source: tags/old_import_filter/GDEHELP/MENUS/fastdnaml.menu

Last change on this file was 7187, checked in by westram, 13 years ago

merges [7099] [7106] [7107] from refactor

  • name+type → FormattedFile
  • simplyfied command line parsing and interactive mode
  • renamed output-format 'phylip2' to 'fastdnaml'
  • fixed broken calls to arb_convert_aln
    • raxml and puzzle expect PHYLIP format
    • arb_dnarates and arb_fastdnaml expect FASTDNAML format
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 949 bytes
Line 
1item:AxML + FastdnaML
2seqtype: N
3itemmeta: A
4itemmethod:(GOTO_LOCAL_DIR ; \
5            arb_export_rates "$RATES" "T 2.0" "Y 1" "$QUICKADD" | \
6                arb_convert_aln -GenBank in1 -fastdnaml infile; \
7            RUN_IN_WINDOW((cp infile last.infile; \
8                           time arb_fastdnaml $PROGRAM;$DISPLAY_FUNC)); \
9            RM_LOCAL_FILES(in1 last.infile) )&
10
11itemhelp:dnaml.help
12
13arg:RATES
14argtype:weights
15arglabel:Select a Weighting Mask
16argchoice:POS_VAR_BY_PAR
17
18arg:PROGRAM
19argtype:choice_menu
20arglabel:Select program to use
21argchoice:AxML:axml
22argchoice:FastdnaML:fastdnaml
23
24arg:QUICKADD
25argtype:choice_menu
26arglabel:Use Quickadd
27argchoice:Yes:
28argchoice:No:Q
29
30arg:DISPLAY_FUNC
31argtype:choice_menu
32arglabel:What to do with the tree?
33argchoice:ARB ('tree_fml_//'):arb_read_tree tree_fml_$$ treefile "PRG=$PROGRAM FILTER=$FILTER RATE=$RATES"3
34argchoice:Treetool:treetool treefile
35
36in:in1
37informat:genbank
38inmask:
39insave:
40
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