Mercurial > repos > cs76 > isotopologue_parameter_optimization

args<-commandArgs(TRUE)

workingDirectory<-args[3]
logFile<-paste(workingDirectory,'/run.log', sep='')
graphsDirectory<-paste(workingDirectory,'/graphs', sep='')
outputCSV<-paste(workingDirectory,'/IPO_PP.csv', sep='')

dir.create(workingDirectory)
zz <- file(logFile, open="wt")
sink(zz)
sink(zz, type="message")

library("xtable")
library(IPO)
#print(args)

peakpickingParameters <- getDefaultXcmsSetStartingParams('centWave')
#setting levels for min_peakwidth to 10 and 20 (hence 15 is the center point)
peakpickingParameters$min_peakwidth <- c(10,20)
peakpickingParameters$max_peakwidth <- c(26,42)
#setting only one value for ppm therefore this parameter is not optimized
peakpickingParameters$ppm <- 20
peakpickingParameters$nSlaves <- 4 # as.numeric(args[3])
type <- "centWave"

resultPP <- optimizeXcmsSet(files=args[1], params=peakpickingParameters, nSlaves=4, subdir=graphsDirectory)

print (resultPP)

graphs<-""
for(i in 1:(length(resultPP)-1))
{
	graphs<-paste(graphs,"<img width='100%' src='graphs/rsm_", i ,".jpg'><hr>",sep='')
}

list <- c(resultPP$best_settings$parameters, as.list(resultPP$best_settings$result), list(type=type))
table <- print(xtable(t(data.frame(list))), type = "html")
write.csv(c(resultPP$best_settings$parameters, as.list(resultPP$best_settings$result), list(type=type)),file=outputCSV)

html<-paste('<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
        <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
        <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
        <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
        <title></title>
        </head>
        <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='')

fileConn<-file(args[2])
writeLines(html, fileConn)
close(fileConn)

sink(type = "message")
sink()
author	cs76
date	Mon, 07 Dec 2015 06:05:53 -0500
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