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_blast... (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.bernt@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.bernt@ufz.de, www.ufz.de
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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.bernt@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 -------------------------------------------