Mercurial > repos > lecorguille > xcms_group

comparison xcms_group.r @ 32:68282292acc4 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
author lecorguille
date Tue, 03 Apr 2018 11:39:07 -0400
parents 020d065edd9e
children 59943e24684b
comparison
equal deleted inserted replaced
31:f248fd3b89d6 32:68282292acc4
27 27
28 # ----- PROCESSING INFILE ----- 28 # ----- PROCESSING INFILE -----
29 cat("\tARGUMENTS PROCESSING INFO\n") 29 cat("\tARGUMENTS PROCESSING INFO\n")
30 30
31 #saving the specific parameters 31 #saving the specific parameters
32 method <- args$method; args$method <- NULL 32 method <- args$method
33 33
34 if (!is.null(args$convertRTMinute)){ 34 if (!is.null(args$convertRTMinute)) convertRTMinute <- args$convertRTMinute
35 convertRTMinute <- args$convertRTMinute; args$convertRTMinute <- NULL 35 if (!is.null(args$numDigitsMZ)) numDigitsMZ <- args$numDigitsMZ
36 } 36 if (!is.null(args$numDigitsRT)) numDigitsRT <- args$numDigitsRT
37 if (!is.null(args$numDigitsMZ)){ 37 if (!is.null(args$intval)) intval <- args$intval
38 numDigitsMZ <- args$numDigitsMZ; args$numDigitsMZ <- NULL
39 }
40 if (!is.null(args$numDigitsRT)){
41 numDigitsRT <- args$numDigitsRT; args$numDigitsRT <- NULL
42 }
43 if (!is.null(args$intval)){
44 intval <- args$intval; args$intval <- NULL
45 }
46 38
47 cat("\n\n") 39 cat("\n\n")
48 40
49 41
50 # ----- ARGUMENTS PROCESSING ----- 42 # ----- ARGUMENTS PROCESSING -----
51 cat("\tINFILE PROCESSING INFO\n") 43 cat("\tINFILE PROCESSING INFO\n")
52 44
53 #image is an .RData file necessary to use xset variable given by previous tools 45 #image is an .RData file necessary to use xset variable given by previous tools
54 load(args$image); args$image=NULL 46 load(args$image)
55 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.*") 47 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.*")
56 48
57 # Handle infiles 49 # Handle infiles
58 if (!exists("singlefile")) singlefile <- NULL 50 if (!exists("singlefile")) singlefile <- NULL
59 if (!exists("zipfile")) zipfile <- NULL 51 if (!exists("zipfile")) zipfile <- NULL
60 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args) 52 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
61 zipfile <- rawFilePath$zipfile 53 zipfile <- rawFilePath$zipfile
62 singlefile <- rawFilePath$singlefile 54 singlefile <- rawFilePath$singlefile
63 args <- rawFilePath$args
64 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) 55 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
65 56
66 # Check some character issues 57 # Check some character issues
67 md5sumList <- list("origin" = getMd5sum(directory)) 58 md5sumList <- list("origin" = getMd5sum(directory))
68 checkXmlStructure(directory) 59 checkXmlStructure(directory)
79 cat("\t\tCOMPUTE\n") 70 cat("\t\tCOMPUTE\n")
80 71
81 72
82 cat("\t\t\tPerform the correspondence\n") 73 cat("\t\t\tPerform the correspondence\n")
83 args$sampleGroups = xdata$sample_group 74 args$sampleGroups = xdata$sample_group
75
76 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
77 args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list(sampleGroups=c(1,2))))]
78
84 groupChromPeaksParam <- do.call(paste0(method,"Param"), args) 79 groupChromPeaksParam <- do.call(paste0(method,"Param"), args)
85 print(groupChromPeaksParam) 80 print(groupChromPeaksParam)
86 xdata <- groupChromPeaks(xdata, param = groupChromPeaksParam) 81 xdata <- groupChromPeaks(xdata, param = groupChromPeaksParam)
87 82
88 83