Thanks for the answer !
 
I compared the two versions of tools. It does not seem to be any major differences indeed. I added these tools to my instance successfully. Additional options in version 6 are not to be integrate to my Galaxy instance immediately. I will update my XML file later if need arises. The old wrappers are perfect for the moment.
 
For the NCBI BLAST+ suite I would like to select multiple databases only from the *.loc files. There is no spaces in the paths in my *.loc files (however there is spaces in the names of these databases, but I guess this is not a problem). I thought I just have to add a tag "multiple=true" in the XML file but it seems a bit more complex. Am I missing something ?
 
F.T

 
2016-01-20 10:33 GMT+01:00 Peter Cock <p.j.a.cock@googlemail.com>:
On Wed, Jan 20, 2016 at 9:19 AM, Floreline TOUCHARD
<floreline.touchard@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