On Thu, Sep 30, 2010 at 11:08 AM, Peter <peter(a)maubp.freeserve.co.uk> wrote:
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...
As an example which I hope clarifies this, looking at blastn and the
dust option (ignoring for the moment the possibility to pass three
values level window linker), we can do this:
blastn ... -dust yes
blastn ... -dust no
or omit the dust option and let blastn follow its own default (which
is to use dust).
Before this patch, I was always explicitly setting the dust option;
After the patch, in "basic" mode I let blastn follow its own default:
Maybe this is a minor issue and is just down to the preferences
of the person writing each wrapper?