Hi Peter,
I hope that subclassing simple data types will be sufficient.
More details:
I'm currently trying to (auto)wrap the checkm suite
https://github.com/Ecogenomics/CheckM. Current state here:
https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/checkm.
These tools often create an output folder which is then the input to
other tools. So I thought to create a (output) data type for each of the
tools and save the folder using extra_files_path. Then I can pass the
folder to downstream tools (and can check for proper input). I hope that
subclassing txt or tabular will be sufficient.
Cheers,
Matthias
On 16.08.2018 17:02, Peter Cock wrote:
More details might help - are you just defining the new datatype as a
subclass in the XML, or do you need to include Python code (e.g. for a
sniffer)?
If you want to see some examples of datatypes using Python code which
are available via the Tool Shed, here are two:
https://github.com/peterjc/galaxy_blast/tree/master/data_managers/ncbi_blastdb
(now also in the Galaxy core)
https://github.com/peterjc/galaxy_mira/tree/master/datatypes/mira_datatypes
Peter
On Thu, Aug 16, 2018 at 3:48 PM, Matthias Bernt <m.be...@ufz.de> wrote:
Dear list,
just a request for links to documentation: How can I realize tool specific
data types. I'm just developing a set of tools that need their own data
types, but I don't want to add them to Galaxy's core data types (yet).
I've seen examples of tools that had a datatypes_conf.xml. So I created one,
but it seems that it is ignored.
Cheers,
Matthias
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
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Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
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--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
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Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
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