annotate macros.xml @ 3:4cc9d85c3bae draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"

<macros>
    <token name="@TOOL_VERSION@">4.0.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">fpocket</requirement>
        </requirements>
    </xml>
    <xml name="inputs">
        <conditional name="inp">
            <param name="pocket_type" type="select" label="Type of pocket to detect" help="Search for different kinds of pockets - or select 'custom' for more fine-grained control">
                <option value="small_mol">Small molecule binding sites</option>
                <option value="channel">Putative channels and small cavities</option>
                <option value="external">Large, external pockets</option>
                <option value="custom">Custom options (advanced)</option>
            </param>
            <when value="custom">
                <param name="min" type="float" value="3" min="0" max="10" label="Minimum radius for an alpha sphere (angstroms)" help="An alpha sphere is an empty sphere in contact with 4 atoms in 3D space."/>
                <param name="max" type="float" value="6" min="0" max="10" label="Maximum radius for an alpha sphere (angstroms)" help="An alpha sphere is an empty sphere in contact with 4 atoms in 3D space."/>
                <param name="i" type="integer" value="35" min="20" max="50" label="Minimum number of alpha spheres a pocket must contain" help="Below this threshold pockets will not be listed in results"/>
                <param name="D" type="float" value="2.4" min="0" max="10" label="Distance threshold for clustering algorithm (angstroms)" help="Alpha spheres may be clustered if they are separated by less than this distance"/>
                <param name="C" type="select" value="s" label="Clustering method for grouping Voronoi vertices" help="Method for clustering alpha spheres">
                    <option value="s">Single linkage clustering</option>
                    <option value="m">Complete linkage clustering</option>
                    <option value="a">Average linkage clustering</option>
                    <option value="c">Centroid linkage clustering</option>
                </param>
                <param name="e" type="select" value="e" label="Distance measure for clustering">
                    <option value="e">Euclidean distance</option>
                    <option value="b">Manhattan distance</option>
                </param>
            </when>
            <when value="small_mol"/>
            <when value="channel"/>
            <when value="external"/>
        </conditional>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1186/1471-2105-10-168</citation>
            <citation type="doi">10.1093/nar/gkq383</citation>
        </citations>
    </xml>
</macros>