source: branches/lib/GDEHELP/MENUS/phyml.menu

Last change on this file was 16469, checked in by westram, 8 years ago
  • reintegrates 'textedit' into 'trunk'
    • fixes #586
      • editor now always started asynchronously
      • uses inotify to track file changes
    • also use inotify to track directory updates (in order to update file selections when needed)
      (./) by [16515] ff.; merged by [16551]
  • adds: log:branches/textedit@16448:16468
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 2.4 KB
Line 
1item:PHYML (DNA)
2seqtype: N
3itemmeta: M
4itemmethod:( GOTO_LOCAL_DIR;GEN_PHYLIP(infile) && \
5             RUN_IN_WINDOW((arb_phyml infile DNA $MODEL $OPTFREQ $BASEFREQEST $TSTVRATIO $PINVAR $INTERACTIVE && \
6                            $DISPLAY_FUNC )); \
7           )&
8itemhelp:phyml.help
9
10arg:DISPLAY_FUNC
11argtype:choice_menu
12arglabel:What to do with the tree?
13argchoice:ARB ('tree_phyml_'):arb_read_tree `/bin/cat arb_read_tree_args` tree_phyml_$$ outtree "PRG=phyml-2.4.5 FILTER=$FILTER STYPE=DNA"
14argchoice:TextEdit:arb_textedit outfile
15argchoice:Treetool:treetool outtree
16
17arg:MODEL
18argtype:choice_menu
19arglabel:Nuc. substitution model
20argchoice:HKY:0
21argchoice:F84:1
22argchoice:TN93:2
23argchoice:GTR:3
24argchoice:custom:4
25argchoice:JC69:5
26argchoice:KP2:6
27argchoice:F81:7
28
29arg:OPTFREQ
30argtype:choice_menu
31arglabel:Optimize equilibrium freq.? [custom]
32argchoice:No:0
33argchoice:Yes:1
34
35arg:BASEFREQEST
36argtype:choice_menu
37arglabel:Base frequency estimates
38argchoice:empirical:0
39argchoice:ML:1
40
41arg:TSTVRATIO
42argtype:choice_menu
43arglabel:Ts/tv ratio
44argchoice:fixed (4.00):0
45argchoice:estimated:1
46
47arg:PINVAR
48argtype:choice_menu
49arglabel:Proportion of invariable sites
50argchoice:fixed (0.00):0
51argchoice:estimated:1
52
53arg:INTERACTIVE
54argtype:choice_menu
55arglabel:Interactive?
56argchoice:No:0
57argchoice:Yes:1
58
59in:TmpInputFile
60informat:genbank
61insave:
62
63// --------------------------------------------------------------------------------
64
65item:PHYML (Amino acids)
66seqtype: A
67itemmeta: L
68itemmethod:( GOTO_LOCAL_DIR;GEN_PHYLIP(infile) && \
69             RUN_IN_WINDOW((arb_phyml infile AA $MODEL $PINVAR $INTERACTIVE && \
70                            $DISPLAY_FUNC )); \
71           )&
72itemhelp:phyml.help
73
74arg:DISPLAY_FUNC
75argtype:choice_menu
76arglabel:What to do with the tree?
77argchoice:ARB ('tree_phyml_'):arb_read_tree `/bin/cat arb_read_tree_args` tree_phyml_$$ outtree "PRG=phyml-2.4.5 FILTER=$FILTER STYPE=AA"
78argchoice:TextEdit:arb_textedit outfile
79argchoice:Treetool:treetool outtree
80
81arg:MODEL
82argtype:choice_menu
83arglabel:AA substitution model
84argchoice:JTT:0
85argchoice:MtRev:1
86argchoice:WAG:2
87argchoice:DCMut:3
88argchoice:RtREV:4
89argchoice:CpREV:5
90argchoice:VT:6
91argchoice:Blosum62:7
92argchoice:MtMam:8
93argchoice:Dayhoff:9
94
95arg:PINVAR
96argtype:choice_menu
97arglabel:Proportion of invariable sites
98argchoice:fixed (0.00):0
99argchoice:estimated:1
100
101arg:INTERACTIVE
102argtype:choice_menu
103arglabel:Interactive?
104argchoice:No:0
105argchoice:Yes:1
106
107in:TmpInputFile
108informat:genbank
109insave:
110
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