Mercurial > repos > tomnl > mspurity_flagremove

comparison purityA.R @ 12:2c8b5a640a04 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 11:49:43 -0400
parents ca0ac330f1a4
children
comparison
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11:7e4a5ce0877d 12:2c8b5a640a04
13 make_option("--exclude_isotopes", action="store_true"), 13 make_option("--exclude_isotopes", action="store_true"),
14 make_option("--isotope_matrix", type="character"), 14 make_option("--isotope_matrix", type="character"),
15 make_option("--mostIntense", action="store_true"), 15 make_option("--mostIntense", action="store_true"),
16 make_option("--plotP", action="store_true"), 16 make_option("--plotP", action="store_true"),
17 make_option("--nearest", action="store_true"), 17 make_option("--nearest", action="store_true"),
18 make_option("--cores", default=4) 18 make_option("--cores", default=4),
19 make_option("--ppmInterp", default=7)
19 ) 20 )
20 21
21 opt <- parse_args(OptionParser(option_list=option_list)) 22 opt <- parse_args(OptionParser(option_list=option_list))
22 print(opt) 23 print(opt)
23 24
95 iwNorm = iwNorm, 96 iwNorm = iwNorm,
96 iwNormFun = iwNormFun, 97 iwNormFun = iwNormFun,
97 ilim = opt$ilim, 98 ilim = opt$ilim,
98 mzRback = "pwiz", 99 mzRback = "pwiz",
99 isotopes = isotopes, 100 isotopes = isotopes,
100 im = im) 101 im = im,
102 ppmInterp = opt$ppmInterp)
101 103
102 104
103 if (!is.null(opt$galaxy_names)){ 105 if (!is.null(opt$galaxy_names)){
104 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]]) 106 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
105 galaxy_names <- galaxy_names[galaxy_names != ""] 107 galaxy_names <- galaxy_names[galaxy_names != ""]