From 9b2d675e85942aa2824ee825bd6f74ccb07a6975 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 24 Jan 2013 21:14:11 +0000 Subject: [PATCH] inprogress --- forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb index 3620fc5..1128be6 100644 --- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb +++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb @@ -23,7 +23,8 @@ module Evoruby class PhylogeniesDecorator #DECORATOR_OPTIONS_SEQ_NAMES = '-r=1 -mdn' - DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -sn' + #DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -sn' + DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -c -tc' # -mdn is a hidden expert option to rename e.g. "6_ORYLA3" to "6_[3]_ORYLA" #DECORATOR_OPTIONS_SEQ_NAMES = '-sn -r=1' #DECORATOR_OPTIONS_DOMAINS = '-r=1' @@ -233,7 +234,7 @@ module Evoruby my_infile = phylogeny_file end cmd = decorator + ' ' + DECORATOR_OPTIONS_SEQ_NAMES + ' ' + - '-f=s ' + my_infile + ' ' + + '-f=n ' + my_infile + ' ' + ids_mapfile_name + ' ' + outfile execute_cmd( cmd, log ) end -- 1.7.10.2