I'm wondering if there is any mechanism in the XML file format
for tool wrappers to access global settings? e.g. something like
$environment.temp to access the temp environment variable,
or something like this for values in universe_wsgi.ini
In particular, I'd like to know if there is a way to know how many
threads a wrapped tool can use - is there a policy here?
Looking at the existing megablast wrapper, this is hard coded
as 8 in the Python script, tools/metag_tools/megablast_wrapper.py
For the BLAST+ wrappers I am writting, I want to set the number
of threads in the XML file - again currently hard coded as 8.
Is there an overall policy on default values when wrapping tools?
e.g. Should defaults be set explicitly in the wrapper (which we can
track in the Galaxy version control under hg), or omitted to let the
command line tool set its own defaults?
I am thinking about pipeline reproducibility as defaults can change...