comparison lib.r @ 36:e309e6af6744 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e

35:2b0a4c7a4a48

}


# This function get the raw file path from the arguments
#@author Gildas Le Corguille [e-mail]
getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
    if (!is.null(args$zipfile))           zipfile <- args$zipfile
    if (!is.null(args$zipfilePositive))   zipfile <- args$zipfilePositive
    if (!is.null(args$zipfileNegative))   zipfile <- args$zipfileNegative

    if (!is.null(args$singlefile_galaxyPath)) {
        singlefile_galaxyPaths <- args$singlefile_galaxyPath;
        singlefile_sampleNames <- args$singlefile_sampleName
    }
    if (!is.null(args$singlefile_galaxyPathPositive)) {
        singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
        singlefile_sampleNames <- args$singlefile_sampleNamePositive
    }
    if (!is.null(args$singlefile_galaxyPathNegative)) {
        singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
        singlefile_sampleNames <- args$singlefile_sampleNameNegative
    }
    if (exists("singlefile_galaxyPaths")){
        singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
        singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))

        singlefile <- NULL
        for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
            singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
            singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
            singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
        }
    }
    return(list(zipfile=zipfile, singlefile=singlefile))
}


# This function retrieve the raw file in the working directory
#   - if zipfile: unzip the file with its directory tree
#   - if singlefiles: set symlink with the good filename
#@author Gildas Le Corguille [e-mail]

        return (xobject)
    # XCMS 3.x
    if (class(xobject) == "XCMSnExp") {
        # Get the legacy xcmsSet object
        suppressWarnings(xset <- as(xobject, 'xcmsSet'))
        sampclass(xset) <- xset@phenoData$sample_group
        return (xset)
    }
}

36:e309e6af6744

}


# This function get the raw file path from the arguments
#@author Gildas Le Corguille [e-mail]
getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") {
  if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")

  if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]]

  if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
    singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]]
    singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]]
  }
  if (exists("singlefile_galaxyPaths")){
    singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
    singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))

    singlefile <- NULL
    for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
      singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
      singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
      # In case, an url is used to import data within Galaxy 
      singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
      singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
    }
  }
  return(list(zipfile=zipfile, singlefile=singlefile))
}

# This function retrieve the raw file in the working directory
#   - if zipfile: unzip the file with its directory tree
#   - if singlefiles: set symlink with the good filename
#@author Gildas Le Corguille [e-mail]

        return (xobject)
    # XCMS 3.x
    if (class(xobject) == "XCMSnExp") {
        # Get the legacy xcmsSet object
        suppressWarnings(xset <- as(xobject, 'xcmsSet'))
        if (!is.null(xset@phenoData$sample_group))
            sampclass(xset) <- xset@phenoData$sample_group
        else
            sampclass(xset) <- "."
        return (xset)
    }
}