Hi,

thanks for your support. This helps.

I have thought a bit about composite data types. And have additional questions.

In my case the additional data is essentially a folder (w subfolders). The contents of the folder vary (it depends on the input of the programs that generate them). So the question is if I can/should

- add a single folder (with all the hirarchy as a single composite data element) .. I have only seen a add_composite_file function.

- add a dynamic number of composite files

- or if it is better to use the extra_files_path mechanism (which seems to be the simplest for me)

In any of these cases my next question would be how to create a test using such a data as input and output (for output I have seen an example somewhere).

Cheers,
Matthias



On 17.08.2018 11:53, Peter Cock wrote:
This is probably a John Chilton question, as the Planemo lead.

The way I do it is to "manually" install the datatype into a Galaxy
test instance (adding entries to the datatypes_conf.xml and Python
files to Galaxy's internal library), and then call ``planemo test``
pointing at this test instance. You can see that approach in action
here:

https://github.com/peterjc/galaxy_blast/blob/579c348ced72d4e6f1ef7fb0cded98e52f454b92/.travis.yml#L106
https://github.com/peterjc/galaxy_blast/blob/579c348ced72d4e6f1ef7fb0cded98e52f454b92/.travis.datatypes_conf.xml#L20

and:

https://github.com/peterjc/galaxy_mira/blob/206259620376b322fc8ed99a6efdd3712f38764b/.travis.yml#L113
https://github.com/peterjc/galaxy_mira/blob/206259620376b322fc8ed99a6efdd3712f38764b/.travis.datatypes_conf.xml#L42

There may be a more elegant solution nowadays using planemo to do some
of the work.

Peter

On Thu, Aug 16, 2018 at 9:30 PM, Matthias Bernt <m.be...@ufz.de> wrote:
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.c...@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.be...@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.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
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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
-------------------------------------------

--

-------------------------------------------
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"
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