annotate purityA.R @ 1:4db043151468 draft

"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
author computational-metabolomics
date Thu, 05 Dec 2019 07:34:21 -0500
parents 5ff9d40c7a42
children fecfe8c80e25
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
1 library(msPurity)
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
2 library(optparse)
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
3 print(sessionInfo())
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
4
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
5 option_list <- list(
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
6 make_option(c("-o", "--out_dir"), type="character"),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
7 make_option("--mzML_files", type="character"),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
8 make_option("--galaxy_names", type="character"),
1
4db043151468 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
parents: 0
diff changeset
9 make_option("--minOffset", type="numeric"),
4db043151468 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
parents: 0
diff changeset
10 make_option("--maxOffset", type="numeric"),
4db043151468 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
parents: 0
diff changeset
11 make_option("--ilim", type="numeric"),
0
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
12 make_option("--iwNorm", default="none", type="character"),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
13 make_option("--exclude_isotopes", action="store_true"),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
14 make_option("--isotope_matrix", type="character"),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
15 make_option("--mostIntense", action="store_true"),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
16 make_option("--plotP", action="store_true"),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
17 make_option("--nearest", action="store_true"),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
18 make_option("--cores", default=4),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
19 make_option("--ppmInterp", default=7)
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
20 )
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
21
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
22 opt <- parse_args(OptionParser(option_list=option_list))
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
23 print(opt)
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
24
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
25
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
26 if (opt$iwNorm=='none'){
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
27 iwNorm = FALSE
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
28 iwNormFun = NULL
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
29 }else if (opt$iwNorm=='gauss'){
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
30 iwNorm = TRUE
1
4db043151468 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
parents: 0
diff changeset
31 if (is.null(opt$minOffset) || is.null(opt$maxOffset)){
4db043151468 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
parents: 0
diff changeset
32 print('User has to define offsets if using Gaussian normalisation')
4db043151468 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
parents: 0
diff changeset
33 }else{
4db043151468 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
parents: 0
diff changeset
34 iwNormFun = msPurity::iwNormGauss(minOff=-as.numeric(opt$minOffset),
4db043151468 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
parents: 0
diff changeset
35 maxOff=as.numeric(opt$maxOffset))
4db043151468 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
parents: 0
diff changeset
36 }
0
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
37 }else if (opt$iwNorm=='rcosine'){
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
38 iwNorm = TRUE
1
4db043151468 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
parents: 0
diff changeset
39 if (is.null(opt$minOffset) || is.null(opt$maxOffset)){
4db043151468 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
parents: 0
diff changeset
40 print('User has to define offsets if using R-cosine normalisation')
4db043151468 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
parents: 0
diff changeset
41 }else{
4db043151468 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
parents: 0
diff changeset
42 iwNormFun = msPurity::iwNormRcosine(minOff=-as.numeric(opt$minOffset),
4db043151468 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
parents: 0
diff changeset
43 maxOff=as.numeric(opt$maxOffset))
4db043151468 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
parents: 0
diff changeset
44 }
0
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
45 }else if (opt$iwNorm=='QE5'){
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
46 iwNorm = TRUE
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
47 iwNormFun = msPurity::iwNormQE.5()
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
48 }
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
49
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
50 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
51 filepaths <- filepaths[filepaths != ""]
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
52
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
53
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
54
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
55 if(is.null(opt$minOffset) || is.null(opt$maxOffset)){
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
56 offsets = NA
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
57 }else{
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
58 offsets = as.numeric(c(opt$minOffset, opt$maxOffset))
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
59 }
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
60
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
61
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
62 if(is.null(opt$mostIntense)){
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
63 mostIntense = FALSE
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
64 }else{
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
65 mostIntense = TRUE
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
66 }
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
67
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
68 if(is.null(opt$nearest)){
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
69 nearest = FALSE
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
70 }else{
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
71 nearest = TRUE
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
72 }
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
73
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
74 if(is.null(opt$plotP)){
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
75 plotP = FALSE
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
76 plotdir = NULL
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
77 }else{
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
78 plotP = TRUE
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
79 plotdir = opt$out_dir
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
80 }
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
81
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
82
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
83 if (is.null(opt$isotope_matrix)){
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
84 im <- NULL
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
85 }else{
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
86 im <- read.table(opt$isotope_matrix,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
87 header = TRUE, sep='\t', stringsAsFactors = FALSE)
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
88 }
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
89
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
90 if (is.null(opt$exclude_isotopes)){
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
91 isotopes <- FALSE
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
92 }else{
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
93 isotopes <- TRUE
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
94 }
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
95
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
96 pa <- msPurity::purityA(filepaths,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
97 cores = opt$cores,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
98 mostIntense = mostIntense,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
99 nearest = nearest,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
100 offsets = offsets,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
101 plotP = plotP,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
102 plotdir = plotdir,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
103 interpol = "linear",
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
104 iwNorm = iwNorm,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
105 iwNormFun = iwNormFun,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
106 ilim = opt$ilim,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
107 mzRback = "pwiz",
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
108 isotopes = isotopes,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
109 im = im,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
110 ppmInterp = opt$ppmInterp)
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
111
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
112
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
113 if (!is.null(opt$galaxy_names)){
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
114 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
115 galaxy_names <- galaxy_names[galaxy_names != ""]
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
116 names(pa@fileList) <- galaxy_names
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
117 }
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
118
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
119 print(pa)
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
120 save(pa, file=file.path(opt$out_dir, 'purityA_output.RData'))
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
121
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
122 pa@puritydf$filename <- sapply(pa@puritydf$fileid, function(x) names(pa@fileList)[as.integer(x)])
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
123
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
124 print(head(pa@puritydf))
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
125 write.table(pa@puritydf, file.path(opt$out_dir, 'purityA_output.tsv'), row.names=FALSE, sep='\t')
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
126
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
127 # removed_peaks <- data.frame(removed_peaks)
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
128 # write.table(data.frame('ID'=rownames(removed_peaks),removed_peaks),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
129 # file.path(opt$out_dir, 'removed_peaks.txt'), row.names=FALSE, sep='\t')