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revision 1.5, Mon Jan 18 23:32:09 2010 UTC revision 1.6, Mon Sep 20 21:38:53 2010 UTC
# Line 9  Line 9 
9  use Data::Dumper;  use Data::Dumper;
10  use Getopt::Long;  use Getopt::Long;
11    
12  my $usage = "Usage: $0 [--url server-url] [--nonActive] [--verbose] [--test] username password < contig-id-list\n";  my $usage = "Usage: $0 [--determineFamily] [--url server-url] [--nonActive] [--verbose] [--test] username password < contig-id-list\n";
13    
14  my $verbose;  my $verbose;
15  my $use_test_server = 0;  my $use_test_server = 0;
16  my $non_active = 0;  my $non_active = 0;
17  my $url;  my $url;
18    my $determine_family = 0;
19  if (!GetOptions('verbose'   => \$verbose,  if (!GetOptions('verbose'   => \$verbose,
20                  "nonActive" => \$non_active,                  "nonActive" => \$non_active,
21                  "url=s" => \$url,                  "url=s" => \$url,
22                    "determineFamily" => \$determine_family,
23                  'test'      => \$use_test_server))                  'test'      => \$use_test_server))
24  {  {
25      die $usage;      die $usage;
# Line 136  Line 138 
138          -keepGeneCalls => 0,          -keepGeneCalls => 0,
139          -geneCaller => 'RAST',          -geneCaller => 'RAST',
140          -nonActive => $non_active,          -nonActive => $non_active,
141            -determineFamily => $determine_family,
142      };      };
143    
144      print "Submitting job to RAST for contigs @$ids with these parameters:\n";      print "Submitting job to RAST for contigs @$ids with these parameters:\n";

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