Mercurial > repos > tomnl > mspurity_createmsp

comparison createMSP.R @ 12:5dd61e94d70d draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
author tomnl
date Fri, 13 Sep 2019 11:53:46 -0400
parents df2efceff4cd
children
comparison
equal deleted inserted replaced
11:4b3b0f5a55d9 12:5dd61e94d70d
2 library(msPurity) 2 library(msPurity)
3 print(sessionInfo()) 3 print(sessionInfo())
4 4
5 # Get the parameter 5 # Get the parameter
6 option_list <- list( 6 option_list <- list(
7 make_option(c("-i","--rdata_input"),type="character"), 7 make_option("--rdata_input",type="character"),
8 make_option(c("-m","--method"),type="character"), 8 make_option("--method",type="character"),
9 make_option(c("-meta","--metadata"),type="character"), 9 make_option("--metadata",type="character"),
10 make_option(c("-metac","--metadata_cols"),type="character"), 10 make_option("--metadata_cols",type="character"),
11 make_option(c("-a","--adduct_split"),type="character"), 11 make_option("--metadata_cols_filter",type="character"),
12 make_option(c("-x","--xcms_groupids"),type="character"), 12 make_option("--adduct_split", action="store_true"),
13 make_option(c("-f","--filter"),action="store_true"), 13 make_option("--xcms_groupids",type="character"),
14 make_option("--filter",action="store_true"),
14 make_option("--intensity_ra",type="character"), 15 make_option("--intensity_ra",type="character"),
16 make_option("--include_adducts",type="character"),
15 make_option("--msp_schema",type="character"), 17 make_option("--msp_schema",type="character"),
16 make_option(c("-o","--out_dir"),type="character", default=".") 18 make_option("--out_dir",type="character", default=".")
17 ) 19 )
18 opt <- parse_args(OptionParser(option_list=option_list)) 20 opt <- parse_args(OptionParser(option_list=option_list))
19 21
20 print(opt) 22 print(opt)
21 23
23 25
24 if (is.null(opt$metadata)){ 26 if (is.null(opt$metadata)){
25 metadata <- NULL 27 metadata <- NULL
26 }else{ 28 }else{
27 metadata <- read.table(opt$metadata, header = TRUE, sep='\t', stringsAsFactors = FALSE, check.names = FALSE) 29 metadata <- read.table(opt$metadata, header = TRUE, sep='\t', stringsAsFactors = FALSE, check.names = FALSE)
28 print(head(metadata)) 30
31 if(!opt$metadata_cols_filter==''){
32 metadata_cols_filter <- strsplit(opt$metadata_cols_filter, ',')[[1]]
33
34 metadata <- metadata[,metadata_cols_filter, drop=FALSE]
35 print(metadata)
36
37 if (!"grpid" %in% colnames(metadata)){
38 metadata$grpid <- 1:nrow(metadata)
39 }
40
41 print(metadata)
42
43 }
44
29 } 45 }
46
47
48
49 if (is.null(opt$metadata_cols) || opt$metadata_cols==''){
50 metadata_cols <- NULL
51 }else{
52 metadata_cols <- opt$metadata_cols
53
54 }
55
30 56
31 if(is.null(opt$adduct_split)){ 57 if(is.null(opt$adduct_split)){
32 adduct_split <- FALSE 58 adduct_split <- FALSE
33 }else{ 59 }else{
34 adduct_split <- TRUE 60 adduct_split <- TRUE
38 xcms_groupids <- NULL 64 xcms_groupids <- NULL
39 }else{ 65 }else{
40 xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ',')[[1]]) 66 xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ',')[[1]])
41 } 67 }
42 68
69 if (opt$include_adducts=='None'){
70 include_adducts <- ''
71 }else{
72 include_adducts <- opt$include_adducts
73 include_adducts <- gsub("__ob__", "[", include_adducts)
74 include_adducts <- gsub("__cb__", "]", include_adducts)
75 include_adducts <- trimws(include_adducts)
76
77 include_adducts <- gsub(",", " ", include_adducts)
78
79 }
80
81
43 if(is.null(opt$filter)){ 82 if(is.null(opt$filter)){
44 filter <- FALSE 83 filter <- FALSE
45 }else{ 84 }else{
46 filter <- TRUE 85 filter <- TRUE
47 } 86 }
48 87
88
89
49 msPurity::createMSP(pa, 90 msPurity::createMSP(pa,
50 msp_file_pth = file.path(opt$out_dir, 'lcmsms_spectra.msp'), 91 msp_file_pth = file.path(opt$out_dir, 'lcmsms_spectra.msp'),
51 metadata = metadata, 92 metadata = metadata,
52 metadata_cols = opt$metadata_cols, 93 metadata_cols = metadata_cols,
53 method = opt$method, 94 method = opt$method,
54 adduct_split = adduct_split, 95 adduct_split = adduct_split,
55 xcms_groupids = xcms_groupids, 96 xcms_groupids = xcms_groupids,
56 filter = filter, 97 filter = filter,
57 intensity_ra=opt$intensity_ra, 98 intensity_ra=opt$intensity_ra,
99 include_adducts=include_adducts,
58 msp_schema=opt$msp_schema) 100 msp_schema=opt$msp_schema)
59 101
60 print('msp created') 102 print('msp created')