Mercurial > repos > tomnl > anticipated_purity_lcms
annotate track_rt_raw.R @ 22:c8b34df46dae draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 04023134d8f28e85927ca293373c506484149ead-dirty
author | tomnl |
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date | Fri, 01 Jun 2018 13:41:15 -0400 |
parents | fd6f8eecdec9 |
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dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
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1 library(optparse) |
5
fd6f8eecdec9
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents:
2
diff
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2 |
2
b83bcc259b76
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
1
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3 print(sessionInfo()) |
b83bcc259b76
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
1
diff
changeset
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4 |
0
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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5 option_list <- list( |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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6 make_option(c("--xset_path"), type="character"), |
5
fd6f8eecdec9
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents:
2
diff
changeset
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7 make_option(c("-o", "--out_dir"), type="character"), |
fd6f8eecdec9
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents:
2
diff
changeset
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8 make_option(c("--extract_peaks"), action="store_true") |
0
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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9 ) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
|
10 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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11 # store options |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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12 opt<- parse_args(OptionParser(option_list=option_list)) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
|
13 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
|
14 load(opt$xset_path) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
|
15 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
|
16 print(xset) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
|
17 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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18 rtraw <- xset@peaks[,c('rt', 'rtmin', 'rtmax')] |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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19 colnames(rtraw) <- c('rt_raw','rtmin_raw','rtmax_raw') |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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20 xset@peaks <- cbind(xset@peaks, rtraw) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
|
21 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
|
22 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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23 print('saving RData') |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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24 save.image(file.path(opt$out_dir, 'xset_rt_raw_tracked.RData')) |
5
fd6f8eecdec9
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents:
2
diff
changeset
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25 |
fd6f8eecdec9
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents:
2
diff
changeset
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26 if(!is.null(opt$extract_peaks)){ |
fd6f8eecdec9
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents:
2
diff
changeset
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27 write.table(xset@peaks, file.path(opt$out_dir, 'xset_peaks.tsv'), row.names=FALSE, sep='\t') |
fd6f8eecdec9
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents:
2
diff
changeset
|
28 } |