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<tool id="rdock" name="rdock" version="1.0">
    <description>tail-to-head</description>
    <command>
        <![CDATA[ 
    	cat $inputmol2 > inputmol2.mol2; cat $inputprm | sed "s|RECEPTOR_FILE.*|RECEPTOR_FILE inputmol2.mol2|g" | sed "s|REF_MOL.*|REF_MOL ligand.sd|g" > new.prm; 
        cp -r $__tool_directory__/tools/rdock/data .;
        mkdir data/ligands; 
        cp $inputsd data/ligands/ligand.sd; 
        LD_LIBRARY_PATH=$__tool_directory__/tools/rdock/lib $__tool_directory__/tools/rdock/bin/rbcavity -r new.prm -was > /tmp/rbcavity.log; 
		LD_LIBRARY_PATH=$__tool_directory__/tools/rdock/lib $__tool_directory__/tools/rdock/bin/rbdock -r new.prm -p dock.prm -n 100 -i $inputsd -o output_docking_out > /tmp/docking_out.log;
        PERL5LIB=$__tool_directory__/tools/rdock/lib/ LD_LIBRARY_PATH=$__tool_directory__/tools/rdock/lib $__tool_directory__/tools/rdock/bin/sdsort -n -f'SCORE' output_docking_out.sd > sorted.sd; 
        PYTHONPATH=/usr/lib/python2.7/dist-packages/ $__tool_directory__/tools/rdock/bin/sdrmsd $inputsd sorted.sd > $output_rdock
    	]]>
    </command>
    <inputs>
        <param name="inputprm" format="prm" type="data" label="PRM file" />
        <param name="inputmol2" format="mol2" type="data" label="MOL2 file" />
        <param name="inputsd" format="sd" type="data" label="SD file" />
    </inputs>
    <outputs>
        <data name="output_rdock" format="data" />
    </outputs>
    <tests>
        <test>
            <param name="inputprm" value="rdock/1sj0_rdock.prm" />
            <param name="inputmol2" value="rdock/1sj0_rdock.mol2" />
            <param name="inputsd" value="rdock/1sj0_ligand.sd" />
            <output name="output_rdock">
                <assert_contents>
                    <has_n_columns n="2" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="inputprm" value="rdock/1nem_rdock.prm" />
            <param name="inputmol2" value="rdock/1nem_rdock.mol2" />
            <param name="inputsd" value="rdock/1nem_lig.sd" />
            <output name="output_rdock">
                <assert_contents>
                    <has_n_columns n="2" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
        rDock tool
    </help>
    <citations>
        <citation type="doi">doi:10.1371/journal.pcbi.1003571</citation>
    </citations>
</tool>