Mercurial > repos > lecorguille > msnbase_readmsdata

comparison msnbase_readmsdata.r @ 13:226fb89cacc4 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
author workflow4metabolomics
date Wed, 12 Feb 2020 08:27:38 -0500
parents 0a0164b8c24d
children 11ab2081bd4a
comparison
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12:f6b2750ea32e 13:226fb89cacc4
36 cat("\tINFILE PROCESSING INFO\n") 36 cat("\tINFILE PROCESSING INFO\n")
37 37
38 # Handle infiles 38 # Handle infiles
39 if (!exists("singlefile")) singlefile <- NULL 39 if (!exists("singlefile")) singlefile <- NULL
40 if (!exists("zipfile")) zipfile <- NULL 40 if (!exists("zipfile")) zipfile <- NULL
41 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args) 41 rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args)
42 zipfile <- rawFilePath$zipfile 42 zipfile <- rawFilePath$zipfile
43 singlefile <- rawFilePath$singlefile 43 singlefile <- rawFilePath$singlefile
44 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) 44 files <- rawFilePath$files
45 45
46 # Check some character issues 46 md5sumList <- list("origin" = getMd5sum(files))
47 md5sumList <- list("origin" = getMd5sum(directory))
48 checkXmlStructure(directory)
49 checkFilesCompatibilityWithXcms(directory)
50
51 47
52 cat("\n\n") 48 cat("\n\n")
53 49
54 50
55 # ----- MAIN PROCESSING INFO ----- 51 # ----- MAIN PROCESSING INFO -----
56 cat("\tMAIN PROCESSING INFO\n") 52 cat("\tMAIN PROCESSING INFO\n")
57 53
58 54
59 cat("\t\tCOMPUTE\n") 55 cat("\t\tCOMPUTE\n")
60
61 ## Get the full path to the files
62 files <- getMSFiles(directory)
63 56
64 cat("\t\t\tCreate a phenodata data.frame\n") 57 cat("\t\t\tCreate a phenodata data.frame\n")
65 s_groups <- sapply(files, function(x) tail(unlist(strsplit(dirname(x),"/")), n=1)) 58 s_groups <- sapply(files, function(x) tail(unlist(strsplit(dirname(x),"/")), n=1))
66 s_name <- tools::file_path_sans_ext(basename(files)) 59 s_name <- tools::file_path_sans_ext(basename(files))
67 pd <- data.frame(sample_name=s_name, sample_group=s_groups, stringsAsFactors=FALSE) 60 pd <- data.frame(sample_name=s_name, sample_group=s_groups, stringsAsFactors=FALSE)