What Bjoern said - unless you meant the older bowtie1 wrappers. Those
have not been updated - I think we decision was made at Penn State to
focus on bowtie2 - but if people are still interested in enhancing the
bowtie1 wrappers I think a PR would be welcome. There have been some
other relatively recent bowtie1 PRs (e.g. from Nicola
https://github.com/galaxyproject/tools-devteam/pull/49).

-John

On Thu, Jun 25, 2015 at 3:46 AM, Bjoern Gruening
<bjoern.gruen...@gmail.com> wrote:
> Hi Ryan,
>
> latest wrappers are here:
> https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2
> And a PR would be great!
>
> But as far as I can see this is already implemented and you can choose as
> option `Paired-end Dataset Collection`, isn't it?
>
> Ciao,
> Bjoern
>
> On 24.06.2015 20:02, Ryan G wrote:
>
> Hi all - It looks like bowtie's wrapper is working incorrectly for a list of
> dataset pairs.  Its expecting all the forward reads in one dataset list and
> the reverse reads in a separate dataset list.
>
> Instead, I have a list of dataset pairs (for paired-end data).  This cannot
> be provided to bowtie as input.  If I correct this, should I create a pull
> request for it?  Alternatively, does someone already have a corrected
> version of this?
>
>
>
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