On Jun 3, 2011, at 5:03 AM, Peter Cock wrote:

> On Thu, Jun 2, 2011 at 6:39 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> On Jun 2, 2011, at 1:29 PM, Nate Coraor wrote:
>>> Peter Cock wrote:
>>>> Hi all,
>>>> Something I've not needed to do until now is define a new file format
>>>> in Galaxy. I understand the basic principle and defining a subclass in
>>>> Python... however, how does this work with new tools on the Tool Shed?
>>>> In particular, if an output format is likely to be used by more than
>>>> one tool, can we get it added to the Galaxy core?
>>> I think people have provided the new subclass as a patch with the tool,
>>> but probably many of them, if well written, could be added to the core.
>>>> As an example, the basic functionality of the Blast2GO for pipelines
>>>> tool (b2g4pipe) takes a BLAST XML input file, and gives a tab
>>>> separated annotation output file. Galaxy already has 'blastxml' and
>>>> 'tabular' file formats defined, so I didn't need to do anything extra.
>>>> However, the tool can also take (a directory of) InterProScan XML
>>>> files as input, so here a new 'interproscanxml' format would useful.
>>>> Then any wrapper using or producing InterProScan XML could take
>>>> advantage of this. e.g. Konrad's InterProScan wrapper could then offer
>>>> the XML output as an option in addition to or instead of the tabular
>>>> output.
>> We will certainly include support for new data formats into the Galaxy
>> core.  In case you haven't seen it, details for adding new formats is
>> available in our wiki at
>> https://bitbucket.org/galaxy/galaxy-central/wiki/AddingDatatypes
>> It's fairly straightforward.  However, glancing at the wiki, it looks like
>> there is no mention of functional tests for the new format.  If we could
>> get a patch that includes a functional test for uploading the format as
>> new method(s) in ~/test/functional/test_get_data.py, it would be great.
> Thanks for the link - I was aware my initial work on adding a generic
> XML filetype was missing some steps, but I ran out of time yesterday:
> https://bitbucket.org/galaxy/galaxy-central/issue/568
> The test information is especially useful - but I don't see any use of
> doctest in test/functional/test_get_data.py - could you clarify if the
> docstring examples within the datatype classes are actually tested,
> and if so how?

The unit tests within the datatype classes are executed via:

%sh run_unit_tests.sh

in the Galaxy root directory, whereas the functional tests are executed via:

%sh run_functional_tests.sh

in the Galaxy root directory.

> Thanks,
> Peter

Greg Von Kuster
Galaxy Development Team

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