| 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 $VERBOSE $TAXFIELD $TAXCODE $METHOD $NUMREPS $CUTOFF $RANDSEED $CORES $SPECIESFIELD; 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 (empty=ignore species) |
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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:TAXCODE |
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| 44 | arglabel:Taxonomic code |
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| 45 | argtype:choice_menu |
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| 46 | argchoice:Bacteriological:bac |
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| 47 | argchoice:Botanical:bot |
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| 48 | argchoice:Zoological:zoo |
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| 49 | argchoice:Virological:vir |
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| 50 | |
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| 51 | arg:METHOD |
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| 52 | arglabel:Reference tree: inference method |
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| 53 | argtype:choice_menu |
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| 54 | argchoice:Thorough (standard RAxML):thorough |
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| 55 | argchoice:Fast (RAxML "-D" option):fast |
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| 56 | argchoice:Ultrafast (RAxML "-f e" option):ultrafast |
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| 57 | |
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| 58 | arg:NUMREPS |
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| 59 | arglabel:Reference tree: number of RAxML searches |
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| 60 | argtype:text |
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| 61 | argtext:1 |
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| 62 | |
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| 63 | arg:CUTOFF |
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| 64 | arglabel:Confidence cut-off |
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| 65 | argtype:text |
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| 66 | argtext:0.51 |
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| 67 | |
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| 68 | arg:RANDSEED |
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| 69 | arglabel:Random seed |
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| 70 | argtype:text |
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| 71 | argtext:12345 |
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| 72 | |
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| 73 | arg:CORES |
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| 74 | arglabel:Number of threads to use (0=auto) |
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| 75 | argtype:text |
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| 76 | argtext:0 |
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| 77 | |
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| 78 | arg:VERBOSE |
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| 79 | arglabel:Verbose output |
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| 80 | argtype:choice_menu |
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| 81 | argchoice:No: |
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| 82 | argchoice:Yes:--verbose |
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| 83 | |
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| 84 | |
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| 85 | //arg:DUPRANKS |
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| 86 | //arglabel:Action for non-unique rank names |
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| 87 | //argtype:choice_menu |
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| 88 | //argchoice:Ignore:ignore |
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| 89 | //#argchoice:Auto-rename:autofix |
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| 90 | //argchoice:Report and exit:abort |
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| 91 | //argchoice:Skip sequences:skip |
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| 92 | |
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| 93 | //arg:BADRANKS |
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| 94 | //arglabel:Action for redundant ranks (subclass, suborder etc.) |
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| 95 | //argtype:choice_menu |
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| 96 | //argchoice:Ignore:ignore |
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| 97 | //#argchoice:"Best guess" fix:autofix |
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| 98 | //argchoice:Report and exit:abort |
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| 99 | //argchoice:Skip sequences:skip |
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