Mercurial > repos > computational-metabolomics > mspurity_createmsp

comparison filterFragSpectra.R @ 7:8512923bdd37 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
author computational-metabolomics
date Tue, 08 Feb 2022 13:56:27 +0000
parents d25273689e04
children b91b9492a4bf
comparison
equal deleted inserted replaced
6:d25273689e04 7:8512923bdd37
15 15
16 make_option("--ra", default = 0.0), 16 make_option("--ra", default = 0.0),
17 make_option("--snr", default = 0.0), 17 make_option("--snr", default = 0.0),
18 18
19 make_option("--rmp", action = "store_true"), 19 make_option("--rmp", action = "store_true"),
20 make_option("--snmeth", default = "median", type = "character") 20 make_option("--snmeth", default = "median", type = "character"),
21 make_option("--allfrag", action = "store_true")
21 ) 22 )
22 23
23 opt <- parse_args(OptionParser(option_list = option_list)) 24 opt <- parse_args(OptionParser(option_list = option_list))
24 print(opt) 25 print(opt)
25 26
37 opt$rmp <- FALSE 38 opt$rmp <- FALSE
38 }else{ 39 }else{
39 opt$rmp <- TRUE 40 opt$rmp <- TRUE
40 } 41 }
41 42
43 if (is.null(opt$allfrag)) {
44 opt$allfrag <- FALSE
45 }else{
46 opt$allfrag <- TRUE
47 }
48
42 pa <- filterFragSpectra(pa, 49 pa <- filterFragSpectra(pa,
43 ilim = opt$ilim, 50 ilim = opt$ilim,
44 plim = opt$plim, 51 plim = opt$plim,
45 ra = opt$ra, 52 ra = opt$ra,
46 snr = opt$snr, 53 snr = opt$snr,
47 rmp = opt$rmp, 54 rmp = opt$rmp,
55 allfrag = opt$allfrag,
48 snmeth = opt$snmeth) 56 snmeth = opt$snmeth)
49 57
50 print(pa) 58 print(pa)
51 save(pa, file = opt$out_rdata) 59 save(pa, file = opt$out_rdata)
52 60