Mercurial > repos > tomnl > create_msp

annotate create_msp.R @ 19:78885fff83a3 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
author tomnl
date Wed, 18 Jul 2018 06:06:32 -0400
parents 4b417094bf71
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
1 suppressWarnings(suppressPackageStartupMessages(require(optparse,quietly = T)))
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
2 suppressWarnings(suppressPackageStartupMessages(require(msPurity)))
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
3 print(sessionInfo())
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
4 # Get the parameter
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
5 option_list <- list(
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
6 make_option(c("-i","--purity"),type="character"),
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
7 make_option(c("-p","--ppm"),type="numeric"),
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
8 make_option(c("-m","--mode"),type="character")
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
9 )
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
10 opt <- parse_args(OptionParser(option_list=option_list))
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
11
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
12 print(opt)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
13
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
14 load(opt$purity)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
15
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
16 grped_df <- pa@grped_df
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
17
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
18 msms <- pa@grped_ms2
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
19
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
20 puritydf <- pa@puritydf
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
21
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
22
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
23
19
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
24 #grped_df$fileid <- sapply(grped_df$filename, function(x) which(basename(pa@fileList)==x))
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
25 #puritydf$fileid <- sapply(puritydf$filename, function(x) which(basename(pa@fileList)==x))
0
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
26
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
27
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
28
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
29
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
30 selfrag <- as.numeric(unique(grped_df$grpid))
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
31
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
32 of <- file(description = "outfile.msp", open = "w+a")
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
33
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
34 write.msp <- function(name,precmz,prectype,spectra,ofile){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
35
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
36 cat(paste("NAME: ", name, "\r\n", sep = ""), file = ofile)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
37
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
38 cat(paste("PRECURSORMZ: ", precmz , "\r\n", sep = ""), file = ofile)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
39
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
40 #cat(paste("PRECURSORTYPE: ", prectype, "\r\n", sep = ""), file = ofile) # No adducts? Annotation
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
41
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
42 cat("Comment:\r\n", file = ofile)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
43
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
44 cat(paste("Num Peaks: ", nrow(spectra), "\r\n", sep = ""), file = ofile)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
45
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
46 cat(paste(paste(spectra[,1], spectra[,2], sep = "\t"), sep = "\r\n"), sep = "\r\n", file = ofile)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
47
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
48 cat("\r\n", file = ofile)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
49 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
50
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
51 for(i in selfrag){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
52
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
53 j <- which(grped_df$grpid==i)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
54
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
55 spec <- msms[[as.character(i)]]
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
56
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
57 if (length(j)>1){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
58
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
59 grpd <- grped_df[j,]
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
60
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
61 if (opt$mode=="all"){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
62
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
63 for(jj in 1:length(j)){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
64
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
65 idj <- paste(i,jj,sep=".")
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
66
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
67 specj <- spec[[jj]]
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
68
19
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
69
0
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
70
19
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
71 grpdj <- grpd[jj,]
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
72 if ('sample' %in% colnames(grpd)){
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
73 fileid = grpdj$sample
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
74 }else{
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
75 fileid = grpdj$fileid
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
76 }
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
77 name = paste(i, fileid, grpdj$pid, sep='-')
0
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
78
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
79 write.msp(name,grpdj$precurMtchMZ,"",specj,of)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
80 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
81
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
82 }else{
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
83
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
84 prec_int <- sapply(grpd$precurMtchID, function(x) puritydf[ which(puritydf$seqNum==x & puritydf$fileid==grpd$fileid[1]), "precursorIntensity"] )
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
85
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
86 if (opt$mode=="max"){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
87
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
88 idx <- which(prec_int==max(prec_int))
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
89
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
90 grpd <- grpd[idx,]
19
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
91 if ('sample' %in% colnames(grpd)){
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
92 fileid = grpd$sample
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
93 }else{
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
94 fileid = grpd$fileid
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
95 }
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
96
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
97 name = paste(i, fileid, grpd$pid, sep='-')
0
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
98 write.msp(name,grpd$precurMtchMZ,"",specj[[idx]], of)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
99 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
100
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
101 if (opt$mode=="average"){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
102
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
103 file_weights <- prec_int/prec_int[which(prec_int==min(prec_int))] # spectra of the most intense precursor, largest weight
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
104
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
105 merged_msms <- do.call("rbind", spec)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
106
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
107 colnames(merged_msms) <- c("mz","int")
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
108
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
109 file_weights <-rep(file_weights,sapply(spec,nrow))
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
110
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
111 merged_msms <- data.frame(cbind(merged_msms,file_weights))
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
112
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
113 umzs <- sort(merged_msms$mz,index.return=T)$ix
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
114
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
115 merged_msms <- merged_msms[umzs,]
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
116
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
117 umzs <- merged_msms$mz
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
118
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
119 mz_groups <- list() # mz windows to bind
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
120
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
121 mz_grouped <- c() # used mzs
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
122
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
123 ppm <- opt$ppm # ppm level to bind mzs
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
124
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
125 for(y in 1:length(umzs)){ # spectra averaging
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
126
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
127 z <- umzs[y]
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
128
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
129 if(!(z %in% mz_grouped)){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
130
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
131 mz_range <- z*(ppm/1e6)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
132
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
133 mz_range <- c(z-mz_range,z+mz_range)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
134
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
135 mz_group <- which(umzs>mz_range[1] & umzs<mz_range[2])
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
136
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
137 if(length(mz_group)>1){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
138
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
139 zz <- umzs[max(mz_group)]
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
140
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
141 mz_range <- zz*(ppm/1e6)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
142
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
143 mz_range <- c(zz-mz_range,zz+mz_range)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
144
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
145 mz_group2 <- which(umzs>mz_range[1] & umzs<mz_range[2])
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
146
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
147 mz_group <- append(mz_group,mz_group2)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
148 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
149
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
150 mz_group <- unique(mz_group)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
151
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
152 mz_grouped <- append(mz_grouped,umzs[mz_group])
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
153
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
154 mz_group <- list(mz_group)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
155
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
156 mz_groups <- append(mz_groups,mz_group)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
157 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
158 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
159
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
160 averaged_spec <- t(sapply(mz_groups,function(x){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
161
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
162 if(length(x)==1){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
163
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
164 mz <- merged_msms$mz[x]
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
165
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
166 nint <- merged_msms[x,]
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
167
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
168 nint <- nint$int*nint$file_weights
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
169
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
170 }else{
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
171
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
172 mz <- mean(merged_msms$mz[x])
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
173
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
174 nint <- sum(sapply(x,function(y){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
175 nint <- merged_msms[y,]
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
176 nint <- nint$int*nint$file_weights
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
177 }))
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
178 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
179 return(c(mz,nint))
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
180 }))
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
181
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
182 write.msp(i,mean(grpd$precurMtchMZ),"",averaged_spec,of)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
183
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
184 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
185 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
186 }else{
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
187 spec <- spec[[1]]
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
188
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
189 grpd <- grped_df[j,]
19
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
190 if ('sample' %in% colnames(grpd)){
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
191 fileid = grpd$sample
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
192 }else{
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
193 fileid = grpd$fileid
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
194 }
78885fff83a3 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
tomnl
parents: 0
diff changeset
195 name = paste(i, fileid, grpd$pid, sep='-')
0
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
196 write.msp(name,grpd$precurMtchMZ,"",spec,of)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
197 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
198 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
199
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
200