Simon and I worked on https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/
trimmomatic_032  during the BOSC 2014 Codefest to add compatibility for
sets of pairs of input files via the then-new dataset collections feature.

I'm not seeing support for that in Peter Briggs version though I am no
expert and happy to be corrected. Hopefully the two will be merged so we
don't lose the enhancements that both bring.

On Mon Dec 01 2014 at 10:52:03 AM Peter Cock <p.j.a.c...@googlemail.com>
wrote:

> Hello all,
>
> I've not heard back from Simon yet (it was the weekend), but in
> the meantime there is a new alternative wrapper from Peter Briggs
> which has skipped the Test Tool Shed and gone straight to the
> main Tool Shed:
>
> https://toolshed.g2.bx.psu.edu/view/pjbriggs/trimmomatic
>
> This one knows Trimmomatic now bundles the Illumina adatpers,
> and has tests too (fingers crossed the Tool Shed tests work
> tonight) :)
>
> @PeterB - My only immediate feedback on scanning the repository
> is to try renaming README.markdown to README.md as currently
> the Tool Shed has not spotted and shown the README file.
>
> Regards
>
> PeterC
>
> On Fri, Nov 28, 2014 at 2:31 PM, Peter Cock <p.j.a.c...@googlemail.com>
> wrote:
> > Hi Simon,
> >
> > I was looking for a Trimmomatic wrapper for Galaxy (which I have thus
> > far only used at the command line outside of Galaxy), and while there
> > does not seem to be one in the main Tool Shed, I see you have been
> > working on this over on the Test Tool Shed:
> >
> > https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/trimmomatic_0_22
> > https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/trimmomatic_032
> >
> > Note that according to http://www.usadellab.org/cms/?page=trimmomatic
> > the Trimmomatic authors have been given permission to redistribute
> > the Illumina adapter sequences now :)
> >
> > It would be nice to have functional tests, but other than that, what
> > status is the wrapper? Are there some issues blocking releasing this
> > via the main Tool Shed for wider use?
> >
> > Thanks,
> >
> > Peter
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