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__eggnogmapper2_exec_command = config.get('eggnogmapper2', {}).get('exec_command', 'emapper.py')
__eggnogmapper2_annotate_options = config.get('eggnogmapper2', {}).get('annotate', {}).get('options', '')
__eggnogmapper2_annotate_threads = config.get('eggnogmapper2', {}).get('annotate', {}).get('threads', 4)

rule eggnogmapper2_annotate:
    """
    Run annotate mode of eggnogmapper v2
    """
    input:
        __eggnogmapper2_annotate_input
    output:
        __eggnogmapper2_annotate_output
    params:
        exec_command = __eggnogmapper2_exec_command + ' --annotate_hits_table',
        output_prefix = __eggnogmapper2_annotate_output_prefix,
        options = __eggnogmapper2_annotate_options
    threads:
        __eggnogmapper2_annotate_threads
    shell:
        """
        {params.exec_command} {input} {params.options} --cpu {threads} -o {params.output_prefix}
        """