Mercurial > repos > tomnl > deconrank
annotate lcms-interval-scheduling.R @ 4:b37f97bda760 draft
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit d4159f1962ef3fe37dd4f3047e4050afe013c15a-dirty
author | tomnl |
---|---|
date | Thu, 03 May 2018 05:20:17 -0400 |
parents | defa57c7775e |
children |
rev | line source |
---|---|
1
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
1 library(XCMSwrapper) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
2 library(optparse) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
3 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
4 option_list <- list( |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
5 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
6 make_option(c("-s", "--sample_peaklist"), type="character"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
7 make_option(c("-b", "--blank_peaklist"), type="character"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
8 make_option(c("-t", "--topn"), type="character"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
9 make_option(c("-o", "--out_dir"), type="character", default=getwd(), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
10 help="Output folder for resulting files [default = %default]" |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
11 ), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
12 make_option("--method", type="character"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
13 make_option("--maxms2", type="numeric"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
14 make_option("--widthFactor", type="numeric"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
15 make_option("--minWidth", type="numeric"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
16 make_option("--ilimit", type="numeric"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
17 make_option("--shift", type="numeric"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
18 make_option("--samplelistNm", type="numeric"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
19 make_option("--overlappingP", type="numeric"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
20 make_option("--fullpw", action="store_true"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
21 make_option("--b_widthFactor", type="numeric"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
22 make_option("--b_shift", type="numeric"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
23 make_option("--b_exclu_limit", type="numeric"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
24 make_option("--b_minWidth", type="numeric"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
25 make_option("--polarity", type="character"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
26 make_option("--fillgaps", type="character"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
27 make_option("--dmaNearline", action="store_true"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
28 make_option("--blankClass", type="character"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
29 make_option("--intensityCN", type="character"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
30 make_option("--sortCN", type="character"), |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
31 make_option("--filterS", type="character") |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
32 ) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
33 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
34 # store options |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
35 opt<- parse_args(OptionParser(option_list=option_list)) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
36 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
37 print(sessionInfo()) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
38 print(opt) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
39 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
40 if(is.null(opt$fullpw)){ |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
41 fullpw = FALSE |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
42 }else{ |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
43 fullpw = TRUE |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
44 } |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
45 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
46 if(is.null(opt$fillgaps)){ |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
47 fillgaps = FALSE |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
48 }else{ |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
49 fillgaps = TRUE |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
50 } |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
51 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
52 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
53 # Nearline processing |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
54 # nearline parameters (sample and blank) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
55 params <- list( |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
56 nl.method = opt$method, |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
57 nl.maxms2 = opt$maxms2, # only used for simple nearline |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
58 nl.widthFactor = opt$widthFactor, |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
59 nl.minWidth = opt$minWidth, # 5 seconds |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
60 nl.ilimit = opt$ilimit, # only used for simple nearline |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
61 nl.shift = opt$shift, |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
62 nl.samplelist_nm = opt$samplelistNm, |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
63 nl.overlappingP = opt$overlappingP, |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
64 nl.fullpw = fullpw, |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
65 nl.fillgaps = fillgaps, # only used for metshot nearline |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
66 #nearline blank parameters |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
67 nl.b_widthFactor = opt$b_widthFactor, # increase the width |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
68 nl.b_minWidth = opt$b_minWidth, |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
69 nl.b.shift = opt$b_shift, |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
70 nl.exclu_limit = opt$b_exclu_limit, |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
71 temp_dir='.', |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
72 intensityCN=opt$intensityCN, |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
73 sortCN=opt$sortCN # column of the sample peaklist to use for |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
74 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
75 ) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
76 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
77 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
78 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
79 # ################################## |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
80 # # Perform Nearline optimisation |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
81 # ################################## |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
82 s_peaklist <- read.table(opt$sample_peaklist, header = TRUE, sep='\t', stringsAsFactors = FALSE) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
83 b_peaklist <- read.table(opt$blank_peaklist, header = TRUE, sep='\t', stringsAsFactors = FALSE) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
84 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
85 if(!is.null(opt$dmaNearline)){ |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
86 # have to do some additional filtering if part of the dma nearline workflow |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
87 blank_class_name <- gsub('-', '.', opt$blankClass) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
88 b_peaklist = b_peaklist[which(b_peaklist[,paste(blank_class_name, '_valid', sep='')]==1),] |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
89 s_peaklist = s_peaklist[s_peaklist[,opt$filterS]==0,] |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
90 } |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
91 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
92 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
93 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
94 topn <- read.table(opt$topn, header = TRUE, sep='\t', stringsAsFactors = FALSE, check.names=FALSE) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
95 topn[is.na(topn)] <- "" |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
96 # colnames(topn) <- c('Mass [m/z]', 'Formula [M]', 'Formula type', 'Species', 'CS [z]', 'Polarity', 'Start [min]', 'End [min]','Comment') |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
97 # colnames(topn) <- gsub('\\.', ' ', colnames(topn)) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
98 print(head(topn)) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
99 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
100 # #Generate inclusions lists for DDA-MS/MS and store in list |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
101 incl.lists = nearline_main(pm = params, peaklist_xcms=s_peaklist, pol=opt$polarity, merge_peaklists=FALSE, peaklist_post=NA) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
102 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
103 # #Generate exclusion lists for each class being analysed |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
104 nearline_main_blank(pm = params, |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
105 plist = b_peaklist, |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
106 incl_list_pos = incl.lists, |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
107 pol = opt$polarity, |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
108 topn = topn) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
109 # |