--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rarefaction/rarefactionCurve.sh	Sun Jun 01 19:46:00 2014 -0400
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+echo $@
+
+filetype=$1
+input=$2
+pctIdent=$3
+label=0$(bc <<< "scale=2; 1-$pctIdent")
+output=$4
+pngOutput=$5
+
+## use Mothur rarefaction.single to calculate rarefaction
+mothur "#rarefaction.single($filetype=$input, label=$label)" 2>1
+
+## get filename only remove the extension and copy to galaxy output file
+file="${input%.*}"
+echo `cp $file.rarefaction $output`