Mercurial > repos > tomnl > dma_filelist_generation
annotate topn.R @ 10:7c54e2862595 draft default tip
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 14435cfc042911bf1ee409f5a0d5ef908f5feec0-dirty
author | tomnl |
---|---|
date | Thu, 21 Jun 2018 08:45:03 -0400 |
parents | 6a2bb42acfe4 |
children |
rev | line source |
---|---|
0
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
1 library(XCMSwrapper) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
2 library(optparse) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
3 |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
4 |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
5 option_list <- list( |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
6 make_option("--sample_metadata", type="character"), |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
7 make_option("--out_dir", type="character"), |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
8 make_option("--class", type="character"), |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
9 make_option("--file_include", type="character"), |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
10 make_option("--cores", type="character"), |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
11 make_option("--scan_dens", type="numeric"), |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
12 make_option("--n", type="numeric"), |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
13 make_option("--ppm", type="numeric"), |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
14 make_option("--snthr", type="numeric"), |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
15 make_option("--minfrac", type="numeric"), |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
16 make_option("--polarity", type="character"), |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
17 make_option("--time_window_choice", type="character"), |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
18 make_option("--files", type="character"), |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
19 make_option("--galaxy_files", type="character") |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
20 |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
21 ) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
22 |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
23 # store options |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
24 opt<- parse_args(OptionParser(option_list=option_list)) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
25 |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
26 |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
27 time_window_choice<- trimws(strsplit(opt$time_window_choice, ';')[[1]]) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
28 time_window_choice <- time_window_choice[time_window_choice != ""] |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
29 tdf <- plyr::ldply(time_window_choice, function(x){trimws(strsplit(x, ',')[[1]])}) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
30 colnames(tdf) <- c('min', 'max') |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
31 tdf$min <- as.numeric(tdf$min) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
32 tdf$max <- as.numeric(tdf$max) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
33 |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
34 # Nearline processing |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
35 params <- list( |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
36 topn.class = opt$class, |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
37 topn.class.files = opt$file_include, |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
38 topn.msPurity = TRUE, |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
39 topn.cores = opt$cores, |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
40 topn.scanDens = opt$scan_dens, # for scan range x to y, take every 'n' scan (i.e. x, x+n, x+2n ... y) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
41 topn.timeRange = tdf, |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
42 topn.chunks = NULL, #list(c = 3, timeWin = c(0,1800)), # e.g. list(c = 3, timeWin = c(0,1800)) #chunk time range 0-1800 in to 3. |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
43 topn.n = opt$n, # number of peaks to take per window |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
44 topn.ppm = opt$ppm, |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
45 topn.snthr = opt$snthr, |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
46 topn.minfrac= opt$minfrac, |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
47 topn.clustType = 'hc', |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
48 topn.camera_xcms = '', |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
49 faahKO=FALSE |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
50 ) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
51 |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
52 |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
53 # |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
54 sample_metadata <- read.table(opt$sample_metadata, sep='\t', stringsAsFactors=FALSE) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
55 |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
56 filepaths <- trimws(strsplit(opt$files, ',')[[1]]) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
57 filepaths <- filepaths[filepaths != ""] |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
58 filepaths_wo_suffix <- unlist(lapply(filepaths, function(x){tools::file_path_sans_ext(basename(x))})) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
59 |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
60 galaxy_files <- trimws(strsplit(opt$galaxy_files, ',')[[1]]) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
61 galaxy_files <- galaxy_files[galaxy_files != ""] |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
62 |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
63 if(!is.null(opt$class)){ |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
64 # print(sample_metadata[,1]) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
65 file_select <- sample_metadata[,1][sample_metadata[,2]==opt$class] |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
66 chosen_files <- galaxy_files[filepaths_wo_suffix %in% file_select] |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
67 }else{ |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
68 chosen_files <- galaxy_files |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
69 } |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
70 print(chosen_files) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
71 |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
72 if(!is.null(opt$file_include)){ |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
73 file_include <- trimws(strsplit(opt$file_include, ',')[[1]]) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
74 file_include <- as.numeric(file_include[file_include != ""]) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
75 print(file_include) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
76 chosen_files <- chosen_files[file_include] |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
77 } |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
78 print(chosen_files) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
79 params$topn.filenames = chosen_files |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
80 |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
81 topn = getTopn(obj=NULL, params) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
82 colnames(topn) = c('mzmed', 'rtmin', 'rtmax') |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
83 topn = create_incl(grps = topn, incl_in = NULL, write_file = F, posneg = opt$polarity, comments='topn') |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
84 |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
85 |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
86 print('HEAD ROWS OF TOPN') |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
87 print(head(topn)) |
6a2bb42acfe4
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
88 write.table(topn, file.path(opt$out_dir, 'topn_peaklist.tsv'), row.names=FALSE, sep='\t') |