Mercurial > repos > tomnl > flag_remove_peaks

annotate track_rt_raw.R @ 14:088f318b2944 draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
author tomnl
date Wed, 18 Jul 2018 05:57:15 -0400
parents cb8dce9812ff
children
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cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
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1 library(optparse)
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
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cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
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3 print(sessionInfo())
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
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5 option_list <- list(
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
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6 make_option(c("--xset_path"), type="character"),
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
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7 make_option(c("-o", "--out_dir"), type="character"),
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
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8 make_option(c("--extract_peaks"), action="store_true")
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
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9 )
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
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cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
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11 # store options
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
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12 opt<- parse_args(OptionParser(option_list=option_list))
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
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cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
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14 load(opt$xset_path)
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
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cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
parents:
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16 print(xset)
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
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18 rtraw <- xset@peaks[,c('rt', 'rtmin', 'rtmax')]
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
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19 colnames(rtraw) <- c('rt_raw','rtmin_raw','rtmax_raw')
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
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20 xset@peaks <- cbind(xset@peaks, rtraw)
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
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23 print('saving RData')
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
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24 save.image(file.path(opt$out_dir, 'xset_rt_raw_tracked.RData'))
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
tomnl
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26 if(!is.null(opt$extract_peaks)){
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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27 write.table(xset@peaks, file.path(opt$out_dir, 'xset_peaks.tsv'), row.names=FALSE, sep='\t')
cb8dce9812ff planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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28 }