updates to OTU picking parameter defaults

~~**NOT READY FOR MERGE**~~

It is still necessary to the enable_rev_strand_match command, and we can't
update the parameters file itself with this release, or it wouldn't work
correctly with 1.8.0 anymore.


On Tue, Jun 17, 2014 at 6:05 AM, Jai Ram Rideout <notifications@github.com>
wrote:

> In doc/tutorials/open_reference_illumina_processing.rst:
>
> >
> >
> > -To apply this analysis to ``seqs1.fna``, picking OTUs against the reference collection ``refseqs.fna`` you can run the following command. Your parameters file should contain the following::
> > -
> > -	pick_otus:otu_picking_method uclust_ref
> > -	pick_otus:enable_rev_strand_
> match True
> > +To apply this analysis to ``seqs1.fna``, picking OTUs against the reference collection ``refseqs.fna`` you can run the following command.
> >
> >  You should *always use full paths* which are represented here by ``$PWD``, but will usually look something like ``$HOME/my_data/`` (in other words, they should start with a ``/``). In this example your input sequences (``seqs1.fna``), and your metadata mapping file (``map.txt``) are all in the same directory represented by ``$PWD``. If you work from the directory containing those files, you can leave ``$PWD`` in the commands instead of specifying the full paths::
> >
> >  	pick_open_reference_otus.py -i $PWD/seqs1.fna,$PWD/seqs2.fna -r $PWD/refseqs.fna -o $PWD/ucrss_iter/ -aO 8 -p $PWD/ucrss_params.txt
>
> Can you please update this command to remove -p $PWD/ucrss_params.txt?
> The parameters file shouldn't be necessary anymore.
>
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> <https://github.com/biocore/qiime/pull/1586/files#r13857046>.
>