diff mothur/tools/mothur/trim.flows.xml @ 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

--- a/mothur/tools/mothur/trim.flows.xml	Tue Jul 30 09:26:31 2013 -0500
+++ b/mothur/tools/mothur/trim.flows.xml	Wed Sep 04 10:51:34 2013 -0500
@@ -44,7 +44,7 @@
    #if $oligo.sdiffs.__str__ != '' and int($oligo.sdiffs.__str__) > 0:
     --sdiffs=$oligo.sdiffs
    #end if
-   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
+   --datasetid='$trim_flow.id' --new_file_path='$__new_file_path__'
    --new_datasets='^\S+?\.(\S+\.flow)$:sff.flow'
   #end if
   $fasta