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 >
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
