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annotate lcms-interval-scheduling.R @ 19:d4081e4160af draft

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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 14435cfc042911bf1ee409f5a0d5ef908f5feec0-dirty
author tomnl
date Thu, 21 Jun 2018 08:47:44 -0400
parents 55aa2dd24828
children
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1 library(XCMSwrapper)
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2 library(optparse)
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3
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4 option_list <- list(
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5
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6 make_option(c("-s", "--sample_peaklist"), type="character"),
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7 make_option(c("-b", "--blank_peaklist"), type="character"),
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8 make_option(c("-t", "--topn"), type="character"),
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9 make_option(c("-o", "--out_dir"), type="character", default=getwd(),
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10 help="Output folder for resulting files [default = %default]"
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11 ),
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12 make_option("--method", type="character"),
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13 make_option("--maxms2", type="numeric"),
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14 make_option("--widthFactor", type="numeric"),
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15 make_option("--minWidth", type="numeric"),
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16 make_option("--ilimit", type="numeric"),
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17 make_option("--shift", type="numeric"),
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18 make_option("--samplelistNm", type="numeric"),
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19 make_option("--overlappingP", type="numeric"),
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20 make_option("--fullpw", action="store_true"),
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21 make_option("--b_widthFactor", type="numeric"),
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22 make_option("--b_shift", type="numeric"),
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23 make_option("--b_exclu_limit", type="numeric"),
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24 make_option("--b_minWidth", type="numeric"),
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25 make_option("--polarity", type="character"),
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26 make_option("--fillgaps", type="character"),
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27 make_option("--dmaNearline", action="store_true"),
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28 make_option("--blankClass", type="character"),
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29 make_option("--intensityCN", type="character"),
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30 make_option("--sortCN", type="character"),
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31 make_option("--filterS", type="character")
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32 )
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34 # store options
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35 opt<- parse_args(OptionParser(option_list=option_list))
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36
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37 print(sessionInfo())
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38 print(opt)
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39
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40 if(is.null(opt$fullpw)){
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41 fullpw = FALSE
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42 }else{
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43 fullpw = TRUE
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44 }
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45
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46 if(is.null(opt$fillgaps)){
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47 fillgaps = FALSE
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48 }else{
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49 fillgaps = TRUE
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50 }
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51
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52
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53 # Nearline processing
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54 # nearline parameters (sample and blank)
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55 params <- list(
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56 nl.method = opt$method,
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57 nl.maxms2 = opt$maxms2, # only used for simple nearline
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58 nl.widthFactor = opt$widthFactor,
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59 nl.minWidth = opt$minWidth, # 5 seconds
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60 nl.ilimit = opt$ilimit, # only used for simple nearline
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61 nl.shift = opt$shift,
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62 nl.samplelist_nm = opt$samplelistNm,
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63 nl.overlappingP = opt$overlappingP,
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64 nl.fullpw = fullpw,
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65 nl.fillgaps = fillgaps, # only used for metshot nearline
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66 #nearline blank parameters
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67 nl.b_widthFactor = opt$b_widthFactor, # increase the width
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68 nl.b_minWidth = opt$b_minWidth,
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69 nl.b.shift = opt$b_shift,
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70 nl.exclu_limit = opt$b_exclu_limit,
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71 temp_dir='.',
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72 intensityCN=opt$intensityCN,
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73 sortCN=opt$sortCN # column of the sample peaklist to use for
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74
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75 )
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77
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78
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79 # ##################################
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80 # # Perform Nearline optimisation
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81 # ##################################
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82 s_peaklist <- read.table(opt$sample_peaklist, header = TRUE, sep='\t', stringsAsFactors = FALSE)
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83 b_peaklist <- read.table(opt$blank_peaklist, header = TRUE, sep='\t', stringsAsFactors = FALSE)
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84
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85 if(!is.null(opt$dmaNearline)){
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86 # have to do some additional filtering if part of the dma nearline workflow
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87 blank_class_name <- gsub('-', '.', opt$blankClass)
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88 b_peaklist = b_peaklist[which(b_peaklist[,paste(blank_class_name, '_valid', sep='')]==1),]
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89 s_peaklist = s_peaklist[s_peaklist[,opt$filterS]==0,]
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90 }
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93
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94 topn <- read.table(opt$topn, header = TRUE, sep='\t', stringsAsFactors = FALSE, check.names=FALSE)
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95 topn[is.na(topn)] <- ""
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96 # colnames(topn) <- c('Mass [m/z]', 'Formula [M]', 'Formula type', 'Species', 'CS [z]', 'Polarity', 'Start [min]', 'End [min]','Comment')
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97 # colnames(topn) <- gsub('\\.', ' ', colnames(topn))
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98 print(head(topn))
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99
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100 # #Generate inclusions lists for DDA-MS/MS and store in list
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101 incl.lists = nearline_main(pm = params, peaklist_xcms=s_peaklist, pol=opt$polarity, merge_peaklists=FALSE, peaklist_post=NA)
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102
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103 # #Generate exclusion lists for each class being analysed
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104 nearline_main_blank(pm = params,
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105 plist = b_peaklist,
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106 incl_list_pos = incl.lists,
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107 pol = opt$polarity,
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108 topn = topn)
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109 #