Mercurial > repos > tomnl > mspurity_createmsp

annotate combineAnnotations.R @ 5:3de08f3c4fb6 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 75d13d0237560528a1c6596a3ea5e327bed3e3a0
author tomnl
date Tue, 18 Jun 2019 10:44:54 -0400
parents 13985cdcf0ba
children 5dd61e94d70d
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df2efceff4cd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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1 library(optparse)
df2efceff4cd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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2 library(msPurity)
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3 print(sessionInfo())
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5 # Get the parameter
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6 option_list <- list(
df2efceff4cd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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7 make_option(c("-s","--sm_resultPth"),type="character"),
df2efceff4cd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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8 make_option(c("-m","--metfrag_resultPth"),type="character"),
df2efceff4cd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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9 make_option(c("-c","--sirius_csi_resultPth"),type="character"),
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10 make_option(c("-p","--probmetab_resultPth"),type="character"),
df2efceff4cd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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11 make_option(c("-sw","--sm_weight"),type="numeric"),
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12 make_option(c("-mw","--metfrag_weight"),type="numeric"),
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13 make_option(c("-cw","--sirius_csi_weight"),type="numeric"),
df2efceff4cd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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14 make_option(c("-pw","--probmetab_weight"),type="numeric"),
df2efceff4cd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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15 make_option("--create_new_database", action="store_true"),
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16 make_option(c("-o","--outdir"),type="character", default="."),
13985cdcf0ba planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e05cb49ba56d359fec34f132d1c9ace582e5b483-dirty
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17 make_option("--eic", action="store_true")
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18 )
df2efceff4cd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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19 opt <- parse_args(OptionParser(option_list=option_list))
df2efceff4cd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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21 print(opt)
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23 if (!is.null(opt$create_new_database)){
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24 sm_resultPth <- file.path(opt$outdir, 'combined_annotations.sqlite')
df2efceff4cd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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25 file.copy(opt$sm_resultPth, sm_resultPth)
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26 }else{
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27 sm_resultPth <- opt$sm_resultPth
df2efceff4cd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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28 }
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31 weights <-list('sm'=opt$sm_weight,
df2efceff4cd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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32 'metfrag'=opt$metfrag_weight,
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33 'sirius_csifingerid'= opt$sirius_csi_weight,
df2efceff4cd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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34 'probmetab'=opt$probmetab_weight
df2efceff4cd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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35 )
df2efceff4cd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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37 if (round(!sum(unlist(weights),0)==1)){
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39 stop(paste0('The weights should sum to 1 not ', sum(unlist(weights))))
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40 }
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42 summary_output <- msPurity::combineAnnotations(sm_resultPth,
df2efceff4cd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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43 opt$metfrag_resultPth,
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44 opt$sirius_csi_resultPth,
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45 opt$probmetab_resultPth,
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46 weights = weights)
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48 write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)
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51 closeAllConnections()
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