What is disappearing (sortof) is the UI for selecting the individual
pieces - I don't think anything in the API has changed yet.

I don't think datatypes have a way of picking apart an archive file
for their pieces - but it would make a lot of sense to implement.

Total Aside: I wonder if testing tools one at a time is always the
best approach - one can imagine (for instance in your indexer's case)
utility in being able to string together some pre-steps or post-steps
for things like conversions to ease testing. For some very yak-shavey
reasons I wrote a little YAML DSL
(https://gist.github.com/jmchilton/3b66f101c53c6734d3c5) for building
Galaxy workflows to test some tool and workflow features. I have been
considering extending it with the ability to specify input and outputs
conditions and adding it to planemo to test repositories . (By
assigning labels at a level above the actual RAW workflow - it solves
the biggest problem that was present with the workflow testing stuff
we briefly discussed last winder). It would be cool for local and CI
testing - but it is more difficult to see how that pattern could work
with the tool shed test framework where the ids are not simple and the
tools may be split across many repositories.</aside>

-John

On Wed, Nov 19, 2014 at 10:39 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hi John, Sam,
>
> I've not done it yet, but was hoping to implement uploading of
> BLAST databases at some point - mainly for use within the
> test framework, rather than expecting it to be useful for the
> end user.
>
> Is the issue here uploading an archive (e.g. .zip or .tar.gz) or
> offering a way to pick multiple files to be treated together as
> a composite dataset?
>
> Peter
>
> On Wed, Nov 19, 2014 at 3:32 PM, John Chilton <jmchil...@gmail.com> wrote:
>> Well there is at least one person using this functionality -
>> http://dev.list.galaxyproject.org/Problem-to-upload-data-to-Galaxy-when-using-pbed-file-format-td4666000.html.
>>
>> Just to make this more concrete - Sam has swapped the "upload file"
>> button to use the new upload widget this release cycle (targeted for
>> December 1st). So barring negative feedback - uploading pbed or velvet
>> report datatypes (or other similar composite datatypes) will no longer
>> be possible via the GUI.
>>
>> -John
>>
>> On Thu, Aug 14, 2014 at 2:32 PM, Aysam Guerler <aysam.guer...@gmail.com> 
>> wrote:
>>> Hello everyone,
>>>
>>> We are considering to disable the deprecated upload tool form which is
>>> currently accessible through Tool panel > Get Data > Upload file. The new
>>> upload feature (icon at the top of the Tool panel) covers all of its
>>> functionality except uploading composite datatypes like e.g. Velvet.
>>>
>>> Please let us know if you are using the composite file upload functionality
>>> of the former tool form.
>>>
>>> Thanks,
>>> Sam
>>>
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