Mercurial > repos > computational-metabolomics > mspurity_averagefragspectra

comparison purityA.R @ 6:52d48bcd3608 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author computational-metabolomics
date Thu, 04 Mar 2021 12:29:17 +0000
parents 4207233ead9c
children e98ae5c1f4e7
comparison
equal deleted inserted replaced
5:e79c1a0654af 6:52d48bcd3608
1 library(msPurity) 1 library(msPurity)
2 library(optparse) 2 library(optparse)
3 print(sessionInfo()) 3 print(sessionInfo())
4 4
5 option_list <- list( 5 option_list <- list(
6 make_option(c("-o", "--out_dir"), type="character"), 6 make_option(c("-o", "--out_dir"), type = "character"),
7 make_option("--mzML_files", type="character"), 7 make_option("--mzML_files", type = "character"),
8 make_option("--galaxy_names", type="character"), 8 make_option("--galaxy_names", type = "character"),
9 make_option("--minOffset", type="numeric"), 9 make_option("--minOffset", type = "numeric"),
10 make_option("--maxOffset", type="numeric"), 10 make_option("--maxOffset", type = "numeric"),
11 make_option("--ilim", type="numeric"), 11 make_option("--ilim", type = "numeric"),
12 make_option("--iwNorm", default="none", type="character"), 12 make_option("--iwNorm", default = "none", type = "character"),
13 make_option("--exclude_isotopes", action="store_true"), 13 make_option("--exclude_isotopes", action = "store_true"),
14 make_option("--isotope_matrix", type="character"), 14 make_option("--isotope_matrix", type = "character"),
15 make_option("--mostIntense", action="store_true"), 15 make_option("--mostIntense", action = "store_true"),
16 make_option("--plotP", action="store_true"), 16 make_option("--plotP", action = "store_true"),
17 make_option("--nearest", action="store_true"), 17 make_option("--nearest", action = "store_true"),
18 make_option("--cores", default=4), 18 make_option("--cores", default = 4),
19 make_option("--ppmInterp", default=7) 19 make_option("--ppmInterp", default = 7)
20 ) 20 )
21 21
22 opt <- parse_args(OptionParser(option_list=option_list)) 22 opt <- parse_args(OptionParser(option_list = option_list))
23 print(opt) 23 print(opt)
24 24
25 25 if (opt$iwNorm == "none") {
26 if (opt$iwNorm=='none'){ 26 iwNorm <- FALSE
27 iwNorm = FALSE 27 iwNormFun <- NULL
28 iwNormFun = NULL 28 }else if (opt$iwNorm == "gauss") {
29 }else if (opt$iwNorm=='gauss'){ 29 iwNorm <- TRUE
30 iwNorm = TRUE 30 if (is.null(opt$minOffset) || is.null(opt$maxOffset)) {
31 if (is.null(opt$minOffset) || is.null(opt$maxOffset)){ 31 print("User has to define offsets if using Gaussian normalisation")
32 print('User has to define offsets if using Gaussian normalisation')
33 }else{ 32 }else{
34 iwNormFun = msPurity::iwNormGauss(minOff=-as.numeric(opt$minOffset), 33 iwNormFun <- msPurity::iwNormGauss(minOff = -as.numeric(opt$minOffset),
35 maxOff=as.numeric(opt$maxOffset)) 34 maxOff = as.numeric(opt$maxOffset))
36 } 35 }
37 }else if (opt$iwNorm=='rcosine'){ 36 }else if (opt$iwNorm == "rcosine") {
38 iwNorm = TRUE 37 iwNorm <- TRUE
39 if (is.null(opt$minOffset) || is.null(opt$maxOffset)){ 38 if (is.null(opt$minOffset) || is.null(opt$maxOffset)) {
40 print('User has to define offsets if using R-cosine normalisation') 39 print("User has to define offsets if using R-cosine normalisation")
41 }else{ 40 }else{
42 iwNormFun = msPurity::iwNormRcosine(minOff=-as.numeric(opt$minOffset), 41 iwNormFun <- msPurity::iwNormRcosine(minOff = -as.numeric(opt$minOffset),
