Hello Jan,

Thanks for the clarification. Not quite what I was expecting so I am
glad I asked - I don't have great answers for either case so hopefully
other people will have some ideas.

For the first use case - I would just specify some default input to
supply to the input wrapper - lets call this N - add a parameter to
the tool wrapper "--limit-size=N" - test that and then allow it to be
overridden via an environment variable - so in your command block use
"--limit-size=\${BLAST_QUERY_LIMIT:N}". This will use N is not limit
is set, but deployers can set limits. There are a number of ways to
set such variables - DRM specific environment files, login rc files,
etc.... Just this last release I added the ability to define
environment variables right in job_conf.xml
(https://bitbucket.org/galaxy/galaxy-central/pull-request/378/allow-specification-of-environment/diff).
I thought the tool shed might have a way to collect such definitions
as well and insert them into package files - but Google failed to find
this for me.

Not sure about how to proceed with the second use case - extending the
.loc file should work locally - I am not sure it is feasible within
the context of the existing tool shed tools, data manager, etc.... You
could certainly duplicate this stuff with your modifications - this
how down sides in terms of interoperability though.

Sorry I don't have great answers for either question,
-John




On Sat, Jun 14, 2014 at 5:12 AM, Jan Kanis <jan.c...@jankanis.nl> wrote:
> I have two use cases: the first is for a modification of the ncbi blast
> wrapper to limit the query input size (for a publically accessible galaxy
> instance), so this needs a configuration option for the query size limit. I
> was thinking about a separate config file in tool-data for this.
>
> The second is is for a tool I have written to convert a blast xml output
> into a html report. The report contains links for each match to a gene bank
> (e.g. the ncbi database). These links should be configurable per database
> that was searched, and preferrably have an option of linking to the location
> of the match within the gene if the gene bank supports such links. One
> option is to add an extra column to the blast .loc files (if that doesn't
> break blast), where the databases are already configured.
>
> Jan
>
> Op 13 jun. 2014 18:02 schreef "John Chilton" <jmchil...@gmail.com> het
> volgende:
>
>> I would have different answers for your depending on what options are
>> available to the server admin. What exactly about the tool is
>> configurable - can you be more specific?
>>
>> -John
>>
>> On Fri, Jun 13, 2014 at 10:59 AM, Jan Kanis <jan.c...@jankanis.nl> wrote:
>> > I am writing a tool that should be configurable by the server admin. I
>> > am
>> > considering adding a configuration file, but where should such a file be
>> > placed? Is the tool-data directory the right place? Is there another
>> > standard way for per-tool configuration?
>> >
>> > Jan
>> >
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