annotate macros.xml @ 0:8b48a608f1df draft

"planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="0.1">ffindex-dbkit</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="ffindex_single_inputs">
        <param name="ffdata" type="data" format="ffdata" label="PDB Database" help="Database Data file." />
        <param name="ffindex" type="data" format="ffindex" label="PDB Database Index" help="Database Index file." />
    </xml>

    <xml name="citations">
        <citations>
            <!--citation type="doi">10.1021/ci300579r</citation-->
        </citations>
    </xml>
    <xml name="logfile">
        <param name="logfile" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output log file" />
    </xml>

    <xml name="db_source">
        <conditional name="db_source">
            <param name="db_source_selector" type="select" label="Custom or built-in ffindex" help="Built-ins have been indexed using ffindex">
                <option value="indexed" selected="true">Use a built-in index</option>
                <option value="history">Use a ffindex from history</option>
            </param>
            <when value="indexed">
                <param name="ffindex" type="select" label="Select ffindex" help="">
                    <options from_data_table="ffindex_indices">
                        <filter type="sort_by" column="0" />
                        <validator type="no_options" message="No indices are available" />
                    </options>
                </param>
            </when>
            <when value="history">
                <expand macro="ffindex_single_inputs" />
            </when>
        </conditional>
    </xml>
    <xml name="db_source2">
        <conditional name="db_source2">
            <param name="db_source_selector" type="select" label="Custom or built-in ffindex" help="Built-ins have been indexed using ffindex">
                <option value="indexed" selected="true">Use a built-in index</option>
                <option value="history">Use a ffindex from history</option>
            </param>
            <when value="indexed">
                <param name="ffindex" type="select" label="Select ffindex" help="">
                    <options from_data_table="ffindex_indices">
                        <filter type="sort_by" column="0" />
                        <validator type="no_options" message="No indices are available" />
                    </options>
                </param>
            </when>
            <when value="history">
                <expand macro="ffindex_single_inputs" />
            </when>
        </conditional>
    </xml>

    <token name="@db_source@">
        #if $db_source.db_source_selector == 'indexed':
            -d '${db_source.ffindex.fields.path}.ffdata'
            -i '${db_source.ffindex.fields.path}.ffindex'
        #else
            -d '$db_source.ffdata'
            -i '$db_source.ffindex'
        #end if
    </token>
    <token name="@db_source2@">
        #if $db_source.db_source_selector == 'indexed':
            -sd '${db_source.ffindex.fields.path}.ffdata'
            -si '${db_source.ffindex.fields.path}.ffindex'
        #else
            -sd '$db_source.ffdata'
            -si '$db_source.ffindex'
        #end if
    </token>
</macros>