Added 'do_not_use_abundance_weigths' option in per_library_stats.py script

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2809 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
cleaned up help text to refer to biom formatted otu tables and updated to use pycogent option types

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2810 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated so output files end with .biom.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2811 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated to use pycogent option types.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2812 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated conversion scripts to use biom formatted otu tables, and pycogent option types.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2813 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated usage examples and changed to pycogent option types.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2814 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
added to documentation.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2815 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
added to documentation.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2816 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated documentation to reflect change to biom format.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2817 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated documentation to reflect change to biom format.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2818 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated to use pycogent option types.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2819 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated docs to refer to biom formatted otu tables.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2820 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Modified option name for otu_counts

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2821 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Modified parameter name to be consisten with per_librar_stats.py

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2822 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
cleaned up the interface (now requires -o rather than randomly generating an output directory name) and modified help text to reflect use of biom format. also takes pycogent option types now.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2823 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated to clean up interface and refer to biom format otu table.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2824 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Modified output to reflect sequences or OTUs depending on --otu_counts

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2825 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2826 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated to refer to biom-formatted tables.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2827 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated to refer to biom-formatted otu tables and use pycogent option types

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2828 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a