columns <- TRUE
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65 }
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66
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67 loadRData <- function(rdata_path, xset_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 print(ls())
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71 return(get(ls()[ls() == xset_name]))
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72 }
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73
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74 target_obj <- loadRData(opt$xset_path, opt$rdata_name)
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75
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76 if (opt$camera_xcms=='camera'){
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77 xset <- target_obj@xcmsSet
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78 }else{
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79 xset <- target_obj
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80 }
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81
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82 print(xset)
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83
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84 minOffset = as.numeric(opt$minOffset)
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85 maxOffset = as.numeric(opt$maxOffset)
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86
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87
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88 if (opt$iwNorm=='none'){
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89 iwNorm = FALSE
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90 iwNormFun = NULL
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91 }else if (opt$iwNorm=='gauss'){
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92 iwNorm = TRUE
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93 iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset)
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94 }else if (opt$iwNorm=='rcosine'){
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
95 iwNorm = TRUE
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
96 iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset)
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
97 }else if (opt$iwNorm=='QE5'){
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
98 iwNorm = TRUE
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
99 iwNormFun = msPurity::iwNormQE.5()
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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100 }
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101
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parents:
diff changeset
102 print(xset@filepaths)
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103
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104
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105
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parents:
diff changeset
106 if (!is.null(opt$files)){
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
107 updated_filepaths <- trimws(strsplit(opt$files, ',')[[1]])
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
108 updated_filepaths <- updated_filepaths[updated_filepaths != ""]
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
109 print(updated_filepaths)
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
110 updated_filenames = basename(updated_filepaths)
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
111 original_filenames = basename(xset@filepaths)
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
112 update_idx = match(updated_filenames, original_filenames)
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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diff changeset
113
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parents:
diff changeset
114 if (!is.null(opt$galaxy_files)){
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
115 galaxy_files <- trimws(strsplit(opt$galaxy_files, ',')[[1]])
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
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116 galaxy_files <- galaxy_files[galaxy_files != ""]
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
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117 xset@filepaths <- galaxy_files[update_idx]
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
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118 }else{
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
119 xset@filepaths <- updated_filepaths[update_idx]
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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120 }
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parents:
diff changeset
121 }
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122
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parents:
diff changeset
123 if (!is.null(opt$choose_class)){
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
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124 classes <- trimws(strsplit(opt$choose_class, ',')[[1]])
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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125
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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126
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127 ignore_files_class <- which(!as.character(xset@phenoData$class) %in% classes)
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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128
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
129 print('choose class')
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
130 print(ignore_files_class)
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
131 }else{
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
132 ignore_files_class <- NA
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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diff changeset
133 }
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diff changeset
134
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parents:
diff changeset
135 if (!is.null(opt$ignore_files)){
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
136 ignore_files_string <- trimws(strsplit(opt$ignore_files, ',')[[1]])
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
137 filenames <- rownames(xset@phenoData)
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
138 ignore_files <- which(filenames %in% ignore_files_string)
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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diff changeset
139
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
140 ignore_files <- unique(c(ignore_files, ignore_files_class))
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
141 ignore_files <- ignore_files[ignore_files != ""]
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
142 }else{
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
143 if (anyNA(ignore_files_class)){
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
144 ignore_files <- NULL
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
145 }else{
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
146 ignore_files <- ignore_files_class
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
147 }
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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148
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diff changeset
149 }
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
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150
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parents:
diff changeset
151 print('ignore_files')
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
152 print(ignore_files)
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153
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parents:
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154
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parents:
diff changeset
155 ppLCMS <- msPurity::purityX(xset=xset,
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
156 offsets=c(minOffset, maxOffset),
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
157 cores=opt$cores,
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
158 xgroups=xgroups,
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
159 purityType=opt$purityType,
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
160 ilim = opt$ilim,
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
161 isotopes = isotopes,
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
162 im = im,
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
163 iwNorm = iwNorm,
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
164 iwNormFun = iwNormFun,
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
165 singleFile = opt$singleFile,
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
166 fileignore = ignore_files,
5
faba6cd56875 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 2
diff changeset
167 rtrawColumns=rtraw_columns)
0
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
168
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parents:
diff changeset
169
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
170 dfp <- ppLCMS@predictions
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
171
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parents:
diff changeset
172 # to make compatable with deconrank
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
173 colnames(dfp)[colnames(dfp)=='grpid'] = 'peakID'
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
174 colnames(dfp)[colnames(dfp)=='median'] = 'medianPurity'
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
175 colnames(dfp)[colnames(dfp)=='mean'] = 'meanPurity'
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
176 colnames(dfp)[colnames(dfp)=='sd'] = 'sdPurity'
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
177 colnames(dfp)[colnames(dfp)=='stde'] = 'sdePurity'
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
178 colnames(dfp)[colnames(dfp)=='RSD'] = 'cvPurity'
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
179 colnames(dfp)[colnames(dfp)=='pknm'] = 'pknmPurity'
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
180 if(sum(is.na(dfp$medianPurity))>0){
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
181 dfp[is.na(dfp$medianPurity),]$medianPurity = 0
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
182 }
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parents:
diff changeset
183
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parents:
diff changeset
184 print('saving tsv')
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
185 print(head(dfp))
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
186 write.table(dfp, file.path(opt$out_dir, 'anticipated_purity_lcms.tsv'), row.names=FALSE, sep='\t')
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
187 print('saving RData')
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
diff changeset
188 save.image(file.path(opt$out_dir, 'anticipated_purity_lcms.RData'))