comparison limma_voom.R @ 12:81796eb60bd0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c

11:7e8af58c8052

    "contrastData", "C", 1, "character",
    "cpmReq", "c", 1, "double",
    "totReq", "y", 0, "logical",
    "cntReq", "z", 1, "integer",
    "sampleReq", "s", 1, "integer",
    "normCounts", "x", 0, "logical",
    "rdaOpt", "r", 0, "logical",
    "lfcReq", "l", 1, "double",
    "pValReq", "p", 1, "double",
    "pAdjOpt", "d", 1, "character",

if (is.null(opt$annoPath)) {
    haveAnno <- FALSE
} else {
    haveAnno <- TRUE
}

if (is.null(opt$normCounts)) {
    wantNorm <- FALSE
} else {

    stripOutPdf[i] <- makeOut(paste0("stripcharts_", con, ".pdf"))
    mdvolOutPng[i] <- makeOut(paste0("mdvolplot_", con, ".png"))
    topOut[i] <- makeOut(paste0(deMethod, "_", con, ".tsv"))
    glimmaOut[i] <- makeOut(paste0("glimma_", con, "/MD-Plot.html"))
}

normOut <- makeOut(paste0(deMethod, "_normcounts.tsv"))
rdaOut <- makeOut(paste0(deMethod, "_analysis.RData"))
sessionOut <- makeOut("session_info.txt")

# Initialise data for html links and images, data frame with columns Label and

        }
    }

    data$counts <- data$counts[keep, ]
    data$genes <- data$genes[keep, , drop=FALSE]

    # Plot Density
    if ("d" %in% plots) {
        # PNG
        png(denOutPng, width=1000, height=500)

12:81796eb60bd0

    "contrastData", "C", 1, "character",
    "cpmReq", "c", 1, "double",
    "totReq", "y", 0, "logical",
    "cntReq", "z", 1, "integer",
    "sampleReq", "s", 1, "integer",
    "filtCounts", "F", 0, "logical",
    "normCounts", "x", 0, "logical",
    "rdaOpt", "r", 0, "logical",
    "lfcReq", "l", 1, "double",
    "pValReq", "p", 1, "double",
    "pAdjOpt", "d", 1, "character",

if (is.null(opt$annoPath)) {
    haveAnno <- FALSE
} else {
    haveAnno <- TRUE
}

if (is.null(opt$filtCounts)) {
    wantFilt <- FALSE
} else {
    wantFilt <- TRUE
}

if (is.null(opt$normCounts)) {
    wantNorm <- FALSE
} else {

    stripOutPdf[i] <- makeOut(paste0("stripcharts_", con, ".pdf"))
    mdvolOutPng[i] <- makeOut(paste0("mdvolplot_", con, ".png"))
    topOut[i] <- makeOut(paste0(deMethod, "_", con, ".tsv"))
    glimmaOut[i] <- makeOut(paste0("glimma_", con, "/MD-Plot.html"))
}
filtOut <- makeOut(paste0(deMethod, "_filtcounts.tsv"))
normOut <- makeOut(paste0(deMethod, "_normcounts.tsv"))
rdaOut <- makeOut(paste0(deMethod, "_analysis.RData"))
sessionOut <- makeOut("session_info.txt")

# Initialise data for html links and images, data frame with columns Label and

        }
    }

    data$counts <- data$counts[keep, ]
    data$genes <- data$genes[keep, , drop=FALSE]

    if (wantFilt) {
        print("Outputting filtered counts")
        filt_counts <- data.frame(data$genes, data$counts)
        write.table(filt_counts, file=filtOut, row.names=FALSE, sep="\t", quote=FALSE)
        linkData <- rbind(linkData, data.frame(Label=paste0(deMethod, "_", "filtcounts.tsv"), Link=paste0(deMethod, "_", "filtcounts.tsv"), stringsAsFactors=FALSE))
    }

    # Plot Density
    if ("d" %in% plots) {
        # PNG
        png(denOutPng, width=1000, height=500)