annotate fpocket.xml @ 1:909c8763f127 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 51f8b6831c513a56bac5aae0d06c936ad6fa8ea8"

<tool id="fpocket" name="fpocket" version="3.1.3">
    <description>- find potential binding sites in protein structures</description>
    <requirements>
        <requirement type="package" version="3.1.3">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>
            <option value="info" selected="true">Log file containing pocket properties</option>
        </param>
    </inputs>

    <outputs>
        <collection type="list" name="atoms_output" label="Atoms in contact with each pocket">
            <discover_datasets pattern="(?P&lt;designation&gt;^pocket\d+)_atm\.pdb$" directory="input_out/pockets" ext="pdb"/>
            <filter>"atoms" in outputs</filter>
        </collection>
        <collection type="list" name="pock_verts_output" label="Voronoi vertices of each pocket">
            <discover_datasets pattern="(?P&lt;designation&gt;^pocket\d+)_vert\.pqr$" directory="input_out/pockets" ext="pqr"/>
            <filter>"pock_verts" in outputs</filter>
        </collection>
        <data format="pqr" name="all_verts_output" label="All Voronoi vertices found" from_work_dir="input_out/input_pockets.pqr">
            <filter>"all_verts" in outputs</filter>
        </data>
        <data format="pdb" name="alpha_pdb_output" label="PDB output with alpha spheres" from_work_dir="input_out/input_out.pdb">
            <filter>"alpha_pdb" in outputs</filter>
        </data>
        <data format="txt" name="info_output" label="Pocket properties" from_work_dir="input_out/input_info.txt">
            <filter>"info" in outputs</filter>
        </data>
    </outputs>

    <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' />
            <output_collection name="pock_verts_output" type="list">
                <element name="pocket2" ftype="pqr" file="pocket2_vert.pqr" lines_diff="2"/>
            </output_collection>
            <output name="all_verts_output" ftype="pqr" file='custom_pockets.pqr'/>
        </test>
        <test>
            <param name="input" ftype="pdb" value="2brc.pdb"/>
            <param name='pocket_type' value='small_mol' />
            <output_collection name="atoms_output" type="list">
                <element name="pocket1" ftype="pdb" file="pocket1_atm.pdb" lines_diff="2"/>
            </output_collection>
            <output name="info_output" ftype="txt" file='2brc_info.txt' lines_diff="20"/>
            <output name="alpha_pdb_output" ftype="pdb">
              <assert_contents>
                <has_text text="ATOM      1    N MET A   1"/>
                <has_text text="HETATM    6 APOL STP C   "/>
              </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

Detect 'pockets' in a protein structure using the fpocket software. A potential use 
of this tool is locating potential binding sites in a protein prior to performing 
protein-ligand docking.

To use, upload a protein structure in PDB format and select the type of pocket to 
detect. 'Custom options' can also be selected - this exposes all internal fpocket 
parameters. Using this option requires some knowledge of the fpocket prediction 
algorithm. Please consult the cited publications for more details.


-----

.. class:: infomark

**Input**

A protein structure in PDB format.

-----

.. class:: infomark

**Output**

Some or all of the following files:

- A collection of PDB files, one for each pocket, each containing the atoms bordering the pocket.
- 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>