we can already specify options that are not tied to parameters. any reason
that wouldn't work?


On Thu, Aug 15, 2013 at 11:40 AM, Jai Ram Rideout
<notifications@github.com>wrote:

> In python-code/biom/commands/summarize_biom_table.py:
>
> > +__credits__ = ["Greg Caporaso"]
> > +__license__ = "GPL"
> > +__version__ = "1.1.2-dev"
> > +__maintainer__ = "Greg Caporaso"
> > +__email__ = "gregcaporaso@gmail.com
> "
> > +
> > +class SummarizeBiomTable(Command):
> > +    """
> > +     Example usage:
> > +      from biom.commands.summarize_biom_table import SummarizeBiomTable
> > +      from biom.parse import parse_biom_table
> > +      c = SummarizeBiomTable()
> > +      t = parse_biom_table(open("table.biom"))
> > +      result = c(table=t)
> > +      result = c(table=t,qualitative=True)
> > +      result = c(table=t,qualitative=True,input_fp="table.biom")
>
> Yes, but how would you hook it up to the current framework that we have in
> place? That's the part that isn't clear to me.
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/biom-format/biom-format/pull/161/files#r5795089>
> .
>