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.c...@googlemail.com>: > 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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