view consensus.r @ 0:0cebe436a553 draft default tip

Initial upload.

#!/usr/bin/env Rscript

#sink(file("/dev/null", "w"), type = "message");

library(pathprint);

# Figure out the relative path to the galaxy-pathprint.r library.
script.args  <- commandArgs(trailingOnly = FALSE);
script.name  <- sub("--file=", "", script.args[grep("--file=", script.args)])
script.base  <- dirname(script.name)
library.path <- file.path(script.base, "galaxy-pathprint.r");
source(library.path)

data(GEO.metadata.matrix);

usage <- function() {
  stop("Usage: consensus.r <input> <threshold> <output>", call. = FALSE)
}

## Get the command line arguments.
args <- commandArgs(trailingOnly = TRUE)

input     <- ifelse(! is.na(args[1]), args[1], usage())
threshold <- ifelse(! is.na(args[2]), as.numeric(args[2]), usage())
output    <- ifelse(! is.na(args[3]), args[3], usage())

fingerprint <- loadFingerprint(input);
consensus   <- consensusFingerprint(fingerprint, threshold);

saveConsensus(consensus, output);

quit("no", 0)