<macros>
    <xml name="requirements">
        <requirement type="package" version="0.8.9">bx-python</requirement>
        <yield />
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioinformatics/btr398</citation>
        </citations>
    </xml>
    <xml name="maf_source">
        <conditional name="maf_source_type">
            <param name="maf_source" type="select" label="MAF Source">
                <option value="cached" selected="true">Locally Cached Alignments</option>
                <option value="user">Alignments in Your History</option>
            </param>
            <when value="user">
                <param format="maf" name="maf_file" label="Choose alignments" type="data">
                    <options>
                        <filter type="data_meta" ref="input1" key="dbkey" />
                    </options>
                    <validator type="dataset_ok_validator" />
                </param>
                <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
                    <options>
                        <filter type="data_meta" ref="maf_file" key="species" />
                    </options>
                </param>
            </when>
            <when value="cached">
                <param name="mafType" type="select" label="Choose alignments">
                    <options from_data_table="maf_indexes">
                        <column name="name" index="0"/>
                        <column name="value" index="1"/>
                        <column name="indexed_for" index="2"/>
                        <column name="exists_in_maf" index="3" />
                        <column name="path" index="4" />
                    </options>
                </param>
                <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment. Results may not be easily predictable if the input species does not exist in the cached multi-alignment">
                    <options from_data_table="maf_indexes">
                        <column name="value" index="3"/>
                        <filter type="multiple_splitter" column="3" separator=","/>
                    </options>
                </param>
            </when>
        </conditional>
    </xml>
</macros>