comparison fpocket.xml @ 3:4cc9d85c3bae draft default tip

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

2:4fb73be7f4cb

<tool id="fpocket" name="fpocket" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <macros>
        <token name="@TOOL_VERSION@">3.1.4.2</token>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <description>- find potential binding sites in protein structures</description>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">fpocket</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

        ln -s '$input' ./input.pdb &&
        fpocket
            -f ./input.pdb
            #if $inp.pocket_type == 'channel':
                -m 2.8 -M 5.5 -i 30
            #elif $inp.pocket_type == 'external':
                -m 3.5 -M 10 -i 30
            #elif $inp.pocket_type == 'custom':
                -m $inp.min -M $inp.max -i $inp.i -D $inp.D -C $inp.C -e $inp.e
            #end if

    ]]></command>
    <inputs>
        <param name="input" type="data" format="pdb" label="Input file" help="Protein structure file (PDB) to search."/>
        <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>
        <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output files">
            <option value="atoms" selected="true">PDB files containing the atoms in contact with each pocket</option>
            <option value="pock_verts">PQR files containing Voronoi vertices of each pocket</option>
            <option value="alpha_pdb" selected="true">PDB file containing alpha spheres found</option>
            <option value="all_verts" selected="true">PQR file containing all Voronoi vertices found</option>

    <tests>
        <!-- lines_diff needed because volume estimates are calculated via a Monte Carlo method and vary with each run -->
        <test>
            <param name="input" ftype="pdb" value="2brc.pdb"/>
            <param name='pocket_type' value='custom' />
            <param name="min" value="4.0"/>
            <param name="max" value="7.0"/>
            <param name="i" value="20" />
            <param name="D" value="2.0"/>
            <param name="C" value="c" />
            <param name="e" value="b" />
            <param name='outputs' value='pock_verts,all_verts' />

- A collection of PQR files, one for each pocket, each containing Voronoi vertices of the pocket.
- A single PQR file containing all Voronoi vertices for all pockets.
- A text file listing properties of all pockets detected.

    ]]></help>
    <citations>
        <citation type="doi">10.1186/1471-2105-10-168</citation>
        <citation type="doi">10.1093/nar/gkq383</citation>
    </citations>
</tool>

3:4cc9d85c3bae

<tool id="fpocket" name="fpocket" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>- find potential binding sites in protein structures</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        ln -s '$input' ./input.pdb &&
        fpocket
            -f ./input.pdb
            #if $inp.pocket_type == 'channel':
                --min_alpha_size 2.8 --max_alpha_size 5.5 --min_spheres_per_pocket 30
            #elif $inp.pocket_type == 'external':
                --min_alpha_size 3.5 --max_alpha_size 10 --min_spheres_per_pocket 30
            #elif $inp.pocket_type == 'custom':
                --min_alpha_size $inp.min
                --max_alpha_size $inp.max
                --min_spheres_per_pocket $inp.i
                --clustering_distance $inp.D
                --clustering_method $inp.C
                --clustering_measure $inp.e
            #end if

    ]]></command>
    <inputs>
        <param name="input" type="data" format="pdb" label="Input file" help="Protein structure file (PDB) to search."/>
        <expand macro="inputs" />
        <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output files">
            <option value="atoms" selected="true">PDB files containing the atoms in contact with each pocket</option>
            <option value="pock_verts">PQR files containing Voronoi vertices of each pocket</option>
            <option value="alpha_pdb" selected="true">PDB file containing alpha spheres found</option>
            <option value="all_verts" selected="true">PQR file containing all Voronoi vertices found</option>

    <tests>
        <!-- lines_diff needed because volume estimates are calculated via a Monte Carlo method and vary with each run -->
        <test>
            <param name="input" ftype="pdb" value="2brc.pdb"/>
            <param name='pocket_type' value='custom' />
            <param name="min" value="1.0"/>
            <param name="max" value="3.0"/>
            <param name="i" value="20" />
            <param name="D" value="2.0"/>
            <param name="C" value="c" />
            <param name="e" value="b" />
            <param name='outputs' value='pock_verts,all_verts' />

- A collection of PQR files, one for each pocket, each containing Voronoi vertices of the pocket.
- A single PQR file containing all Voronoi vertices for all pockets.
- A text file listing properties of all pockets detected.

    ]]></help>
    <expand macro="citations" />
</tool>