comparison CAMERA.r @ 19:608b4b95818b draft

planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00

18:78d267387462

# CAMERA.r version="2.2.1"



# ----- PACKAGE -----
cat("\tPACKAGE INFO\n")

setRepositories(graphics=F, ind=31)

#pkgs=c("xcms","batch")
pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","igraph","CAMERA","multtest","batch")
for(p in pkgs) {
    suppressPackageStartupMessages(suppressWarnings(library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
    cat(p,"\t",as.character(packageVersion(p)),"\n",sep="")
}
source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }

cat("\n\n");

rplotspdf = "Rplots.pdf"
if (!is.null(listArguments[["rplotspdf"]])){
    rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
}

dataMatrixOutput = "dataMatrix.tsv"
if (!is.null(listArguments[["dataMatrixOutput"]])){
    dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL
}

variableMetadataOutput = "variableMetadata.tsv"
if (!is.null(listArguments[["variableMetadataOutput"]])){
    variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL
}

    singlefile = rawFilePath$singlefile
    listArguments = rawFilePath$listArguments
    directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
}


#addition of xset object to the list of arguments in the first position
if (exists("xset") != 0){
    listArguments=append(list(xset), listArguments)
}

cat("\n\n")

cat("\tMAIN PROCESSING INFO\n")

#change the default display settings
pdf(file=rplotspdf, width=16, height=12)


if (thefunction %in% c("annotatediff")) {
    results_list=annotatediff(xset=xset,listArguments=listArguments,variableMetadataOutput=variableMetadataOutput,dataMatrixOutput=dataMatrixOutput)
    xa=results_list[["xa"]]
    diffrep=results_list[["diffrep"]]
    variableMetadata=results_list[["variableMetadata"]]

    cat("\n\n")

19:608b4b95818b

# CAMERA.r version="2.2.1"



# ----- PACKAGE -----
cat("\tSESSION INFO\n")

pkgs=c("CAMERA","multtest","batch")
for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))

sessioninfo = sessionInfo()
cat(sessioninfo$R.version$version.string,"\n")
cat("Main packages:\n")
for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
cat("Other loaded packages:\n")
for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")

source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }

cat("\n\n");

rplotspdf = "Rplots.pdf"
if (!is.null(listArguments[["rplotspdf"]])){
    rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
}

variableMetadataOutput = "variableMetadata.tsv"
if (!is.null(listArguments[["variableMetadataOutput"]])){
    variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL
}

    singlefile = rawFilePath$singlefile
    listArguments = rawFilePath$listArguments
    directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
}

# Because so far CAMERA isn't compatible with the new XCMSnExp object
if (exists("xdata")){
    xset <- getxcmsSetObject(xdata)
}

# addition of xset object to the list of arguments in the first position
if (exists("xset")){
    listArguments=append(list(xset), listArguments)
}

cat("\n\n")

cat("\tMAIN PROCESSING INFO\n")

#change the default display settings
pdf(file=rplotspdf, width=16, height=12)

if (thefunction %in% c("annotatediff")) {
    results_list=annotatediff(xset=xset,listArguments=listArguments,variableMetadataOutput=variableMetadataOutput)
    xa=results_list[["xa"]]
    diffrep=results_list[["diffrep"]]
    variableMetadata=results_list[["variableMetadata"]]

    cat("\n\n")