You'll need to add the display_in_upload attribute to your local version of the
datatypes_conf.xml file installed with your emboss_datatypes repository from
the tool shed.
This may result in a merge at some point if the contents of the
datatypes_conf.xml file changes in the emboss_datatypes repository in the main
tool shed and you pull the updates to your local repository.
Greg Von Kuster
On Aug 3, 2012, at 10:51 AM, Marc Logghe wrote:
> Hi Björn,
> I think the issue is that the genbank datatype is coming in via the tool shed
> and is not taken into account by the upload tool. The genbank datatype is
> defined in
> I have added the display_in_upload attribute in the latter file for the
> genbank datatype, restarted Galaxy but the type did not appear in the
> Should the genbank datatype be added to the main galaxy datatypes_conf.xml ?
> Or is it better to explicitly add the emboss' datatypes_conf.xml to the
> universe_wsgi.ini (but this will break the tool shed update system, right) ?
> -----Original Message-----
> From: Björn Grüning [mailto:bjoern.gruen...@pharmazie.uni-freiburg.de]
> Sent: Friday, August 03, 2012 4:14 PM
> To: Marc Logghe
> Cc: firstname.lastname@example.org
> Subject: Re: [galaxy-dev] Upload File: how to see all registered formats ?
> Hi Marc,
> please have a look at the datatypes_conf.xml file in your galaxy directory.
> There should be something like that:
> <datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile"
> Try to add 'display_in_upload="true"' to the genbank datatype.
> The 'good' solution would be to define a datatype genbank, with a sniff
> function, so that galaxy can guess the filetype when you are uploading it.
> Please find attached my first attempt for that. Im working on some datatypes
> and converteres, but its not ready yet :(
>> Hi again,
>> Emboss_datatypes is installad via tool shed. The ‘View datatypes
>> registry’ in the Adminstration page, shows all registered data types,
>> including the emboss ones, like e.g. genbank.
>> However, the ‘Upload File’ tool does not show genbank in the ‘File
>> Format’ dropdown. How can one configure the upload1 tool so that all
>> registered formats are listed ?
>> I don’t understand the from_parameter hocus-pocus in this line
>> transform_lines="[ "%s%s%s" % ( line, self.separator, line )
>> for line in obj ]">
>> The workaround which is used up to now is upload genbank sequences as
>> txt format and change the format later via the history. But that is a
>> 2-step operation, guess there should be a way taking only 1 step ?
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> Björn Grüning
> Albert-Ludwigs-Universität Freiburg
> Institute of Pharmaceutical Sciences
> Pharmaceutical Bioinformatics
> Hermann-Herder-Strasse 9
> D-79104 Freiburg i. Br.
> Tel.: +49 761 203-4872
> Fax.: +49 761 203-97769
> E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
> Web: http://www.pharmaceutical-bioinformatics.org/
> THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY
> TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED,
> CONFIDENTIAL AND EXEMPT FROM DISCLOSURE.
> If the reader of this E-mail message is not the intended recipient, you are
> hereby notified that any dissemination, distribution or copying of this
> communication is strictly prohibited. If you have received this communication
> in error, please notify us immediately at abl...@ablynx.com. Thank you for
> your co-operation.
> "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V.
> 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:
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: