<tool id="rdock" name="rDock" version="1.0">
    <description>Binding Mode Prediction in Proteins/RNA</description>
    <requirements>
        <requirement type="package" version="2013.1">rDock</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
ln -s '$inputmol2' inputmol2.mol2 &&
ln -s '$inputsd' ligand.sd &&
sed 's|RECEPTOR_FILE.*|RECEPTOR_FILE inputmol2.mol2|g' < '$inputprm' | sed 's|REF_MOL.*|REF_MOL ./ligand.sd|g' > new.prm &&
rbcavity -r new.prm -was &&
rbdock -r new.prm -p dock.prm -n 100 -i '$inputsd' -o output_docking_out &&
sdsort -n -f'SCORE' output_docking_out.sd > sorted.sd &&
sdrmsd '$inputsd' sorted.sd > '$output_rdock'
    ]]></command>
    <inputs>
        <param name="inputprm" argument="-r" type="data" format="prm" label="Receptor param file (contains active site params)" />
        <param name="inputmol2" type="data" format="mol2" label="MOL2 file" />
        <param name="inputsd" argument="-i" type="data" format="sdf" label="Ligand SD file" />
    </inputs>
    <outputs>
        <data name="output_rdock" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="inputprm" value="1sj0_rdock.prm" />
            <param name="inputmol2" value="1sj0_rdock.mol2" />
            <param name="inputsd" value="1sj0_ligand.sd" />
            <output name="output_rdock">
                <assert_contents>
                    <has_n_columns n="2" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

`rDock`_ is a fast and versatile open source docking program that can be used to dock small molecules against proteins and nucleic acids.
It is designed for High Throughput Virtual Screening (HTVS) campaigns and Binding Mode prediction studies.

.. _rDock: https://rdock.github.io/
    ]]></help>
    <citations>
        <citation type="doi">10.1371/journal.pcbi.1003571</citation>
    </citations>
</tool>