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stderr_should_have($script_name,'-a', 'Looking for');

my $current_cwd = getcwd();
stderr_should_have($script_name,'-v --output_directory t/data/directory_which_doesnt_exist  t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff', 'Output directory created');
ok( ( -e 't/data/directory_which_doesnt_exist/clustered_proteins' ), 'pan genome files should be in directory' );
is(getcwd(),$current_cwd , 'current working directory should not have changed after script is finished'); 

SKIP:
{
    skip "prank not installed", 11 unless ( which('prank') );

    %scripts_and_expected_files =
      ( '-j Local --dont_delete_files --dont_split_groups  --output_multifasta_files t/data/real_data_1.gff t/data/real_data_2.gff' =>
          [ 'pan_genome_sequences/mdoH.fa.aln', 't/data/mdoH.fa.aln' ], );
    mock_execute_script_and_check_output( $script_name, \%scripts_and_expected_files );

    ok( -e 'core_gene_alignment.aln', 'Core gene alignment exists' );

    ok(
        my $seq_len = Bio::Roary::SequenceLengths->new(
            fasta_file => 'core_gene_alignment.aln',
        ),
        'Check size of the core_gene_alignment.aln init'
    );

    my @keys = keys %{ $seq_len->sequence_lengths };
    is( $seq_len->sequence_lengths->{ $keys[0] }, 64983, 'length of first sequence' );
		
		ok( -e 'core_alignment_header.embl', 'Core gene alignment header exists' );

    ok( -e 'accessory.tab' );
    ok( -e 'core_accessory.tab' );
    ok( -e 'number_of_conserved_genes.Rtab' );
    ok( -e 'number_of_genes_in_pan_genome.Rtab' );
    ok( -e 'number_of_new_genes.Rtab' );
    ok( -e 'number_of_unique_genes.Rtab' );
    ok( -e 'blast_identity_frequency.Rtab' );

    cleanup_files();
    %scripts_and_expected_files =
      (
'-j Local --output_multifasta_files t/data/core_alignment_gene_lookup/query_1.gff t/data/core_alignment_gene_lookup/query_2.gff t/data/core_alignment_gene_lookup/query_3.gff'
          => [ 'core_gene_alignment.aln', 't/data/core_alignment_gene_lookup/expected_core_gene_alignment.aln' ], );
    mock_execute_script_and_check_output( $script_name, \%scripts_and_expected_files );

    cleanup_files();
}

SKIP:
{
	skip "extended tests not run",  40 unless ( defined($ENV{ROARY_FULL_TESTS}));

    %scripts_and_expected_files = (
        '-o some_different_output -i 90 -p 2 --translation_table 1 t/data/real_data_1.gff t/data/real_data_2.gff' => [ 'some_different_output', 't/data/expected_some_different_output' ],
    	);
    mock_execute_script_and_check_output_sorted( $script_name, \%scripts_and_expected_files, [ 0 ] );
    
    stderr_should_have($script_name,'--translation_table 1  -o some_different_output --core_definition 60 -p 2 -e --mafft  --group_limit 10 t/data/real_data_1.gff t/data/real_data_2.gff', 'Exiting early because number of clusters is too high');
    stderr_should_have($script_name,'--verbose_stats --group_limit 10 -e t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff', 'Exiting early because number of clusters is too high');
    stderr_should_not_have($script_name,'-e --group_limit 10 t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff ', 'Cant access the multifasta base directory');
    stderr_should_have($script_name,'-i 90 --core_definition 60 -p 2 -v t/data/real_data_1.gff t/data/real_data_2.gff ','Cleaning up files'); 
    stderr_should_have($script_name,'-i 30 t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff','The percentage identity is too low');
    stderr_should_not_have($script_name,'--dont_delete_files -v t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff ','Cleaning up files');
    stderr_should_have($script_name,'-v --group_limit 100000 -e t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff ' ,'Running command: pan_genome_core_alignment');
    stderr_should_have($script_name,'--translation_table 1 -v t/data/real_data_1.gff t/data/real_data_2.gff ' ,'Cleaning up files');
    stderr_should_have($script_name,'-e -v t/data/real_data_1.gff t/data/real_data_2.gff ','Creating files with the nucleotide sequences for every cluster');
    
    SKIP:
    {
        skip "kraken not installed",        2 unless ( which('kraken') );
        skip "kraken-report not installed", 2 unless ( which('kraken-report') );
        stderr_should_have($script_name,'-v --qc t/data/real_data_1.gff t/data/real_data_2.gff' ,'Running Kraken on each input assembly');
    }
    
    %scripts_and_expected_files = (
        # output
        '-o some_different_output -e --dont_delete_files t/data/real_data_1.gff t/data/real_data_2.gff' =>
          [ 'pan_genome_sequences/mdoH.fa.aln', 't/data/mdoH.fa.aln' ],
        '-o some_different_output --core_definition 60 t/data/real_data_1.gff t/data/real_data_2.gff' =>
          [ 'summary_statistics.txt', 't/data/expected_core_60_summary_statistics.txt' ],
        '-e -i 95.3 --translation_table 1 -v --group_limit 100000 --qc t/data/real_data_1.gff t/data/real_data_2.gff'   => [ 'core_gene_alignment.aln', 't/data/expected_real_data_core_gene_alignment.aln' ],
	
        '-e --verbose_stats t/data/real_data_1.gff t/data/real_data_2.gff'            => [ 'core_gene_alignment.aln', 't/data/expected_real_data_core_gene_alignment.aln' ],
        '--core_definition 60 t/data/real_data_1.gff t/data/real_data_2.gff'          => [ 'summary_statistics.txt', 't/data/expected_core_60_summary_statistics.txt' ],
        '-p 2 -e --dont_delete_files t/data/real_data_1.gff t/data/real_data_2.gff'   => [ 'pan_genome_sequences/mdoH.fa.aln', 't/data/mdoH.fa.aln' ],
        '-p 2 --core_definition 60 t/data/real_data_1.gff t/data/real_data_2.gff'     => [ 'summary_statistics.txt', 't/data/expected_core_60_summary_statistics.txt' ],
        '-p 2 -e --mafft t/data/real_data_1.gff t/data/real_data_2.gff'               => [ 'core_gene_alignment.aln', 't/data/expected_mafft_real_data_core_gene_alignment.aln' ],

    );
    mock_execute_script_and_check_output_sorted( $script_name, \%scripts_and_expected_files );

}

cleanup_files();

done_testing();

sub cleanup_files {
    remove_tree('pan_genome_sequences');
    remove_tree('fixed_input_files');
    remove_tree('t/data/directory_which_doesnt_exist');
    remove_tree('locus_tags_gffs_output');
    unlink('_blast_results');
    unlink('_clustered');
    unlink('_clustered.bak.clstr');
    unlink('_clustered.clstr');
    unlink('_combined_files');
    unlink('_combined_files.groups');
    unlink('_fasta_files');
    unlink('_gff_files');
    unlink('_inflated_mcl_groups');
    unlink('_inflated_unsplit_mcl_groups');
    unlink('_labeled_mcl_groups');
    unlink('_uninflated_mcl_groups');
    unlink('accessory.header.embl');
    unlink('accessory.header.tab');
    unlink('accessory.tab');
    unlink('blast_identity_frequency.Rtab');
    unlink('clustered_proteins');
    unlink('core_accessory.header.embl');
    unlink('core_accessory.header.tab');
    unlink('core_accessory.tab');
    unlink('core_gene_alignment.aln');