#
# ama test
#
my $ama_ignore = [
 'cis-element-search:parameters:command-line#value',
 'cis-element-search:parameters:pattern-file',
 'cis-element-search:parameters:sequence-file',
 'cis-element-search:parameters:background-seq-file',
];

&test(
  'ama1', 'max-odds, no p-values',
  'ama', '',
  ['--verbosity', 1, '--scoring', 'max-odds', make_test_src_path('gomo/motif.meme.txt'),
    make_test_src_path('gomo/seqs.fasta'), make_test_src_path('gomo/seqs.bg')],
  [
    {output => '-', reference => make_test_src_path('gomo/ama.withMaxodds.xml'), type => 'xml', ignore => $ama_ignore
    }
  ],
  'results/ama1'
);
&test(
  'ama2', 'avg-odds, combine sequences, calculate p-values',
  'ama', '',
  ['--pvalues', '--verbosity', 1, '--cs', make_test_src_path('gomo/motif.meme.txt'), 
    make_test_src_path('gomo/seqs_red.fasta'), make_test_src_path('gomo/seqs.norc.bg')],
  [ 
    {
      output => '-', reference => make_test_src_path('gomo/ama.redundant.xml'), type => 'xml', ignore => $ama_ignore
    }
  ],
  'results/ama2'
);
