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