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?


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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