Last change
on this file was
19501,
checked in by westram, 3 weeks 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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