# HG changeset patch
# User fangly
# Date 1318918523 14400
# Node ID bac7e652a9aaa4fd38942be0fb18e2ff807eb5d8
# Parent  68576b1d2d8bb66e7dd9e6bc9cae5aaf7b4ed62e
Added mate orientation option

diff -r 68576b1d2d8b -r bac7e652a9aa grinder.xml
--- a/grinder.xml	Tue Oct 18 01:48:14 2011 -0400
+++ b/grinder.xml	Tue Oct 18 02:15:23 2011 -0400
@@ -28,6 +28,9 @@
       #if str($insert_dist):
         -insert_dist      $insert_dist
       #end if
+      #if str($mate_orientation):
+        -mate_orientation $mate_orientation
+      #end if
       #if str($exclude_chars):
         -exclude_chars    $exclude_chars
       #end if
@@ -133,8 +136,9 @@
    0 : off,
    or: insert size distribution in bp, in the same format as the read length
        distribution (a typical value is 2,500 bp)
-Two distinct reads are generated whether or not the mate pair overlaps.
-Default: insert_dist.default" />
+Two distinct reads are generated whether or not the mate pair overlaps." />
+
+    <param name="mate_orientation" type="text" value="FR" optional="true" label="Mate orientation" help="When generating paired-end or mate-pair reads (see the insert distribution parameter), specify the orientation of the reads (F: forward, R: reverse): FR for Sanger or Illumina paired-end, FF for 454, RF for Illumina mate-pairs, or RR" />
 
     <param name="exclude_chars" type="text" optional="true" label="Characters to exclude" help="Do not create reads containing any of the specified characters (case insensitive), e.g. 'N-' to prevent reads with gaps (-) or ambiguities (N)." />