annotate macros.xml @ 1:5b96db0a313e draft

"planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">springsuite</requirement>
            <yield />
        </requirements>
    </xml>
    <token name="@TOOL_VERSION@">0.2</token>
    <token name="@VERSION_SUFFIX@">0</token>

    <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="ffindex_single_inputs_hhr">
        <param name="ffdata" type="data" format="ffdata" label="HHR Database" help="Database Data file." />
        <param name="ffindex" type="data" format="ffindex" label="HHR 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="pdb_source">
        <conditional name="pdb_source">
            <param name="pdb_source_selector" type="select" label="Custom or built-in PDB" help="Built-ins have been indexed using ffindex">
                <option value="indexed" selected="true">Use a built-in index</option>
                <option value="history">Use a PDB index from history</option>
            </param>
            <when value="indexed">
                <param name="pdb" type="select" label="Select PDB database" help="">
                    <options from_data_table="ffindex_indices">
                        <filter type="sort_by" column="0" />
                        <filter type="static_value" column="3" value="pdb" />
                        <validator type="no_options" message="No indices are available" />
                    </options>
                </param>
                <param name="zipped" type="select" label="Zipped entries in PDB database?" help="">
                    <option value="" selected="true">No</option>
                    <option value="gz">Yes</option>
                </param>
            </when>
            <when value="history">
                <expand macro="ffindex_single_inputs" />
            </when>
        </conditional>
    </xml>
    <xml name="hhr_source">
        <conditional name="hhr_source">
            <param name="hhr_source_selector" type="select" label="Custom or built-in HHR index" help="Built-ins have been indexed using ffindex">
                <option value="indexed" selected="true">Use a built-in index</option>
                <option value="history">Use a HHR index from history</option>
            </param>
            <when value="indexed">
                <param name="hhr" type="select" label="Select HHR database" help="">
                    <options from_data_table="ffindex_indices">
                        <filter type="sort_by" column="0" />
                        <filter type="static_value" column="3" value="hhr" />
                        <validator type="no_options" message="No indices are available" />
                    </options>
                </param>
            </when>
            <when value="history">
                <expand macro="ffindex_single_inputs_hhr" />
            </when>
        </conditional>
    </xml>

    <token name="@pdb_source@">
        #if $pdb_source.pdb_source_selector == 'indexed':
            -d '${pdb_source.pdb.fields.path}.ffdata'
            -i '${pdb_source.pdb.fields.path}.ffindex'
            -z '$pdb_source.zipped'
        #else
            -d '$pdb_source.ffdata'
            -i '$pdb_source.ffindex'
        #end if
    </token>
    <token name="@hhr_source@">
        #if $hhr_source.hhr_source_selector == 'indexed':
            -dh '${hhr_source.hhr.fields.path}.ffdata'
            -ih '${hhr_source.hhr.fields.path}.ffindex'
        #else
            -dh '$hhr_source.ffdata'
            -ih '$hhr_source.ffindex'
        #end if
    </token>
</macros>