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 ?


2016-01-20 10:33 GMT+01:00 Peter Cock <>:

> On Wed, Jan 20, 2016 at 9:19 AM, Floreline TOUCHARD
> <> 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
> > (
> ).
> >
> > 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:
> 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:
> Thanks,
> Peter
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