menu:Print

item:[experimental] Validate taxonomy (SATIVA)
itemmethod: (mkdir -p ~/.arb_tmp/sativa_$$; cd ~/.arb_tmp/sativa_$$ ; arb_convert_aln --arb-notify -GenBank TmpInputFile -phylip sativa_in.phy; ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; arb_sativa.pl $MARKEDONLY $MARKMIS $RANKTEST $TAXFIELD $SPECIESFIELD $DUPRANKS $BADRANKS; arb_wait@@; cd ~/.arb_tmp; rm -rf sativa_$$) & 
seqtype:*
itemmeta:v
itemhelp:sativa.help

#arb_export_tree $TREE > reftree.tre

in:TmpInputFile
informat:genbank
insave:

arg:MARKEDONLY
arglabel:Process marked species only ?
argtype:choice_menu
argchoice:Yes:--marked-only
argchoice:No:

arg:MARKMIS
arglabel:Mark found misplaced species ?
argtype:choice_menu
argchoice:Yes:--mark-misplaced
argchoice:No:

arg:RANKTEST
arglabel:Test for misplaced higher ranks ?
argtype:choice_menu
argchoice:No:
argchoice:Yes:--rank-test

arg:TAXFIELD
arglabel:Taxonomy path field
argtype:text
argtext:tax_slv

arg:SPECIESFIELD
arglabel:Species name field
argtype:text
argtext:full_name

arg:DUPRANKS
arglabel:Action for non-unique rank names
argtype:choice_menu
argchoice:Ignore:ignore
#argchoice:Auto-rename:autofix
argchoice:Report and exit:abort
argchoice:Skip sequences:skip

arg:BADRANKS
arglabel:Action for redundant ranks (subclass, suborder etc.)
argtype:choice_menu
argchoice:Ignore:ignore
#argchoice:"Best guess" fix:autofix
argchoice:Report and exit:abort
argchoice:Skip sequences:skip