Mercurial > repos > computational-metabolomics > mspurity_frag4feature

comparison purityA.R @ 0:85bc606fd219 draft default tip

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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 12:22:55 +0000
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-1:000000000000 0:85bc606fd219
1 library(msPurity)
2 library(optparse)
3 print(sessionInfo())
4
5 option_list <- list(
6 make_option(c("-o", "--out_dir"), type = "character"),
7 make_option("--mzML_files", type = "character"),
8 make_option("--galaxy_names", type = "character"),
9 make_option("--minOffset", type = "numeric"),
10 make_option("--maxOffset", type = "numeric"),
11 make_option("--ilim", type = "numeric"),
12 make_option("--iwNorm", default = "none", type = "character"),
13 make_option("--exclude_isotopes", action = "store_true"),
14 make_option("--isotope_matrix", type = "character"),
15 make_option("--mostIntense", action = "store_true"),
16 make_option("--plotP", action = "store_true"),
17 make_option("--nearest", action = "store_true"),
18 make_option("--cores", default = 4),
19 make_option("--ppmInterp", default = 7)
20 )
21
22 opt <- parse_args(OptionParser(option_list = option_list))
23 print(opt)
24
25 if (opt$iwNorm == "none") {
26 iwNorm <- FALSE
27 iwNormFun <- NULL
28 }else if (opt$iwNorm == "gauss") {
29 iwNorm <- TRUE
30 if (is.null(opt$minOffset) || is.null(opt$maxOffset)) {
31 print("User has to define offsets if using Gaussian normalisation")
32 }else{
33 iwNormFun <- msPurity::iwNormGauss(minOff = -as.numeric(opt$minOffset),
34 maxOff = as.numeric(opt$maxOffset))
35 }
36 }else if (opt$iwNorm == "rcosine") {
37 iwNorm <- TRUE
38 if (is.null(opt$minOffset) || is.null(opt$maxOffset)) {
39 print("User has to define offsets if using R-cosine normalisation")
40 }else{
41 iwNormFun <- msPurity::iwNormRcosine(minOff = -as.numeric(opt$minOffset),
42 maxOff = as.numeric(opt$maxOffset))
43 }
44 }else if (opt$iwNorm == "QE5") {
45 iwNorm <- TRUE
46 iwNormFun <- msPurity::iwNormQE.5()
47 }
48
49 filepaths <- trimws(strsplit(opt$mzML_files, ",")[[1]])
50 filepaths <- filepaths[filepaths != ""]
51
52
53
54 if (is.null(opt$minOffset) || is.null(opt$maxOffset)) {
55 offsets <- NA
56 }else{
57 offsets <- as.numeric(c(opt$minOffset, opt$maxOffset))
58 }
59
60
61 if (is.null(opt$mostIntense)) {
62 mostIntense <- FALSE
63 }else{
64 mostIntense <- TRUE
65 }
66
67 if (is.null(opt$nearest)) {
68 nearest <- FALSE
69 }else{
70 nearest <- TRUE
71 }
72
73 if (is.null(opt$plotP)) {
74 plotP <- FALSE
75 plotdir <- NULL
76 }else{
77 plotP <- TRUE
78 plotdir <- opt$out_dir
79 }
80
81
82 if (is.null(opt$isotope_matrix)) {
83 im <- NULL
84 }else{
85 im <- read.table(opt$isotope_matrix,
86 header = TRUE, sep = "\t", stringsAsFactors = FALSE)
87 }
88
89 if (is.null(opt$exclude_isotopes)) {
90 isotopes <- FALSE
91 }else{
92 isotopes <- TRUE
93 }
94
95 pa <- msPurity::purityA(filepaths,
96 cores = opt$cores,
97 mostIntense = mostIntense,
98 nearest = nearest,
99 offsets = offsets,
100 plotP = plotP,
101 plotdir = plotdir,
102 interpol = "linear",
103 iwNorm = iwNorm,
104 iwNormFun = iwNormFun,
105 ilim = opt$ilim,
106 mzRback = "pwiz",
107 isotopes = isotopes,
108 im = im,
109 ppmInterp = opt$ppmInterp)
110
111
112 if (!is.null(opt$galaxy_names)) {
113 galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]])
114 galaxy_names <- galaxy_names[galaxy_names != ""]
115 names(pa@fileList) <- galaxy_names
116 }
117
118 print(pa)
119 save(pa, file = file.path(opt$out_dir, "purityA_output.RData"))
120
121 pa@puritydf$filename <- sapply(pa@puritydf$fileid, function(x) names(pa@fileList)[as.integer(x)])
122
123 print(head(pa@puritydf))
124 write.table(pa@puritydf, file.path(opt$out_dir, "purityA_output.tsv"), row.names = FALSE, sep = "\t")