Mercurial > repos > computational-metabolomics > mspurity_purityx

comparison createMSP.R @ 3:1cba235b1972 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
author computational-metabolomics
date Thu, 09 Apr 2020 14:15:03 -0400
parents a141be614e76
children 6b9a83e08467
comparison
equal deleted inserted replaced
2:d7c5fa406ea8 3:1cba235b1972
13 make_option("--xcms_groupids",type="character"), 13 make_option("--xcms_groupids",type="character"),
14 make_option("--filter",action="store_true"), 14 make_option("--filter",action="store_true"),
15 make_option("--intensity_ra",type="character"), 15 make_option("--intensity_ra",type="character"),
16 make_option("--include_adducts",type="character"), 16 make_option("--include_adducts",type="character"),
17 make_option("--msp_schema",type="character"), 17 make_option("--msp_schema",type="character"),
18 make_option("--include_adducts_custom",type="character", default=""),
18 make_option("--out_dir",type="character", default=".") 19 make_option("--out_dir",type="character", default=".")
19 ) 20 )
20 opt <- parse_args(OptionParser(option_list=option_list)) 21 opt <- parse_args(OptionParser(option_list=option_list))
21 22
22 print(opt) 23 print(opt)
64 xcms_groupids <- NULL 65 xcms_groupids <- NULL
65 }else{ 66 }else{
66 xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ',')[[1]]) 67 xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ',')[[1]])
67 } 68 }
68 69
70
71
72
73
74 if (is.null(opt$include_adducts_custom)){
75 include_adducts_custom <- ''
76 }else{
77 include_adducts_custom <- opt$include_adducts_custom
78 }
79
80
69 if (opt$include_adducts=='None'){ 81 if (opt$include_adducts=='None'){
70 include_adducts <- '' 82 include_adducts <- ''
71 }else{ 83 }else{
72 include_adducts <- opt$include_adducts 84 include_adducts <- opt$include_adducts
73 include_adducts <- gsub("__ob__", "[", include_adducts) 85 }
74 include_adducts <- gsub("__cb__", "]", include_adducts)
75 include_adducts <- trimws(include_adducts)
76 86
77 include_adducts <- gsub(",", " ", include_adducts) 87 include_adducts_all <- paste(include_adducts_custom, ',', include_adducts, sep="")
78 88
79 } 89 include_adducts_all <- gsub("^,", "", include_adducts_all)
90 include_adducts_all <- gsub(",$", "", include_adducts_all)
91
92 include_adducts_all <- gsub("__ob__", "[", include_adducts_all)
93 include_adducts_all <- gsub("__cb__", "]", include_adducts_all)
94 include_adducts_all <- trimws(include_adducts_all)
95 include_adducts_all <- gsub(",", " ", include_adducts_all)
96
80 97
81 98
82 if(is.null(opt$filter)){ 99 if(is.null(opt$filter)){
83 filter <- FALSE 100 filter <- FALSE
84 }else{ 101 }else{
94 method = opt$method, 111 method = opt$method,
95 adduct_split = adduct_split, 112 adduct_split = adduct_split,
96 xcms_groupids = xcms_groupids, 113 xcms_groupids = xcms_groupids,
97 filter = filter, 114 filter = filter,
98 intensity_ra=opt$intensity_ra, 115 intensity_ra=opt$intensity_ra,
99 include_adducts=include_adducts, 116 include_adducts=include_adducts_all,
100 msp_schema=opt$msp_schema) 117 msp_schema=opt$msp_schema)
101 118
102 print('msp created') 119 print('msp created')