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annotate assess_purity_msms.R @ 3:8b043ee376db draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a598583947118bd50cfe5ae12d955c20d6e502a6
author tomnl
date Tue, 17 Jul 2018 12:32:50 -0400
parents 58ee3687f776
children
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58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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1 library(msPurity)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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2 library(optparse)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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3 print(sessionInfo())
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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4
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5 option_list <- list(
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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6 make_option(c("-o", "--out_dir"), type="character"),
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7 make_option("--mzML_files", type="character"),
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8 make_option("--galaxy_names", type="character"),
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9 make_option("--minOffset", default=0.5),
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10 make_option("--maxOffset", default=0.5),
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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11 make_option("--ilim", default=0.05),
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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12 make_option("--iwNorm", default="none", type="character"),
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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13 make_option("--exclude_isotopes", action="store_true"),
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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14 make_option("--isotope_matrix", type="character"),
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15 make_option("--mostIntense", action="store_true"),
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16 make_option("--plotP", action="store_true"),
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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17 make_option("--nearest", action="store_true"),
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18 make_option("--cores", default=4)
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19 )
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21 # store options
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22 opt<- parse_args(OptionParser(option_list=option_list))
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24 minOffset = as.numeric(opt$minOffset)
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25 maxOffset = as.numeric(opt$maxOffset)
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27 if (opt$iwNorm=='none'){
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28 iwNorm = FALSE
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29 iwNormFun = NULL
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30 }else if (opt$iwNorm=='gauss'){
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31 iwNorm = TRUE
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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32 iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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33 }else if (opt$iwNorm=='rcosine'){
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34 iwNorm = TRUE
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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35 iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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36 }else if (opt$iwNorm=='QE5'){
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37 iwNorm = TRUE
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38 iwNormFun = msPurity::iwNormQE.5()
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39 }
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40
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41 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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42 filepaths <- filepaths[filepaths != ""]
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43
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44
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45
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46 if(is.null(opt$minOffset) || is.null(opt$maxOffset)){
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47 offsets = NA
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48 }else{
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49 offsets = as.numeric(c(opt$minOffset, opt$maxOffset))
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50 }
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51
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52
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53 if(is.null(opt$mostIntense)){
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54 mostIntense = FALSE
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55 }else{
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56 mostIntense = TRUE
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57 }
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58
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59 if(is.null(opt$nearest)){
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60 nearest = FALSE
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61 }else{
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62 nearest = TRUE
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63 }
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64
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65 if(is.null(opt$plotP)){
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66 plotP = FALSE
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67 plotdir = NULL
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68 }else{
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69 plotP = TRUE
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70 plotdir = opt$out_dir
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71 }
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72
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73
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74 if (is.null(opt$isotope_matrix)){
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75 im <- NULL
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76 }else{
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77 im <- read.table(opt$isotope_matrix,
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78 header = TRUE, sep='\t', stringsAsFactors = FALSE)
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79 }
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80
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81 if (is.null(opt$exclude_isotopes)){
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82 isotopes <- FALSE
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83 }else{
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84 isotopes <- TRUE
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85 }
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86
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87 pa <- msPurity::purityA(filepaths,
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88 cores = opt$cores,
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89 mostIntense = mostIntense,
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90 nearest = nearest,
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91 offsets = offsets,
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92 plotP = plotP,
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93 plotdir = plotdir,
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94 interpol = "linear",
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95 iwNorm = iwNorm,
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96 iwNormFun = iwNormFun,
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97 ilim = opt$ilim,
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98 mzRback = "pwiz",
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99 isotopes = isotopes,
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100 im = im)
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101
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102
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103 if (!is.null(opt$galaxy_names)){
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104 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
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105 galaxy_names <- galaxy_names[galaxy_names != ""]
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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106 names(pa@fileList) <- galaxy_names
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107 }
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108
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109 print(pa)
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110
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111 save(pa, file=file.path(opt$out_dir, 'purity_msms.RData'))
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112
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113 print(head(pa@puritydf))
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114 write.table(pa@puritydf, file.path(opt$out_dir, 'purity_msms.tsv'), row.names=FALSE, sep='\t')
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115
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116 # removed_peaks <- data.frame(removed_peaks)
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117 # write.table(data.frame('ID'=rownames(removed_peaks),removed_peaks),
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118 # file.path(opt$out_dir, 'removed_peaks.txt'), row.names=FALSE, sep='\t')