diff phylostatistics/ses-mpd-galaxy.r @ 0:5b9a38ec4a39 draft default tip

First commit of old repositories

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylostatistics/ses-mpd-galaxy.r	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,28 @@
+#!/sw/math/R-2.15.3-shlib/bin/Rscript
+
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+# NOTE: since picante is licensed under the GPL, and this program relies on 
+# picante, the program is licensed under the GPL regardless
+#
+# See: http://cran.r-project.org/web/packages/picante/picante.pdf,
+# http://www.gnu.org/licenses/old-licenses/gpl-2.0-faq.html#IfLibraryIsGPL
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+library('picante') 
+
+args <- commandArgs(trailingOnly = TRUE)
+
+sample <- read.table(file = args[1])
+tree <- read.tree(file = args[2])
+
+# get community data matrix of sample
+comm <- sample2matrix(sample)
+# get phylogenetic distance matrix of tree
+phydist <- cophenetic(tree)
+
+# finally, run the processed info through ses.mpd to get the result we want
+result <- ses.mpd(comm, phydist)
+
+# capture result and output to file
+out <- capture.output(result)
+cat(out, file = args[3], sep = "\n")