source: tags/svn.1.5.4/GDEHELP/MENUS/dnamlrates.menu

Last change on this file was 7189, checked in by westram, 14 years ago

merges [7108] [7146] [7147] [7148] [7150] [7151] [7152] [7153] [7155] [7156] [7161] [7162] [7163] from refactor

  • arb_dnarates
    • may read from file (instead of STDIN)
    • if dbname is given on command line, expect dbsavename as following argument and save db with that name.
    • removed old debug code
    • adds a SAI counter to DB
    • no longer uses PID for SAI name, instead uses counter
    • no longer overwrites existing SAIs
  • arb_swap_rnastr (unused, uncommented → unlinked)
  • arb_read_tree
    • command line options may appear anywhere / in any order
    • new option -db to specify db (load/save).
  • arb_export_rates
    • new option -d to specify db.
    • handle more errors
  • arb_export_tree
    • optional CLI-argument 'DBNAME' (to specify a DB for unittests)
  • arb_gene_probe
    • error handling fixes
    • do not write debugging-data to gene-ptserver-db (+fixed expected result-db)
  • arb_primer
    • optional CLI-argument 'dbname'
    • replaced scattered exit()-calls by proper error-handling
  • arb_probe
    • forward errors to top level, to enable error check in unit-test
    • allow usage of TEST_SERVER_ID if compiled with UNIT_TESTS==1
  • added unit tests for mosts tools in TOOLS. Tests do not try to test complete functionality - they only check that one or a few calls to the tools do not fail.
  • fixed sourcefile list
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 1.0 KB
Line 
1item:Positional Variability by Olsons dnamlrates (max 5000 Species, 8000 seqlength)
2seqtype: N
3itemmeta: O
4itemmethod:(GOTO_LOCAL_DIR ; \
5            arb_export_rates "" "M $RESIDUES" "T $TTRATIO" "U" $LENGTHS "F" | \
6                arb_convert_aln -GenBank in1 -fastdnaml in1.ph; \
7            ( echo 1; arb_export_tree $TREE ) >>in1.ph; \
8            RUN_IN_WINDOW(arb_dnarates in1.ph); \
9            RM_LOCAL_FILES(in1) )&
10
11itemhelp:DNAml_rates.help
12
13arg:TREE
14argtype:tree
15arglabel:Base Tree
16argchoice:tree_main
17
18arg:RESIDUES
19argtype:text
20arglabel:Number of informative residues
21argtext:10
22
23arg:TTRATIO
24argtype:text
25arglabel:Transition/transversion ratio
26argtext:2.0
27
28arg:LENGTHS
29argtype:choice_menu
30arglabel:Use branchlengths?
31argchoice:Yes:"L"
32argchoice:No:
33
34// arg:USERRATES
35// argtype:text(20)
36// arglabel:User frequency rates
37// argtext:F
38
39// arg:USERRATES
40// argtype:choice_menu
41// arglabel:Choose frequency rates
42// argchoice:Calculate frequencies:F
43// argchoice:Estimate equal frequencies:F 0.25 0.25 0.25 0.25
44
45in:in1
46informat:genbank
47inmask:
48insave:
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