annotate rbcavity.xml @ 2:7fac8e7a12d5 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1"

<tool id="rxdock_rbcavity" name="rxDock cavity definition" version="0.1.5">
    <description>- generate the active site definition needed for rxDock docking</description>
    <macros>
        <import>rxdock_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command><![CDATA[
        ln -s '$receptor_prm' receptor.prm &&
        ln -s '$receptor' receptor.mol2 &&
        ln -s '$ligand' ligand.sdf &&
        rbcavity -W -d -r receptor.prm &&
        ls -l
    ]]></command>

    <configfiles>
        <configfile name="receptor_prm">RBT_PARAMETER_FILE_V1.00
RECEPTOR_FILE receptor.mol2
RECEPTOR_FLEX 3.0
SECTION MAPPER
    SITE_MAPPER RbtLigandSiteMapper
    REF_MOL ligand.sdf
    RADIUS $radius
    SMALL_SPHERE $sphere
    MIN_VOLUME $min_volume
    MAX_CAVITIES 1
    VOL_INCR $vol_incr
    GRIDSTEP $gridstep
END_SECTION
SECTION CAVITY
    SCORING_FUNCTION RbtCavityGridSF
    WEIGHT $weight
END_SECTION
        </configfile>
    </configfiles>

    <inputs>
        <param type="data" name="receptor" format="mol2" label="Receptor" help="Select a receptor (Mol2 format)."/>
        <param type="data" name="ligand" format="mol,sdf" label="Reference ligand" help="Single ligand in Mol or SDF format"/>
        <param name="radius" type="float" value="6.0" min="0" label="Mapper sphere radius"
            help="Mapper radius of large sphere in angstroms; rxDock will search for cavities to the small sphere but not to the large sphere"/>
        <param name="sphere" type="float" value="1.0" min="0" label="Mapper small sphere radius"
            help="Mapper radius of small sphere in angstroms; rxDock will search for cavities accessible to the small sphere but not to the large sphere"/>
        <param name="min_volume" type="integer" value="100" min="0" label="Mapper minimum volume"
            help="Mapper minimum volume in cubic angstroms. rxDock will ignore cavities which are smaller than this value"/>
        <param name="vol_incr" type="float" value="0.0" min="0" label="Mapper volume increment"
            help="Mapper volume increment in angstroms. When excluding the volume occupied by the receptor from the cavity search, rxDock will temporarily increase the radius of receptor atoms by this amount"/>
        <param name="gridstep" type="float" value="0.5" min="0" label="Mapper grid step" help="Grid resolution for mapping in angstroms"/>
        <param name="weight" type="float" value="1.0" min="0" label="Cavity weight" help="Cavity weight"/>
    </inputs>
    <outputs>
        <data name="activesite" format="rdock_as" from_work_dir="receptor.as" label="rbcavity active site on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="receptor" value="receptor.mol2"/>
            <param name="ligand" value="ligand.sdf"/>
            <output name="activesite" file="receptor.as" compare="sim_size"/>
        </test>
        <test>
            <param name="receptor" value="receptor.mol2"/>
            <param name="ligand" value="ligand.mol"/>
            <output name="activesite" file="receptor.as" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

This tool generates the cavity definition for rxDock docking (the receptor.as file) using the rbcavity program.
See https://www.rxdock.org for more details about rxDock and associated programs.
Only a subset of the parameters are currently exposed. Read the rxDock docs for a full understanding.

-----

.. class:: infomark

**Inputs**

1. The protein receptor to dock into as a file in Mol2 format.
2. A reference ligand used to define the location of the active site in Molfile or SDF format.
3. Various parameters for the mapper and cavity generation. Sensible defaults are provided for all.

-----

.. class:: infomark

**Outputs**

An active site definition binary file (receptor.as) that is needed by the rxDock docking program to guide the docking.

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