On Wed, Jan 20, 2016 at 9:19 AM, Floreline TOUCHARD
<floreline.touch...@gmail.com> wrote:
> Hi,
>
> I would like to add some tools of the EMBOSS suite (6.6.0) to my Galaxy
> instance. It seems that the only wrapper available for Galaxy is for the
> 5.0.0 version
> (http://dev.list.galaxyproject.org/Galaxy-with-EMBOSS-5-or-EMBOSS-6-td4658043.html).
>
> I would like to know if someone has already tried (successfully or not) to
> wrap this tools base on the old wrappers to estimate the workload that
> awaits me (for prettyseq and water mostly).

There is work in progress here, see:
https://github.com/galaxyproject/tools-iuc/issues/65
https://github.com/galaxyproject/tools-iuc/pull/131

Have you compared the API options to see if anything changed
here in EMBOSS? I don't recall any major changes to water,
but I don't use prettyseq at all.

> Could there be an invalid datatype format for example ?

Many datatypes were already defined for the EMBOSS 5.0.0
wrappers, so that is less likely to be a problem for EMBOSS 6.6.0

> I have another question regarding the NCBI BLAST+ suite : is there a way to
> edit the XML file to enable the selection of multiple databases as proposed
> by the command lines tool ?

Possible by editing the wrappers, yes. However it will likely break
if any of the paths have spaces in them due to the NCBI wanting
a space separated list of database paths - a potential problem
already in the makeblastdb wrapper.

Are you wanting to use multiple databases from the *.loc files at
once, multiple databases from the current history, or both? Please
log this as an enhancement request here:

https://github.com/peterjc/galaxy_blast/issues

Thanks,

Peter
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