diff oases_optimiser.sh @ 0:53e887dda799 default tip

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/oases_optimiser.sh	Tue Jun 07 17:41:37 2011 -0400
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+min_k=$1
+max_k=$2
+input=$3
+args=$#
+if [$args -gt 3]; then
+	velvetoptions=$4
+	oasesoptions=$5
+else
+	velvetoptions=''
+	oasesoptions=''
+fi
+
+for i in `seq $min_k 2 $max_k`
+do
+     velveth . $i $input
+     velvetg . -read_trkg yes 
+     oases . $oasesoptions
+     mv transcripts.fa transcripts_$i.fa 
+done
+
+velveth . $max_k -long transcripts_*.fa $input 
+velvetg . -read_trkg yes $velvetoptions 
+oases . -amos_file yes -unused_reads yes $oasesoptions 
+