I think it is probably a pair of bugs you are seeing:

The wrong database being selected is probably this:
https://trello.com/c/72WuZ8mu. It would be interesting to know if
reverting this pull request
https://bitbucket.org/galaxy/galaxy-central/pull-request/433/fix-allow-editing-workflows-on-the-fly-for/diff
fixes it - that would be a good indication this is the problem.

The tool running even though no valid inputs are found - is a sort of
known-ish issue but I cannot find any Trello card on it. I know I have
some WIP on a fix here:
https://github.com/jmchilton/galaxy/commit/900b7bbbf7f0084a86da9b737967fd8eb9d9f5fe

... and a related failing test case here.
https://github.com/galaxyproject/galaxy/blob/dev/test/api/test_tools.py#L223

The fix unfortunately is messy and will likely break stuff.

-John

On Tue, Mar 31, 2015 at 1:03 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Thanks Dan,
>
> That's very reassuring - will you file a Trello issue, or should I?
>
> Peter
>
>
> On Tue, Mar 31, 2015 at 5:56 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote:
>>
>> Hi Peter,
>>
>> I just wanted to chime in and say that I have been able to reproduce
>> this issue locally (on a different tool), and I’d consider it a pretty
>> significant bug for reproducibility, etc.
>>
>> Thanks,
>>
>> Dan
>
>>>> On Tue, Mar 31, 2015 at 11:31 AM, Peter Cock <p.j.a.c...@googlemail.com> 
>>>> wrote:
>>>>> ...
>>>>>
>>>>> Summary: Workflow requesting key entry "xxx" from example.loc
>>>>> (a) example.loc empty, gets empty path, fails cleanly.
>>>>> (b) example.loc contains xxx, gets correct path, works.
>>>>> (c) example.loc non empty but lacks xxx, runs with WRONG path.
>>>>>
>>>>> Peter
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