Mercurial > repos > fangly > grinder
changeset 7:bac7e652a9aa
Added mate orientation option
| author | fangly |
|---|---|
| date | Tue, 18 Oct 2011 02:15:23 -0400 |
| parents | 68576b1d2d8b |
| children | 43def9fa33b9 |
| files | grinder.xml |
| diffstat | 1 files changed, 6 insertions(+), 2 deletions(-) [+] |
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--- 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)." />