<macros>
    <xml name="tests">
        <tests>
            <test expect_num_outputs="1">
                <param name="protein_alignment" value="inputs/test.aln" ftype="clustal" />
                <param name="nucleotide_fastas" value="inputs/test.nuc" ftype="fasta" />
                <param name="output_format" value="paml" />
                <output name="output_file" file="outputs/expected_paml.paml" ftype="phylip" />
            </test>
            <test expect_num_outputs="1">
                <param name="protein_alignment" value="inputs/test.aln" ftype="clustal" />
                <param name="nucleotide_fastas" value="inputs/test.nuc" ftype="fasta" />
                <param name="output_format" value="clustal" />
                <output name="output_file" file="outputs/expected_clustal.aln" ftype="clustal" />
            </test>
            <test expect_num_outputs="1">
                <param name="protein_alignment" value="inputs/test.aln" ftype="clustal" />
                <param name="nucleotide_fastas" value="inputs/test.nuc" ftype="fasta" />
                <param name="output_format" value="fasta" />
                <param name="remove_gaps" value="true" />
                <output name="output_file" file="outputs/expected_nogap.fasta" ftype="fasta" />
            </test>
            <test expect_num_outputs="1">
                <param name="protein_alignment" value="inputs/test.aln" ftype="clustal" />
                <param name="nucleotide_fastas" value="inputs/test.nuc" ftype="fasta" />
                <param name="output_format" value="codon" />
                <output name="output_file" file="outputs/expected_codon.txt" ftype="txt" />
            </test>
            <test expect_num_outputs="1">
                <param name="protein_alignment" value="inputs/test.aln" ftype="clustal" />
                <param name="nucleotide_fastas" value="inputs/test_bc070280.fasta,inputs/test_pseudogene.fasta" ftype="fasta" />
                <param name="output_format" value="clustal" />
                <output name="output_file" file="outputs/expected_clustal_multi.aln" ftype="clustal" />
            </test>
            <test expect_num_outputs="2">
                <param name="protein_alignment" value="inputs/test.aln" ftype="clustal" />
                <param name="nucleotide_fastas" value="inputs/test.nuc" ftype="fasta" />
                <param name="output_format" value="clustal" />
                <param name="show_only_blocks" value="true" />
                <param name="remove_mismatches" value="true" />
                <param name="genetic_code" value="2" />
                <param name="html_output" value="true" />
                <param name="suppress_stderr" value="true" />
                <output name="output_file" file="outputs/expected_block_nomismatch.aln" ftype="clustal" />
                <output name="html_output_file" file="outputs/expected_html.html" ftype="html" />
            </test>
        </tests>
    </xml>
</macros>