view openduck_run_smd.xml @ 0:05c95b16823b draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"

<tool id="openduck_run_smd" name="Run OpenDUck" version="@VERSION@">
    <description>steered molecular dynamics runs</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        ## to run on GPU set OPENDUCK_GPU_PARAM to something like "--gpu-id 1"
        cp '$ligand' ./ligand.sdf &&
        
        duck_prepare_sys
            -p '$protein'
            -l ./ligand.sdf
            -c '$chunk'
            ## -i is interaction, e.g. A_ASP_156_OD2
            -i '${ia.chain_sel}'_'${ia.res_sel}'_'${ia.resid_sel}'_'${ia.atom_sel}' 
            \${OPENDUCK_GPU_PARAM} &&

        mv equil.chk eql.chk &&
        mv complex_system.pickle cs.pickle &&

        duck_smd_runs
            -i eql.chk
            -p cs.pickle
            -n '$num'
            -l '$mdlen'
            -d '$start_dist'
            -v '$vel'
            \${OPENDUCK_GPU_PARAM} &&
        #if $return_tar:
            tar -czf allfiles.tar.gz --exclude=allfiles.tar.gz * &&
        #end if
        get_wqb -l '$ligand' -o '$ligand_wqb'
    ]]></command>
    <inputs>
        <param argument="protein" type="data" format='pdb' label="PDB file for apoprotein"/>
        <param argument="chunk" type="data" format='pdb' label="Chunk (in PDB format)" help="PDB file produced by chunk tool."/>
        <param argument="ligand" type="data" format='sdf,mol' label="SDF/MOL file containing a single ligand"/>
        <expand macro="interaction_params" />
        <param argument="mdlen" type="float" min="0" value="0.05" label="MD run length (ns)" help="Length of initial MD run (prior to steered molecular dynamics runs)."/>
        <param argument="start_dist" type="float" min="0" value="2.5" label="Starting distance" help="Initial length of the selected interaction between protein and ligand."/>
        <param argument="num" type="integer" min="0" value="1" label="Number of SMD runs" help="Number of steered molecular dynamics runs to perform."/>
        <param argument="vel" type="float" min="0" value="0.00001" label="Velocity" help="Distance (in angstroms) to perturb the system per simulation step in the SMD runs. Decreasing this value will increase simulation time."/>
        <expand macro="tar_param" />
    </inputs>
    <outputs>
        <data name="ligand_wqb" format="sdf" label="SD-file with DUck score"/>
        <expand macro="tar_output" />
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="protein" value="1n2v_apo.pdb" />
            <param name="ligand" value="ligand.mol" />
            <param name="chunk" value="protein_out_prot.pdb" />
            <param name="chain_sel" value="A" />
            <param name="res_sel" value="ASP" />
            <param name="resid_sel" value="156" />
            <param name="atom_sel" value="OD2" />
            <param name="num" value="1" />
            <param name="mdlen" value="0.05" />
            <param name="start_dist" value="2.5" />
            <param name="vel" value="0.00001" />
            <output name="ligand_wqb" file="ligand_wqb.mol" lines_diff="2" />
            <output name="tar" >
                <assert_contents>
                    <has_size value="6718500" delta="500"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

Perform steered molecular dynamics runs for dynamic undocking (DUck), performing system preparation (topology calculation and minimization), an initial MD run, and SMD runs.

This Galaxy tool uses OpenDUck, an open-source implementation of the original DUck method, using OpenMM and AmberTools.

_____

.. class:: infomark

**Input**

       - PDB file for apoprotein
       - PDB file for chunk
       - SDF/MOL file for ligand
       - Parameters defining the protein-ligand interaction
       - Parameters for MD and SMD runs

_____


.. class:: infomark

**Output**

       - Ligand in SDF/MOL format, with added `<SCORE.DUCK_WQB>` parameter.

A tar file is also produced as a optional output, containing all files produced by the tool.

    ]]></help>

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