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| 1 | menu:Print |
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| 2 | |
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| 3 | item:[experimental] Validate taxonomy (SATIVA) |
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| 4 | 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_$$) & |
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| 5 | seqtype:* |
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| 6 | itemmeta:v |
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| 7 | itemhelp:sativa.help |
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| 8 | |
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| 9 | #arb_export_tree $TREE > reftree.tre |
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| 10 | |
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| 11 | in:TmpInputFile |
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| 12 | informat:genbank |
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| 13 | insave: |
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| 14 | |
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| 15 | arg:MARKEDONLY |
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| 16 | arglabel:Process marked species only ? |
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| 17 | argtype:choice_menu |
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| 18 | argchoice:Yes:--marked-only |
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| 19 | argchoice:No: |
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| 20 | |
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| 21 | arg:MARKMIS |
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| 22 | arglabel:Mark found misplaced species ? |
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| 23 | argtype:choice_menu |
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| 24 | argchoice:Yes:--mark-misplaced |
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| 25 | argchoice:No: |
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| 26 | |
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| 27 | arg:RANKTEST |
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| 28 | arglabel:Test for misplaced higher ranks ? |
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| 29 | argtype:choice_menu |
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| 30 | argchoice:No: |
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| 31 | argchoice:Yes:--rank-test |
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| 32 | |
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| 33 | arg:TAXFIELD |
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| 34 | arglabel:Taxonomy path field |
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| 35 | argtype:text |
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| 36 | argtext:tax_slv |
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| 37 | |
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| 38 | arg:SPECIESFIELD |
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| 39 | arglabel:Species name field |
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| 40 | argtype:text |
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| 41 | argtext:full_name |
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| 42 | |
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| 43 | arg:DUPRANKS |
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| 44 | arglabel:Action for non-unique rank names |
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| 45 | argtype:choice_menu |
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| 46 | argchoice:Ignore:ignore |
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| 47 | #argchoice:Auto-rename:autofix |
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| 48 | argchoice:Report and exit:abort |
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| 49 | argchoice:Skip sequences:skip |
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| 50 | |
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| 51 | arg:BADRANKS |
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| 52 | arglabel:Action for redundant ranks (subclass, suborder etc.) |
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| 53 | argtype:choice_menu |
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| 54 | argchoice:Ignore:ignore |
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| 55 | #argchoice:"Best guess" fix:autofix |
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| 56 | argchoice:Report and exit:abort |
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| 57 | argchoice:Skip sequences:skip |
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