Dear Peter,

you are right. I hope that this will be much less in the end (I'm still learning about the package).

The main question still remains, how do I get `planemo test` to include the data types defined in the xml file?

Best,
Matthias



Am 16/08/18 18:32 schrieb Peter Cock <p.j.a.cock@googlemail.com>:
Defining 20 different text-based formats does not look ideal (if that
is what you are doing).

Do you have sample output in the repository? Perhaps at least some of
these can be better defined as tabular instead?

Or, perhaps you can define one composite datatype for the folder of
output instead?

Peter

On Thu, Aug 16, 2018 at 4:18 PM, Matthias Bernt <m.bernt@ufz.de> wrote:
> 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.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
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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
> -------------------------------------------