Mercurial > repos > lecorguille > xcms_fillpeaks

comparison xcms_fillpeaks.r @ 24:999f9db0ca2c draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
author workflow4metabolomics
date Wed, 12 Feb 2020 08:28:33 -0500
parents 3bc94c3abb28
children 26d77e9ceb49
comparison
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23:3bc94c3abb28 24:999f9db0ca2c
51 if (!hasFeatures(xdata)) stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step") 51 if (!hasFeatures(xdata)) stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step")
52 52
53 # Handle infiles 53 # Handle infiles
54 if (!exists("singlefile")) singlefile <- NULL 54 if (!exists("singlefile")) singlefile <- NULL
55 if (!exists("zipfile")) zipfile <- NULL 55 if (!exists("zipfile")) zipfile <- NULL
56 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args) 56 rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args)
57 zipfile <- rawFilePath$zipfile 57 zipfile <- rawFilePath$zipfile
58 singlefile <- rawFilePath$singlefile 58 singlefile <- rawFilePath$singlefile
59 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
60
61 # Check some character issues
62 md5sumList <- list("origin" = getMd5sum(directory))
63 checkXmlStructure(directory)
64 checkFilesCompatibilityWithXcms(directory)
65 59
66 60
67 cat("\n\n") 61 cat("\n\n")
68 62
69 # ----- MAIN PROCESSING INFO ----- 63 # ----- MAIN PROCESSING INFO -----