Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tool-data/mothur_taxonomy.loc.sample @ 32:ec8df51e841a
Fixes courtesy of Peter Briggs:
metagenomics.py:
- Groups class: Fix for when second column not present
- Axes class: make 'sniff' method more sensitive to try and restrict arbitrary tabular
data uploads being sniffed as this type
mothur_wrapper.py:
- update cmd_dict['chimera.perseus'], to use correct inputs
- add --beta option (needed for chimera.perseus tool)
- add function for converting input floats from scientific notation (e.g. 1e-6,
which mothur can't handle) to decimal format (e.g. 0.00001, which it can)
chimera.perseus.xml:
- add output data item for the "accnos" file (not previous captured in the
history)
trim.flows.xml:
- cosmetic change: base name for additional output data items is now "trim.flows",
rather than "logfile" (clarifies history items)
shhh.flows.xml:
- cosmetic change: update default value specified in help for mindiff to be
consistent with that given in the mothur documentation
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 04 Sep 2013 10:51:34 -0500 (2013-09-04) |
| parents | 09740be2bc9c |
| children |
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#This is a sample file distributed with Galaxy that enables tools #to use a directory of metagenomics files. #file has this format (white space characters are TAB characters): # # Silva reference files: http://www.mothur.org/wiki/Silva_reference_files # #<taxonomyname> <file_base> # #archaea.gg /project/db/galaxy/mothur/Silva.archaea/silva.archaea.gg.tax #archaea.silva /project/db/galaxy/mothur/Silva.archaea/silva.archaea.silva.tax #archaea.rdp /project/db/galaxy/mothur/Silva.archaea/silva.archaea.rdp.tax #archaea.ncbi /project/db/galaxy/mothur/Silva.archaea/silva.archaea.ncbi.tax #bacteria.gg /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.gg.tax #bacteria.silva /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.silva.tax #bacteria.ncbi /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.ncbi.tax #bacteria.rdp /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp.tax #bacteria.rdp6 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp6.tax #eukarya.silva /project/db/galaxy/mothur/silva.eukarya.silva.tax #eukarya.ncbi /project/db/galaxy/mothur/silva.eukarya.ncbi.tax #trainset6_032010.rdp.tax /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.tax #trainset7_112011.pds.tax /project/db/galaxy/mothur/RDP/trainset7_112011.pds.tax #trainset7_112011.rdp.tax /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.tax #FungiLSU_train_1400bp_8506_mod.tax /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.tax #