__graphlan_annotate_exec_command = config['graphlan_annotate'].get('exec_command', 'graphlan_annotate.py')
__graphlan_annotate_options = config['graphlan_annotate'].get('options', "")

rule graphlan_annotate:
    input:
        tree = __graphlan_annotate_input_tree,
        annot = __graphlan_annotate_input_annotation
    output:
        __graphlan_annotate_output
    params:
        exec_command = __graphlan_annotate_exec_command,
        options = __graphlan_annotate_options
    shell:
        "{params.exec_command} {params.options} --annot {input.annot} {input.tree} {output}"