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annotate cameradims.R @ 0:aa55ff1d76d4 draft

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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit dcfc95273101a7ef0405c2efb8d83f5d456ccd15
author tomnl
date Thu, 10 May 2018 07:20:04 -0400
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0
aa55ff1d76d4 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit dcfc95273101a7ef0405c2efb8d83f5d456ccd15
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1 library(optparse)
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2 library(cameraDIMS)
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3
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4 option_list <- list(
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5 make_option(c("-i", "--in_file"), type="character"),
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6 make_option(c("-o", "--out_dir"), type="character"),
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7 make_option("--ppm_iso", default=5),
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8 make_option("--ppm_adduct", default=5),
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9 make_option("--maxiso", default=4),
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10 make_option("--mzabs_iso", default=0.015),
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11 make_option("--mzabs_adduct", default=0.015),
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12 make_option("--maxcharge", default=3),
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13 make_option("--maxmol", default=3),
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14 make_option("--polarity", default='pos'),
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15 make_option("--rule_path"),
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16 make_option("--rule_type"),
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17 make_option("--export_ruleset", action="store_true"),
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18 make_option("--intensity_filter", default=0)
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19 )
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21
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22 # store options
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23 opt<- parse_args(OptionParser(option_list=option_list))
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25 print(sessionInfo())
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26 print(opt)
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28 df <- read.table(opt$in_file, header = TRUE, sep='\t', stringsAsFactors=FALSE)
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29
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30 print('IN DATA')
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31 print(nrow(df))
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32 print(head(df))
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33
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34 devppm_adduct <- opt$ppm_adduct / 1000000
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35 devppm_iso <- opt$ppm_iso / 1000000
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36
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37 paramiso <- list("ppm"=opt$ppm_iso,
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38 "filter"=TRUE,
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39 "maxcharge"=opt$maxcharge,
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40 "maxiso"=opt$maxiso,
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41 "mzabs"=opt$mzabs_iso,
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42 "intval"='maxo',
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43 "minfrac"=0.5,
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44 'IM'=NULL,
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45 'devppm'=devppm_iso)
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46
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47 paramadduct <- list("maxCharge"= opt$maxcharge,
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48 "maxMol"= opt$maxmol,
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49 'devppm'=devppm_adduct,
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50 "mzabs"=opt$mzabs_adduct,
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51 'IM'=NULL,
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52 "filter"=TRUE,
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53 'ppm'=opt$ppm_adduct,
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54 "quasimolion"= c(1, 6, 8),
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55 'polarity'=opt$polarity)
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56
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57
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58
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59
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60 if(is.null(opt$export_ruleset)){
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61 rule_export <- FALSE
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62 }else{
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63 rule_export <- TRUE
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64 }
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65
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66 df$mz <- as.numeric(df$mz)
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67
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68 print(head(df$mz))
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69
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70 if ('intensity' %in% colnames(df)){
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71 colnames(df)[colnames(df)=='intensity'] = 'i'
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72 }
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73
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74 if (!'peakID' %in% colnames(df)){
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75 df <- cbind('peakID'=1:nrow(df), df)
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76 }
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77
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78 df$i <- as.numeric(df$i)
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79
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80 df <- df[df$i>opt$intensity_filter,]
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81
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82 if (nrow(df)==0){
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83 print('No peaks left after filtering')
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84 quit()
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85 }
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86
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87
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88 if (opt$rule_type=='extended_large'){
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89
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90 rule_sep=','
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91 opt$rule_type <- 'user'
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92 if(opt$polarity=='pos'){
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93 opt$rule_path <- system.file("rules", "CAMERA_rules_PosFinal_PlusLi.csv", package = "cameraDIMS")
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94 }else{
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95 opt$rule_path <- system.file("rules", "CAMERA_rules_NegFinal_PlusLi.csv", package = "cameraDIMS")
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96 }
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97 }else{
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98 rule_sep='\t'
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99 }
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100
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101 cameraOut <- cameraDIMS(data=df,
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102 params_iso=paramiso,
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103 params_adduct=paramadduct,
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104 rule_type=opt$rule_type,
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105 rule_pth=opt$rule_path,
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106 rule_sep=rule_sep,
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107 rule_export=rule_export)
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108
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109
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110 print(head(cameraOut[[1]]))
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111 print(head(cameraOut[[2]]))
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112
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113
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114 out_file1 <- file.path(opt$out_dir, 'camera_annotated_peaklist.txt')
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115 out_file2 <- file.path(opt$out_dir, 'camera_annotated_map.txt')
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116 out_file3 <- file.path(opt$out_dir, 'ruleset.txt')
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117
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118 write.table(cameraOut[[1]], out_file1, row.names=FALSE, sep='\t')
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119 write.table(cameraOut[[2]], out_file2, row.names=FALSE, sep='\t')
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120
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121 if (rule_export){
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122 write.table(cameraOut[[3]], out_file3, row.names=FALSE, sep='\t')
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123 }