<macros>
    <token name="@WRAPPER_VERSION@">1.0.0</token>
    <token name="@VERSION_SUFFIX@">1.0.0</token>
    <token name="@PROFILE@">20.09</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="38.92">bbmap</requirement>
        </requirements>
    </xml>
    <macro name="dbKeyActionsBBMap">
        <expand macro="dbKeyActions">
            <option type="from_data_table" name="fasta_indexes" column="1" offset="0">
                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                <filter type="param_value" ref="ref_source_cond.reference" column="1"/>
            </option>
        </expand>
    </macro>
    <macro name="dbKeyActions">
        <actions>
            <conditional name="ref_source_cond.ref_source">
                <when value="cached">
                    <action type="metadata" name="dbkey">
                        <yield/>
                    </action>
                </when>
                <when value="history">
                    <action type="metadata" name="dbkey">
                        <option type="from_param" name="ref_source_cond.reference" param_attribute="dbkey"/>
                    </action>
                </when>
            </conditional>
        </actions>
    </macro>
    <macro name="reference_source_cond">
        <conditional name="ref_source_cond">
            <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history">
                <option value="cached" selected="True">Use a cached reference</option>
                <option value="history">Use a reference from the history</option>
            </param>
            <when value="cached">
                <param name="reference" type="select" label="Using reference genome">
                    <options from_data_table="fasta_indexes">
                        <filter type="sort_by" column="2"/>
                        <validator type="no_options" message="A built-in reference genome is not available"/>
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="reference" type="data" format="fasta" label="Using reference genome">
                    <validator type="no_options" message="The current history does not include a fasta dataset"/>
                </param>
            </when>
        </conditional>
    </macro>
    <xml name="citations">
        <citations>
            <citation type="doi">
                https://doi.org/10.1371/journal.pone.0185056
            </citation>
        </citations>
    </xml>
</macros>