#
# dreme.test
#
use File::Which;
my %paths;

# xml parts to ignore in DREME output
my $dreme_xml_ignore = [
    '^dreme@(release|version)$', '^dreme:model:command_line#value$', 
    '^dreme:model:(positives|negatives)@(file|last_mod_date)$',
    '^dreme:model:host#value$', '^dreme:model:when#value$',
    '^dreme:run_time@.*$'
  ];  

&test('dreme1', 'testing both strands',
  'dreme', '',
  [
    '-oc', 'results/dreme1', 
    '-verbosity', 1, 
    '-p', 
    'common/Klf1-200-100.fa', 
    '-n', 
    'common/Klf1-200-100-shuffled.py2.fa'
  ],
  [
    {
      output => 'results/dreme1/dreme.xml', 
      reference => make_test_src_path('dreme/basic.xml'), 
      type => 'xml', ignore => $dreme_xml_ignore
    }
  ], 
  'results/dreme1', 'scripts'
);

# test DREME with a single strand
&test('dreme2', 'testing single strand',
  'dreme', '',
  [
    '-norc', 
    '-oc', 'results/dreme2', 
    '-verbosity', 1, 
    '-p', 
    'common/Klf1-200-100.fa',
    '-n', 
    'common/Klf1-200-100-shuffled.py2.fa'
  ],
  [
    {
      output => 'results/dreme2/dreme.xml', 
      reference => make_test_src_path('dreme/norc.xml'), 
      type => 'xml', ignore => $dreme_xml_ignore
    }
  ],
  'results/dreme2', 'scripts'
);