|
Last change
on this file was
19501,
checked in by westram, 10 months ago
|
- implements #865:
- allows to match species and
 rows, using list entries (in cells and/or fields).
|
-
Property svn:eol-style set to
native
-
Property svn:keywords set to
Author Date Id Revision
|
|
File size:
1.9 KB
|
| Line | |
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| 1 | item:Import sequences using Readseq (slow) ... |
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| 2 | itemmeta: R |
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| 3 | itemmethod:arb_readseq $INPUTFILE -a -f2 > TmpOutputFile |
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| 4 | itemhelp:readseq.help |
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| 5 | |
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| 6 | arg:INPUTFILE |
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| 7 | argtype:filename |
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| 8 | arglabel:Name of file to import |
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| 9 | |
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| 10 | out:TmpOutputFile |
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| 11 | outformat:genbank |
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| 12 | |
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| 13 | |
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| 14 | |
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| 15 | item:Import fields from calc-sheet |
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| 16 | itemmeta: c |
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| 17 | itemmethod:( \ |
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| 18 | import_from_table.pl "$FROMFILE" \ |
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| 19 | --match "$MATCHCOL,$MATCHFIELD" \ |
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| 20 | --write "$WRITECOL,$WRITEFIELD" \ |
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| 21 | --mode "$MATCHMODE" \ |
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| 22 | $SEPARATOR \ |
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| 23 | $OVERWRITE \ |
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| 24 | $SKIPUNKNOWN \ |
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| 25 | $SKIPEMPTY \ |
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| 26 | $MARKEDONLY \ |
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| 27 | $MARK \ |
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| 28 | $ASINT \ |
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| 29 | )& |
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| 30 | itemhelp:import_calc.help |
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| 31 | |
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| 32 | arg:FROMFILE |
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| 33 | argtype:filename |
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| 34 | arglabel:Import from CSV |
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| 35 | argtext:csv |
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| 36 | |
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| 37 | arg:WRITECOL |
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| 38 | arglabel:Write content of column |
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| 39 | argtype:slider |
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| 40 | argmin:1 |
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| 41 | argmax:9999 |
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| 42 | |
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| 43 | arg:WRITEFIELD |
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| 44 | arglabel:to field |
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| 45 | argtype:text |
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| 46 | |
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| 47 | arg:MATCHFIELD |
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| 48 | arglabel:of species for which field |
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| 49 | argtype:text |
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| 50 | |
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| 51 | arg:MATCHCOL |
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| 52 | arglabel:matches content of column |
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| 53 | argtype:slider |
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| 54 | argmin:1 |
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| 55 | argmax:9999 |
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| 56 | |
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| 57 | arg:MATCHMODE |
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| 58 | arglabel:using match mode |
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| 59 | argtype:text |
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| 60 | argtext:= |
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| 61 | |
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| 62 | arg:SEPARATOR |
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| 63 | argtype:choice_menu |
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| 64 | arglabel:Columns are separated by |
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| 65 | argchoice:tabs: |
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| 66 | argchoice:commas:--csv |
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| 67 | |
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| 68 | arg:OVERWRITE |
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| 69 | argtype:chooser |
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| 70 | arglabel:Overwrite existing fields |
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| 71 | argchoice:no: |
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| 72 | argchoice:yes:--overwrite |
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| 73 | |
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| 74 | arg:SKIPUNKNOWN |
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| 75 | argtype:choice_menu |
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| 76 | arglabel:Unmatched entries will |
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| 77 | argchoice:abort importing: |
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| 78 | argchoice:be skipped:--skip-unknown |
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| 79 | |
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| 80 | arg:SKIPEMPTY |
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| 81 | argtype:choice_menu |
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| 82 | arglabel:Empty entries will |
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| 83 | argchoice:be handled normally: |
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| 84 | argchoice:be skipped:--skip-empty |
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| 85 | |
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| 86 | arg:MARKEDONLY |
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| 87 | argtype:choice_menu |
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| 88 | arglabel:Import to |
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| 89 | argchoice:all species: |
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| 90 | argchoice:marked species:--marked-only |
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| 91 | |
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| 92 | arg:MARK |
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| 93 | argtype:choice_menu |
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| 94 | arglabel:Mark |
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| 95 | argchoice:dont change: |
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| 96 | argchoice:species when writing field (unmark rest):--mark |
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| 97 | |
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| 98 | arg:ASINT |
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| 99 | arglabel:Field type |
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| 100 | argtype:choice_menu |
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| 101 | argchoice:Text: |
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| 102 | argchoice:Numeric:--as-integer |
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| 103 | |
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| 104 | |
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| 105 | |
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