I recommend adding:

``action='store_true'`` to

https://github.com/biocore/American-Gut/blob/master/scripts/make_phyla_plots_AGP.py#L239


On Sun, Apr 13, 2014 at 5:36 PM, J W Debelius <notifications@github.com>wrote:

> In scripts/make_phyla_plots_AGP.py:
>
> > @@ -297,7 +297,7 @@ def main(otu_table, mapping_data, cat_tables, output_dir, sample_type='fecal',
> >           cat_tables=categories,
> >           samples_to_plot=samples,
> >           sample_type=sample_type,
> > -         debug=args.debug)
> > +         debug=eval(args.debug))
>
> I tried it that way, but when I passed only -d it triggered an error. And,
> args.debug was a string.
>
> --
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> .
>