source: tags/arb_5.2/GDEHELP/MENUS/phylip_pars.menu

Last change on this file was 5077, checked in by westram, 16 years ago
  • typo
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 2.9 KB
Line 
1item:Phylip DNAPARS
2seqtype: N
3itemmeta: D
4itemmethod:(GEN_INFILE(in1);\
5            RUN_IN_WINDOW((arb_dnapars $BOOTSTRP $SEARCH $VIEWOUT $RANDOM $TRANSVERSION_PARS $THRESHOLD_PARS $INTERACTIVE;$DISPLAY_FUNC));\
6            RM_LOCAL_FILES(in1) )&
7itemhelp:dnapars.help
8
9arg:DISPLAY_FUNC
10argtype:choice_menu
11arglabel:What to do with the tree?
12argchoice:ARB ('tree_ph_'):arb_read_tree `/bin/cat arb_read_tree_args` tree_ph_$$ outtree "PRG=dnapars FILTER=$FILTER PKG=phylip BOOT=$BOOTSTRP"
13argchoice:TextEdit:arb_textedit outfile &
14argchoice:Treetool:treetool outtree
15
16arg:SEARCH
17argtype:choice_menu
18arglabel:Search depth
19argchoice:More thorough search:0
20argchoice:Less thorough search:1
21argchoice:Rearrange on one best tree:2
22
23arg:RANDOM
24argtype:choice_menu
25arglabel:Randomize sequence order
26argchoice:Yes:1
27argchoice:No:0
28
29arg:TRANSVERSION_PARS
30argtype:choice_menu
31arglabel:Use transversion parsimony?
32argchoice:No:0
33argchoice:Yes:1
34
35arg:THRESHOLD_PARS
36argtype:text
37arglabel:Use threshold parsimony (0=no)
38argtext:0
39
40arg:BOOTSTRP
41argtype:choice_menu
42arglabel:How many bootstraps ?
43argchoice:Do not bootstrap:0
44argchoice:10:10
45argchoice:100:100
46argchoice:500:500
47argchoice:1000:1000
48argchoice:5000:5000
49argchoice:10000:10000
50
51arg:VIEWOUT
52argtype:choice_menu
53arglabel:View report
54argchoice:No:0
55argchoice:Yes:1
56
57arg:INTERACTIVE
58argtype:choice_menu
59arglabel:Interactive? (no for bootstrap)
60argchoice:No:0
61argchoice:Yes:1
62
63in:in1
64informat:genbank
65inmask:
66insave:
67
68// --------------------------------------------------------------------------------
69
70item:Phylip PROTPARS
71seqtype: A
72itemmeta: P
73itemmethod:(GEN_INFILE(in1);\
74            RUN_IN_WINDOW((arb_protpars $BOOTSTRP $GENETIC_CODE $VIEWOUT $RANDOM $THRESHOLD_PARS $INTERACTIVE;$DISPLAY_FUNC));\
75            RM_LOCAL_FILES(in1) )&
76itemhelp:protpars.help
77
78arg:DISPLAY_FUNC
79argtype:choice_menu
80arglabel:What to do with the tree?
81argchoice:ARB ('tree_ph_'):arb_read_tree `/bin/cat arb_read_tree_args` tree_ph_$$ outtree "PRG=protpars FILTER=$FILTER PKG=phylip BOOT=$BOOTSTRP CODE=$GENETIC_CODE"
82argchoice:TextEdit:arb_textedit outfile &
83argchoice:Treetool:treetool outtree
84
85arg:GENETIC_CODE
86argtype:choice_menu
87arglabel:Genetic code
88argchoice:Universal:U
89argchoice:Mitochondrial:M
90argchoice:Vertebrate mitochondrial:V
91argchoice:Fly mitochondrial:F
92argchoice:Yeast mitochondrial:Y
93
94arg:RANDOM
95argtype:choice_menu
96arglabel:Randomize sequence order
97argchoice:Yes:1
98argchoice:No:0
99
100arg:THRESHOLD_PARS
101argtype:text
102arglabel:Use threshold parsimony (0=no)
103argtext:0
104
105arg:BOOTSTRP
106argtype:choice_menu
107arglabel:How many bootstraps ?
108argchoice:Do not bootstrap:0
109argchoice:10:10
110argchoice:100:100
111argchoice:500:500
112argchoice:1000:1000
113argchoice:5000:5000
114argchoice:10000:10000
115
116arg:VIEWOUT
117argtype:choice_menu
118arglabel:View report
119argchoice:No:0
120argchoice:Yes:1
121
122arg:INTERACTIVE
123argtype:choice_menu
124arglabel:Interactive? (no for bootstrap)
125argchoice:No:0
126argchoice:Yes:1
127
128in:in1
129informat:genbank
130inmask:
131insave:
132
133
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