annotate smina.xml @ 0:bc03dbb6eb37 draft

planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty

<tool id="smina" name="smina" version="0.1.0">
    <requirements>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command>
        <![CDATA[ 
        cat $receptor > receptor.pdbqt;
        cat $ligand > ligand.pdbqt;
        $__tool_directory__/tools/smina/smina.static 
                                                    --receptor receptor.pdbqt 
                                                    --ligand ligand.pdbqt 

                                                    #if $flex
                                                    --flex $flex
                                                    #end if
                                                    #if $flexres
                                                    --flexres $flexres
                                                    #end if
                                                    #if $flexdist_ligand
                                                    --flexdist_ligand $flexdist_ligand
                                                    #end if
                                                    #if $flexdist
                                                    --flexdist $flexdist
                                                    #end if

                                                    --center_x $center_x 
                                                    --center_y $center_y
                                                    --center_z $center_z 
                                                    --size_x $size_x
                                                    --size_y $size_y
                                                    --size_z $size_z

                                                    #if $autobox_ligand
                                                    --autobox_ligand $autobox_ligand 
                                                    #end if 
                                                    #if $autobox_add 
                                                    --autobox_add $autobox_add
                                                    #end if
                                                    #if $no_lig=="true"
                                                    --no_lig
                                                    #end if 

                                                    --scoring $scoring 
                                                    #if $custom_scoring
                                                    --custom_scoring $custom_scoring
                                                    #end if
                                                    #if $custom_atoms
                                                    --custom_atoms $custom_atoms 
                                                    #end if
                                                    #if $score_only=="true"
                                                    --score_only 
                                                    #end if
                                                    #if $local_only=="true"
                                                    --local_only 
                                                    #end if
                                                    #if $minimize=="true"
                                                    --minimize 
                                                    #end if 
                                                    #if $randomize_only=="true"    
                                                    --randomize_only  
                                                    #end if 
                                                    #if $minimize_iters  
                                                    --minimize_iters $minimize_iters 
                                                    #end if

                                                    --seed 1000 > $output;
                                                    cat $output > /tmp/ouput
    ]]>
    </command>
    <inputs>
        <param name="receptor" type="data" format="pdbqt" label="receptor: rigid part of the receptore" />
        <param name="ligand" type="data" format="data" label="ligand: ligand(s)" />

        <param name="flex" type="data" format="pdbqt" label="flex: flexible side chains, if any" optional="true" />
        <param name="flexres" type="text" label="flexres: flexible side chains specified by comma separated list of chain:resid" optional="true" />
        <param name="flexdist_ligand" type="data" format="data" label="flexdist_ligand: Ligand to use for flexdist" optional="true" />
        <param name="flexdist" type="float" label="flexdist: set all side chains within specified distance to flexdist_ligand to flexible" optional="true" />

        <param name="center_x" type="float" value="0" label="center_x: X coordinate of the center" />
        <param name="center_y" type="float" value="0" label="center_y: Y coordinate of the center" />
        <param name="center_z" type="float" value="0" label="center_z: Z coordinate of the center" />
        <param name="size_x" type="integer" value="1" label="size_x: size in the X dimension" />
        <param name="size_y" type="integer" value="1" label="size_y: size in the Y dimension" />
        <param name="size_z" type="integer" value="1" label="size_z: size in the Z dimension" />

        <param name="autobox_ligand" type="data" format="data" label="autobox_ligand: Ligand to use for autobox" optional="true" />
        <param name="autobox_add" type="float" value="4" label="autobox_add: Amount of buffer space to add to auto-generated box text(default +4 on all six sides)" optional="true" />
        <param name="no_lig" type="select" label="no_lig: no ligand; for sampling/minimizing flexible residues (Type true if you want to use it)" optional="true">
            <option value="false" selected="true">Don't use this option</option>
            <option value="true">Use this option</option>
        </param>

        <param name="scoring" type="select" label="scoring: specify alternative builtin scoring function" optional="true">
            <option value="default" selected="true">default</option>
            <option value="ad4_scoring">ad4_scoring</option>
            <option value="dkoes_fast">dkoes_fast</option>
            <option value="dkoes_scoring">dkoes_scoring</option>
            <option value="dkoes_scoring_old">dkoes_scoring_old</option>
            <option value="vina">vina</option>
            <option value="vinardo">vinardo</option>
        </param>
        <param name="custom_scoring" type="data" format="data" label="custom_scoring: custom scoring function file" optional="true" />
        <param name="custom_atoms" type="data" format="data" label="custom_atoms: custom atom type parameters file" optional="true" />
        <param name="score_only" type="select" label="score_only: score provided ligand pose" optional="true">
            <option value="false" selected="true">Don't use this option</option>
            <option value="true">Use this option</option>
            </param>
        <param name="local_only" type="select" label="local_only: local search only using autobox (you probably want to use --minimize)" optional="true">
            <option value="false" selected="true">Don't use this option</option>
            <option value="true">Use this option</option>
        </param>
        <param name="minimize" type="select" label="minimize: energy minimization" optional="true">
            <option value="false" selected="true">Don't use this option</option>
            <option value="true">Use this option</option>
        </param>
        <param name="randomize_only" type="select" label="randomize_only: generate random poses, attempting to avoid clashes" optional="true">
            <option value="false" selected="true">Don't use this option</option>
            <option value="true">Use this option</option>
        </param>
        <param name="minimize_iters" type="integer" label="minimize_iters: number iterations of steepest descent; default scales with rotors and usually isn't sufficient for convergence" optional="true" />
    </inputs>
    <outputs>
        <data name="output" format="data" />
    </outputs>
    <tests>
        <test>
            <param name="receptor" value="smina/protein.pdbqt" />
            <param name="ligand" value="smina/ligand.pdbqt" />
            <param name="center_x" value="11" />
            <param name="center_y" value="90.5" />
            <param name="center_z" value="57.5" />
            <param name="size_x" value="22" />
            <param name="size_y" value="24" />
            <param name="size_z" value="28" />
            <output name="output" file="smina/output_smina" />
        </test>
    </tests>
    <help>
        "Smina help"
    </help>
    <citations>
        <citation type="bibtex">
            @misc{renameTODO, author = {LastTODO, FirstTODO}, year = {TODO}, title = {TODO}, url = {https://sourceforge.net/projects/smina/}, }
        </citation>
    </citations>
</tool>