Mercurial > repos > workflow4metabolomics > mzxmlshaper

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
author workflow4metabolomics
date Mon, 07 Oct 2024 11:40:19 +0000
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7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
workflow4metabolomics
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1 #!/usr/bin/env Rscript
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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3 # R version 4.3.3
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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4 # Conversion tool mzXMLShaper.R (former cdf2mzml)
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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5 # Author: Quentin RUIN
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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6 # Creation date: 25/04/2023
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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7 # Last updated: 09/09/2024
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
workflow4metabolomics
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9 cat("\nJob starting time:\n", format(Sys.time(), "%a %d %b %Y %X"), "\n\n")
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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11 library(mzR)
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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12 library(msdata)
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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13 library("W4MRUtils")
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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14 library("tools")
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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16 args <- W4MRUtils::parse_args(args = commandArgs())
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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18 cat("\n\n--------------------------------------------------------------------",
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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19 "\nParameters used by the 'mz(X)MLShaper' tool:\n\n")
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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20 cat("--------------------------------------------------------------------\n\n")
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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21 print(args)
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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23 inputfilename <- args[[1]]
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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24 outputfileformat <- args[[2]]
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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25 outputfilename <- args[[3]]
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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26 spectrum <- mzR::openMSfile(inputfilename)
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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28 ## Get the spectra
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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29 pks <- mzR::spectra(spectrum)
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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31 ## Get the header
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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32 hdr <- mzR::header(spectrum)
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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34 if (outputfileformat == "mzml") {
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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35 writeMSData(pks, file = outputfilename, outformat = "mzml", header = hdr)
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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36 }
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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38 if (outputfileformat == "mzXml") {
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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39 writeMSData(pks, file = outputfilename, outformat = "mzxml", header = hdr)
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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40 }
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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42 cat("\n--------------------------------------------------------------------",
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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43 "\nInformation about R (version, Operating System, attached or loaded packages):\n\n")
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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44 sessionInfo()
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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45 cat("--------------------------------------------------------------------\n",
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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46 "\nJob ending time:\n", format(Sys.time(), "%a %d %b %Y %X"))