diff distance.r @ 0:0cebe436a553 draft default tip

Initial upload.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/distance.r	Fri May 17 14:29:33 2013 -0400
@@ -0,0 +1,33 @@
+#!/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: distance.r <input> <output> <output2>", call. = FALSE)
+}
+
+## Get the command line arguments.
+args <- commandArgs(trailingOnly = TRUE)
+
+input  <- ifelse(! is.na(args[1]), args[1], usage())
+output <- ifelse(! is.na(args[2]), args[2], usage())
+output2 <- ifelse(! is.na(args[3]), args[3], usage())
+
+fingerprint <- loadFingerprint(input);
+distance    <- calculateDistanceToPluripotent(fingerprint, verbose = 0);
+saveDistance(distance, output);
+
+generateHistograms(distance, output2);
+
+quit("no", 0)