comparison limma_voom.R @ 19:c9c6427edfe9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5

18:97e06a4c7c75

#       filesPath", "j", 2, "character"     -JSON list object if multiple files input
#       matrixPath", "m", 2, "character"    -Path to count matrix
#       factFile", "f", 2, "character"      -Path to factor information file
#       factInput", "i", 2, "character"     -String containing factors if manually input
#       annoPath", "a", 2, "character"      -Path to input containing gene annotations
#       contrastData", "C", 1, "character"  -String containing contrasts of interest
#       cpmReq", "c", 2, "double"           -Float specifying cpm requirement
#       cntReq", "z", 2, "integer"          -Integer specifying minimum total count requirement
#       sampleReq", "s", 2, "integer"       -Integer specifying cpm requirement
#       normCounts", "x", 0, "logical"      -String specifying if normalised counts should be output
#       rdaOpt", "r", 0, "logical"          -String specifying if RData should be output

    "filesPath", "j", 2, "character",
    "matrixPath", "m", 2, "character",
    "factFile", "f", 2, "character",
    "factInput", "i", 2, "character",
    "annoPath", "a", 2, "character",
    "contrastData", "C", 1, "character",
    "cpmReq", "c", 1, "double",
    "totReq", "y", 0, "logical",
    "cntReq", "z", 1, "integer",
    "sampleReq", "s", 1, "integer",
    "filtCounts", "F", 0, "logical",

}

#Create output directory
dir.create(opt$outPath, showWarnings=FALSE)

# Split up contrasts seperated by comma into a vector then sanitise
contrastData <- unlist(strsplit(opt$contrastData, split=","))
contrastData <- sanitiseEquation(contrastData)
contrastData <- gsub(" ", ".", contrastData, fixed=TRUE)
# in case input groups start with numbers this will make the names valid R names, required for makeContrasts
cons <- NULL
for (i in contrastData) {
    i <- strsplit(i, split="-")
    i <- lapply(i, make.names)
    i <- lapply(i, paste, collapse="-")

19:c9c6427edfe9

#       filesPath", "j", 2, "character"     -JSON list object if multiple files input
#       matrixPath", "m", 2, "character"    -Path to count matrix
#       factFile", "f", 2, "character"      -Path to factor information file
#       factInput", "i", 2, "character"     -String containing factors if manually input
#       annoPath", "a", 2, "character"      -Path to input containing gene annotations
#       contrastFile", "C", 1, "character"  -Path to contrasts information file
#       contrastInput", "D", 1, "character" -String containing contrasts of interest
#       cpmReq", "c", 2, "double"           -Float specifying cpm requirement
#       cntReq", "z", 2, "integer"          -Integer specifying minimum total count requirement
#       sampleReq", "s", 2, "integer"       -Integer specifying cpm requirement
#       normCounts", "x", 0, "logical"      -String specifying if normalised counts should be output
#       rdaOpt", "r", 0, "logical"          -String specifying if RData should be output

    "filesPath", "j", 2, "character",
    "matrixPath", "m", 2, "character",
    "factFile", "f", 2, "character",
    "factInput", "i", 2, "character",
    "annoPath", "a", 2, "character",
    "contrastFile", "C", 1, "character",
    "contrastInput", "D", 1, "character",
    "cpmReq", "c", 1, "double",
    "totReq", "y", 0, "logical",
    "cntReq", "z", 1, "integer",
    "sampleReq", "s", 1, "integer",
    "filtCounts", "F", 0, "logical",

}

#Create output directory
dir.create(opt$outPath, showWarnings=FALSE)

# Process contrasts
if (is.null(opt$contrastInput)) {
    contrastData <- read.table(opt$contrastFile, header=TRUE, sep="\t", quote= "", strip.white=TRUE, stringsAsFactors=FALSE)
    contrastData <- contrastData[, 1, drop=TRUE]
}  else {
    # Split up contrasts seperated by comma into a vector then sanitise
    contrastData <- unlist(strsplit(opt$contrastInput, split=","))
}

# in case input groups start with numbers this will make the names valid R names, required for makeContrasts
contrastData <- sanitiseEquation(contrastData)
contrastData <- gsub(" ", ".", contrastData, fixed=TRUE)
cons <- NULL
for (i in contrastData) {
    i <- strsplit(i, split="-")
    i <- lapply(i, make.names)
    i <- lapply(i, paste, collapse="-")