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annotate combineAnnotations.R @ 0:ca0ac330f1a4 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
author tomnl
date Fri, 24 May 2019 09:13:42 -0400
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children 28fb8befb3b2
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ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
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1 library(optparse)
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
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2 library(msPurity)
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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3 print(sessionInfo())
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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5 # Get the parameter
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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6 option_list <- list(
ca0ac330f1a4 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"),
ca0ac330f1a4 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"),
ca0ac330f1a4 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"),
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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10 make_option(c("-p","--probmetab_resultPth"),type="character"),
ca0ac330f1a4 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"),
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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12 make_option(c("-mw","--metfrag_weight"),type="numeric"),
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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13 make_option(c("-cw","--sirius_csi_weight"),type="numeric"),
ca0ac330f1a4 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"),
ca0ac330f1a4 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"),
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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16 make_option(c("-o","--outdir"),type="character", default=".")
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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17 )
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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18 opt <- parse_args(OptionParser(option_list=option_list))
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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20 print(opt)
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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22 if (!is.null(opt$create_new_database)){
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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23 sm_resultPth <- file.path(opt$outdir, 'combined_annotations.sqlite')
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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24 file.copy(opt$sm_resultPth, sm_resultPth)
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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25 }else{
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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26 sm_resultPth <- opt$sm_resultPth
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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27 }
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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30 weights <-list('sm'=opt$sm_weight,
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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31 'metfrag'=opt$metfrag_weight,
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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32 'sirius_csifingerid'= opt$sirius_csi_weight,
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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33 'probmetab'=opt$probmetab_weight
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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34 )
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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36 if (round(!sum(unlist(weights),0)==1)){
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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38 stop(paste0('The weights should sum to 1 not ', sum(unlist(weights))))
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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39 }
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ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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41 summary_output <- msPurity::combineAnnotations(sm_resultPth,
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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42 opt$metfrag_resultPth,
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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43 opt$sirius_csi_resultPth,
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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44 opt$probmetab_resultPth,
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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45 weights = weights)
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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47 write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)