On Wed, Mar 30, 2016 at 9:46 PM, Molik, David <dmo...@cshl.edu> wrote:
> We're uploading a tool to the Galaxy Toolshed and were wondering about sample 
> files:
> Should .loc.sample files refer to sample data ( test-data )
> or should they be generalized for integration into other instances of Galaxy?

Any sample loc files should be provided named tool-data/example.loc.sample
and will be copied as example.loc to give default values for the system. This
may just mean a section of comment lines with no actual values, or perhaps
you can give useful defaults?

Here's an example where useful defaults made sense - and these are
also used in the tool's functional tests:


If you want to write functional tests using test entries in the example.loc file
(i.e. entries not in the default values provided in your
example.loc.sample file),
use tests-data/example.loc instead and the special value ${__HERE__} to
take case of giving a full path.

e.g. sample file with no real entries:
vs. test file pointing at some test entries:

I'm not sure if this last part has made it into the official
documentation yet...

> Also, how should dependencies be noted?

Can you be a bit more precise?

Probably the answer is tool_dependencies.xml etc, e.g.

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