emtpy samples should be (optionally) filtered after subsample-* actions

[gregcaporaso]

@brett-van-tussler discovered that if a sample has 0 reads following qiime demux subsample-paired (or subsample-single), the sample will still be retained in the output. There should be an option to drop these samples from the resulting artfiact.

A workaround is as follows (once #151 is merged):

# subsample the Moving Pictures demux.qza such that all samples will likely have zero read count
qiime demux subsample-single --i-sequences demux.qza --p-fraction 0.0000000000000000000000001 --o-subsampled-sequences demux-empty.qza

# generate counts of reads on a per-sample basis (this is what we're waiting on #151 for)
qiime demux tabulate-read-counts --i-sequences demux-empty.qza --o-counts demux-empty-counts.qza

# tabulate those into a .qzv, just to confirm counts are zero
qiime metadata tabulate --m-input-file demux-empty-counts.qza --o-visualization demux-empty-counts.qzv

# filter all samples with a count of zero (this will fail if no samples have a count greater than 0)
qiime demux filter-samples --i-demux demux-empty.qza --m-metadata-file demux-empty-counts.qza --p-where "[Demultiplexed sequence count] > 0" --o-filtered-demux demux-empty-filtered.qza

# generate read counts on the filtered artifact
qiime demux tabulate-read-counts --i-sequences demux-empty-filtered.qza --o-counts demux-empty-filtered-counts.qza

# tabulate those into a .qzv to confirm that no samples are left
qiime metadata tabulate --m-input-file demux-empty-filtered-counts.qza --o-visualization demux-empty-filtered-counts.qzv