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1
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1 args<-commandArgs(TRUE)
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2
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3 workingDirectory<-args[3]
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4 logFile<-paste(workingDirectory,'/run.log', sep='')
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5 graphsDirectory<-paste(workingDirectory,'/graphs', sep='')
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6 outputCSV<-paste(workingDirectory,'/IPO_PP.csv', sep='')
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7
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8 dir.create(workingDirectory)
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9 zz <- file(logFile, open="wt")
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10 sink(zz)
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11 sink(zz, type="message")
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12
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13 library("xtable")
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14 library(IPO)
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15 #print(args)
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16
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17 peakpickingParameters <- getDefaultXcmsSetStartingParams('centWave')
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18 #setting levels for min_peakwidth to 10 and 20 (hence 15 is the center point)
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19 peakpickingParameters$min_peakwidth <- c(10,20)
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20 peakpickingParameters$max_peakwidth <- c(26,42)
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21 #setting only one value for ppm therefore this parameter is not optimized
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22 peakpickingParameters$ppm <- 20
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23 peakpickingParameters$nSlaves <- 4 # as.numeric(args[3])
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24 type <- "centWave"
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25
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26 resultPP <- optimizeXcmsSet(files=args[1], params=peakpickingParameters, nSlaves=4, subdir=graphsDirectory)
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27
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28 print (resultPP)
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29
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30 graphs<-""
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31 for(i in 1:(length(resultPP)-1))
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32 {
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33 graphs<-paste(graphs,"<img width='100%' src='graphs/rsm_", i ,".jpg'><hr>",sep='')
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34 }
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35
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36 list <- c(resultPP$best_settings$parameters, as.list(resultPP$best_settings$result), list(type=type))
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37 table <- print(xtable(t(data.frame(list))), type = "html")
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38 write.csv(c(resultPP$best_settings$parameters, as.list(resultPP$best_settings$result), list(type=type)),file=outputCSV)
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39
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40 html<-paste('<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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41 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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42 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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43 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
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44 <title></title>
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45 </head>
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46 <body> <div class="container-fluid"><h1 class="text-center">IPO optimization - Output</h1><hr>',table,'<br><span class="label label-primary"><a href="IPO_PP.csv">Output</a></span><br><span class="label label-danger"><a href="run.log">Job log</a></span><hr>',graphs,'</div>', sep='')
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47
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48 fileConn<-file(args[2])
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49 writeLines(html, fileConn)
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50 close(fileConn)
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51
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52 sink(type = "message")
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53 sink() |
