Mercurial > repos > lecorguille > xcms_group

comparison xcms_group.r @ 24:761913919c21 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
author workflow4metabolomics
date Wed, 12 Feb 2020 08:29:15 -0500
parents 6842c495da6d
children d45a786cbc40
comparison
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23:fe4002ac5193 24:761913919c21
48 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") 48 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
49 49
50 # Handle infiles 50 # Handle infiles
51 if (!exists("singlefile")) singlefile <- NULL 51 if (!exists("singlefile")) singlefile <- NULL
52 if (!exists("zipfile")) zipfile <- NULL 52 if (!exists("zipfile")) zipfile <- NULL
53 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args) 53 rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args)
54 zipfile <- rawFilePath$zipfile 54 zipfile <- rawFilePath$zipfile
55 singlefile <- rawFilePath$singlefile 55 singlefile <- rawFilePath$singlefile
56 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
57
58 # Check some character issues
59 md5sumList <- list("origin" = getMd5sum(directory))
60 checkXmlStructure(directory)
61 checkFilesCompatibilityWithXcms(directory)
62
63 56
64 cat("\n\n") 57 cat("\n\n")
65 58
66 59
67 # ----- MAIN PROCESSING INFO ----- 60 # ----- MAIN PROCESSING INFO -----