Mercurial > repos > tomnl > create_sqlite_db
comparison anticipated_purity_dims.R @ 5:9ab472c5714c draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
author | tomnl |
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date | Mon, 23 Apr 2018 06:10:07 -0400 |
parents | 1a88758357ed |
children | 3d8bde261c95 |
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4:ff61a6fb23bf | 5:9ab472c5714c |
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12 make_option("--ppm", default=4), | 12 make_option("--ppm", default=4), |
13 make_option("--dimspy", action="store_true"), | 13 make_option("--dimspy", action="store_true"), |
14 make_option("--sim", action="store_true"), | 14 make_option("--sim", action="store_true"), |
15 make_option("--remove_nas", action="store_true"), | 15 make_option("--remove_nas", action="store_true"), |
16 make_option("--iwNorm", default="none", type="character"), | 16 make_option("--iwNorm", default="none", type="character"), |
17 make_option("--dimspy_file_num", default=1), | 17 make_option("--file_num_dimspy", default=1), |
18 make_option("--exclude_isotopes", action="store_true"), | 18 make_option("--exclude_isotopes", action="store_true"), |
19 make_option("--isotope_matrix", type="character") | 19 make_option("--isotope_matrix", type="character") |
20 ) | 20 ) |
21 | 21 |
22 # store options | 22 # store options |
23 opt<- parse_args(OptionParser(option_list=option_list)) | 23 opt<- parse_args(OptionParser(option_list=option_list)) |
24 | 24 |
25 print(sessionInfo()) | 25 print(sessionInfo()) |
26 print(opt) | 26 print(opt) |
27 | 27 |
28 if (opt$dimspy){ | 28 if (is.null(opt$dimspy)){ |
29 | |
30 df <- read.table(opt$peaks_file, header = TRUE, sep='\t') | |
31 filename = NA | |
32 }else{ | |
29 indf <- read.table(opt$peaks_file, | 33 indf <- read.table(opt$peaks_file, |
30 header = TRUE, sep='\t', stringsAsFactors = FALSE) | 34 header = TRUE, sep='\t', stringsAsFactors = FALSE) |
31 filename = colnames(indf)[8:ncol(indf)][opt$dimspy_file_num] | 35 filename = colnames(indf)[8:ncol(indf)][opt$dimspy_file_num] |
32 # check if the data file is mzML or RAW (can only use mzML currently) so | 36 # check if the data file is mzML or RAW (can only use mzML currently) so |
33 # we expect an mzML file of the same name in the same folder | 37 # we expect an mzML file of the same name in the same folder |
47 df[df$mz=='nan',]$mz <- NA | 51 df[df$mz=='nan',]$mz <- NA |
48 } | 52 } |
49 df$mz <- as.numeric(df$mz) | 53 df$mz <- as.numeric(df$mz) |
50 | 54 |
51 | 55 |
52 }else{ | 56 |
53 df <- read.table(opt$peaks_file, header = TRUE, sep='\t') | 57 |
54 filename = NA | |
55 } | 58 } |
56 | 59 |
57 if (!is.null(opt$remove_nas)){ | 60 if (!is.null(opt$remove_nas)){ |
58 df <- df[!is.na(df$mz),] | 61 df <- df[!is.na(df$mz),] |
59 } | 62 } |