Hi Assaf,

I placed the patch into a ticket for us to be able to track status more easily:
https://bitbucket.org/galaxy/galaxy-central/issue/635/patch-bwa-wrapper-with-illumina-13-fastq

Thank you!

Jen
Galaxy team

On 7/28/11 2:26 PM, Assaf Gordon wrote:
Hello Peter and all,

Peter Cock wrote, On 07/28/2011 05:08 PM:
It concerns me that you're doing this for both "fastqillumina" format
(good) and "fastqsolexa" (bad). Treating the later as fastqillumina
would give negative scores and probably cause trouble. Unless BWA
copes but if so it is a poor choice of argument name?

In the XML wrapper you've not updated the help text for the
FASTQ parameters to indicate it would now accept Illumina
FASTQ as well as Sanger FASTQ.

Peter

P.S. It is a patch file, but it has extension xml??

These are all valid comments, here's an updated patch (with a ".patch" 
extension :) ).

Thanks!
  -gordon




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