first pass at adding run() functionality
some changes to get logging working
working on cleaning up run() functionality
Merge pull request #38 from gregcaporaso/death-march

updates to get logging working
Merge pull request #39 from wasade/death-march

Death march
Make command-line parser work (maybe)
Merge branch 'death-march' of github.com:bipy/qcli into death-march

Conflicts:
	qcli/interface/cli.py
Remove print statement
Merge pull request #40 from jrrideout/death-march

Work on command-line parser
updated to use logger rather than cl-specific option parser
Merge branch 'death-march' of github.com:bipy/qcli into death-march
updates to get to the point where we can (at least partially) print help text
Merge pull request #41 from wasade/death-march

Death march
Merge branch 'death-march' of github.com:bipy/qcli into death-march

Conflicts:
	qcli/interface/cli.py
added beginning of filter_samples_from_otu_table script config file
updated to fix printing of command line output
first working version of basic filter samples from otu table command
updated to support no short name
added remaining ParameterConversions to fill out this command
added cl types