Mercurial > repos > tomnl > assess_purity_msms

annotate track_rt_raw.R @ 13:eea94e398c26 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
author tomnl
date Tue, 08 May 2018 05:30:13 -0400
parents faba6cd56875
children
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b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
1 library(optparse)
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faba6cd56875 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
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146699c00d38 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 1
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3 print(sessionInfo())
146699c00d38 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
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b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
5 option_list <- list(
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
6 make_option(c("--xset_path"), type="character"),
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faba6cd56875 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 2
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7 make_option(c("-o", "--out_dir"), type="character"),
faba6cd56875 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 2
diff changeset
8 make_option(c("--extract_peaks"), action="store_true")
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b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
9 )
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
11 # store options
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
12 opt<- parse_args(OptionParser(option_list=option_list))
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
14 load(opt$xset_path)
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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16 print(xset)
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
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b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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18 rtraw <- xset@peaks[,c('rt', 'rtmin', 'rtmax')]
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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19 colnames(rtraw) <- c('rt_raw','rtmin_raw','rtmax_raw')
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
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20 xset@peaks <- cbind(xset@peaks, rtraw)
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
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23 print('saving RData')
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
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24 save.image(file.path(opt$out_dir, 'xset_rt_raw_tracked.RData'))
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faba6cd56875 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 2
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faba6cd56875 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 2
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26 if(!is.null(opt$extract_peaks)){
faba6cd56875 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 2
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27 write.table(xset@peaks, file.path(opt$out_dir, 'xset_peaks.tsv'), row.names=FALSE, sep='\t')
faba6cd56875 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 2
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28 }