43 maxOff=as.numeric(opt$maxOffset)) 42 maxOff = as.numeric(opt$maxOffset))
44 } 43 }
45 }else if (opt$iwNorm=='QE5'){ 44 }else if (opt$iwNorm == "QE5") {
46 iwNorm = TRUE 45 iwNorm <- TRUE
47 iwNormFun = msPurity::iwNormQE.5() 46 iwNormFun <- msPurity::iwNormQE.5()
48 } 47 }
49 48
50 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]]) 49 filepaths <- trimws(strsplit(opt$mzML_files, ",")[[1]])
51 filepaths <- filepaths[filepaths != ""] 50 filepaths <- filepaths[filepaths != ""]
52 51
53 52
54 53
55 if(is.null(opt$minOffset) || is.null(opt$maxOffset)){ 54 if (is.null(opt$minOffset) || is.null(opt$maxOffset)) {
56 offsets = NA 55 offsets <- NA
57 }else{ 56 }else{
58 offsets = as.numeric(c(opt$minOffset, opt$maxOffset)) 57 offsets <- as.numeric(c(opt$minOffset, opt$maxOffset))
59 } 58 }
60 59
61 60
62 if(is.null(opt$mostIntense)){ 61 if (is.null(opt$mostIntense)) {
63 mostIntense = FALSE 62 mostIntense <- FALSE
64 }else{ 63 }else{
65 mostIntense = TRUE 64 mostIntense <- TRUE
66 } 65 }
67 66
68 if(is.null(opt$nearest)){ 67 if (is.null(opt$nearest)) {
69 nearest = FALSE 68 nearest <- FALSE
70 }else{ 69 }else{
71 nearest = TRUE 70 nearest <- TRUE
72 } 71 }
73 72
74 if(is.null(opt$plotP)){ 73 if (is.null(opt$plotP)) {
75 plotP = FALSE 74 plotP <- FALSE
76 plotdir = NULL 75 plotdir <- NULL
77 }else{ 76 }else{
78 plotP = TRUE 77 plotP <- TRUE
79 plotdir = opt$out_dir 78 plotdir <- opt$out_dir
80 } 79 }
81 80
82 81
83 if (is.null(opt$isotope_matrix)){ 82 if (is.null(opt$isotope_matrix)) {
84 im <- NULL 83 im <- NULL
85 }else{ 84 }else{
86 im <- read.table(opt$isotope_matrix, 85 im <- read.table(opt$isotope_matrix,
87 header = TRUE, sep='\t', stringsAsFactors = FALSE) 86 header = TRUE, sep = "\t", stringsAsFactors = FALSE)
88 } 87 }
89 88
90 if (is.null(opt$exclude_isotopes)){ 89 if (is.null(opt$exclude_isotopes)) {
91 isotopes <- FALSE 90 isotopes <- FALSE
92 }else{ 91 }else{
93 isotopes <- TRUE 92 isotopes <- TRUE
94 } 93 }
95 94
108 isotopes = isotopes, 107 isotopes = isotopes,
109 im = im, 108 im = im,
110 ppmInterp = opt$ppmInterp) 109 ppmInterp = opt$ppmInterp)
111 110
112 111
113 if (!is.null(opt$galaxy_names)){ 112 if (!is.null(opt$galaxy_names)) {
114 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]]) 113 galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]])
115 galaxy_names <- galaxy_names[galaxy_names != ""] 114 galaxy_names <- galaxy_names[galaxy_names != ""]
116 names(pa@fileList) <- galaxy_names 115 names(pa@fileList) <- galaxy_names
117 } 116 }
118 117
119 print(pa) 118 print(pa)
120 save(pa, file=file.path(opt$out_dir, 'purityA_output.RData')) 119 save(pa, file = file.path(opt$out_dir, "purityA_output.RData"))
121 120
122 pa@puritydf$filename <- sapply(pa@puritydf$fileid, function(x) names(pa@fileList)[as.integer(x)]) 121 pa@puritydf$filename <- sapply(pa@puritydf$fileid, function(x) names(pa@fileList)[as.integer(x)])
123 122
124 print(head(pa@puritydf)) 123 print(head(pa@puritydf))
125 write.table(pa@puritydf, file.path(opt$out_dir, 'purityA_output.tsv'), row.names=FALSE, sep='\t') 124 write.table(pa@puritydf, file.path(opt$out_dir, "purityA_output.tsv"), row.names = FALSE, sep = "\t")
126
127 # removed_peaks <- data.frame(removed_peaks)
128 # write.table(data.frame('ID'=rownames(removed_peaks),removed_peaks),
129 # file.path(opt$out_dir, 'removed_peaks.txt'), row.names=FALSE, sep='\t')