Fixing --input_fps option for count_seqs.py. Not finished (currently does not support filepath pattern expansions)
Update denoise_wrapper.py

Fixed filepaths-problem when using multiple flowgram-files in the commandline. 
Lines 47,99-113
Update denoise_wrapper.py

Sorry for editing so late. I am pretty much noobish in this github-game :-). I just tried this code on some samples and it worked well. Hopefully it workes for you, too. Have a nice weekend all together.
Merge branch 'master' of github.com:josenavas/qiime into count_seqs
update qiime config parser to expand env variables

Fixes #937
Merge pull request #896 from paulomat/patch-1

Update denoise_wrapper.py
Fixing count_seqs.py option types
Merge branch 'master' of github.com:josenavas/qiime into count_seqs
Fixing existing_filepaths option to handle wildcards
Fixes issue 289

Retrieve the absolute path for the db_FASTA and the db_NAST parameters.

Fixes #289
Merge pull request #940 from ElDeveloper/issue_289

Fixes issue 289
Remove deprecated options in split_otu_table.py

Two un-used options have been removed from the script interface, this is
related to #941.

Fixes #417.
Fixing Greg's comments
Merge branch 'master' of github.com:qiime/qiime into count_seqs
Merge pull request #942 from ElDeveloper/issue_417

Remove deprecated options in split_otu_table.py
Merge pull request #939 from josenavas/count_seqs

Fix input_fps option type for count_seqs.py
Merge pull request #938 from gregcaporaso/issue-937

update qiime config parser to expand env variables