annotate smina.xml @ 0:7c0bb0c48a27 draft default tip

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty

<tool id="smina" name="smina" version="1.0">
    <description>Scoring and Minimization with AutoDock Vina</description>
    <requirements>
        <requirement type="package" version="2017.11.9">smina</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
ln -s '$input.receptor' receptor.pdbqt &&
ln -s '$input.ligand' ligand.pdbqt &&
smina
--receptor receptor.pdbqt
--ligand ligand.pdbqt
#if $input.flex
    --flex '$input.flex'
#end if
#if $input.flexres
    --flexres '$input.flexres'
#end if
#if $input.flexdist_ligand
    --flexdist_ligand '$input.flexdist_ligand'
#end if
#if str($input.flexdist)
    --flexdist $input.flexdist
#end if

--center_x $search_space.center_x
--center_y $search_space.center_y
--center_z $search_space.center_z
--size_x $search_space.size_x
--size_y $search_space.size_y
--size_z $search_space.size_z
#if $search_space.autobox_ligand
    --autobox_ligand '$search_space.autobox_ligand'
#end if
#if str($search_space.autobox_add)
    --autobox_add $search_space.autobox_add
#end if
$search_space.no_lig

--out ligand_out.pdbqt
#if $output_sect.out_flex
    --out_flex '$out_flex_output'
#end if
#if $output_sect.log
    --log '$output_log'
#end if
#if $output_sect.atom_terms
    --atom_terms '$atom_terms_output'
#end if
$output_sect.atom_term_data

--scoring $scoring_and_minimization.scoring
#if $scoring_and_minimization.custom_scoring
    --custom_scoring '$scoring_and_minimization.custom_scoring'
#end if
#if $scoring_and_minimization.custom_atoms
    --custom_atoms '$scoring_and_minimization.custom_atoms'
#end if
$scoring_and_minimization.score_only
$scoring_and_minimization.local_only
$scoring_and_minimization.minimize
$scoring_and_minimization.randomize_only
--minimize_iters $scoring_and_minimization.minimize_iters
$scoring_and_minimization.accurate_line
$scoring_and_minimization.minimize_early_term
#if $scoring_and_minimization.approximation
    --approximation $scoring_and_minimization.approximation
#end if
#if $scoring_and_minimization.factor
    --factor $scoring_and_minimization.factor
#end if
#if str($scoring_and_minimization.force_cap)
    --force_cap $scoring_and_minimization.force_cap
#end if
#if str($scoring_and_minimization.user_grid)
    --user_grid $scoring_and_minimization.user_grid
#end if
--user_grid_lambda $scoring_and_minimization.user_grid_lambda
$scoring_and_minimization.print_terms
$scoring_and_minimization.print_atom_types

--cpu \${GALAXY_SLOTS:-1}
#if str($misc.seed)
    --seed $misc.seed
#end if
--exhaustiveness $misc.exhaustiveness
--num_modes $misc.num_modes
--energy_range $misc.energy_range
--min_rmsd_filter $misc.min_rmsd_filter
$misc.addH
    ]]></command>
    <inputs>
        <section name="input" title="Input" expanded="True">
            <param argument="--receptor" type="data" format="pdbqt" label="Rigid part of the receptore" />
            <param argument="--ligand" type="data" format="pdbqt" label="Ligand(s)" />
            <param argument="--flex" type="data" format="pdbqt" optional="true" label="Flexible side chains, if any" />
            <param argument="--flexres" type="text" optional="true" label="Flexible side chains specified by comma separated list of chain:resid" />
            <param argument="--flexdist_ligand" type="data" format="data" optional="true" label="Ligand to use for flexdist" />
            <param argument="--flexdist" type="float" optional="true" label="Set all side chains within specified distance to flexdist_ligand to flexible" />
        </section>
        <section name="search_space" title="Search space" expanded="True">
            <param argument="--center_x" type="float" value="0" label="X coordinate of the center" />
            <param argument="--center_y" type="float" value="0" label="Y coordinate of the center" />
            <param argument="--center_z" type="float" value="0" label="Z coordinate of the center" />
            <param argument="--size_x" type="integer" value="1" label="Size in the X dimension" />
            <param argument="--size_y" type="integer" value="1" label="Size in the Y dimension" />
            <param argument="--size_z" type="integer" value="1" label="Size in the Z dimension" />

            <param argument="--autobox_ligand" type="data" format="data" optional="true" label="Ligand to use for autobox" />
            <param argument="--autobox_add" type="float" optional="true" label="Amount of buffer space to add to auto-generated box text" />
            <param argument="--no_lig" type="boolean" truevalue="--no_lig" falsevalue="" label="No ligand; for sampling/minimizing flexible residues" />
        </section>
        <section name="output_sect" title="Output">
            <param argument="--out_flex" type="boolean" label="Write flexible receptor residues" />
            <param argument="--log" type="boolean" label="Write log file" />
            <param argument="--atom_terms" type="boolean" label="Write per-atom interaction term values" />
            <param argument="--atom_term_data" type="boolean" truevalue="--atom_term_data" falsevalue="" label="Embedded per-atom interaction terms in output sd data" />
        </section>
        <section name="scoring_and_minimization" title="Scoring and minimization options">
            <param argument="--scoring" type="select" label="Specify alternative builtin scoring function">
                <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 argument="--custom_scoring" type="data" format="data" optional="true" label="Custom scoring function file" />
            <param argument="--custom_atoms" type="data" format="data" optional="true" label="Custom atom type parameters file" />
            <param argument="--score_only" type="boolean" truevalue="--score_only" falsevalue="" label="Score provided ligand pose" />
            <param argument="--local_only" type="boolean" truevalue="--local_only" falsevalue="" label="Local search only using autobox" />
            <param argument="--minimize" type="boolean" truevalue="--minimize" falsevalue="" label="Energy minimization" />
            <param argument="--randomize_only" type="boolean" truevalue="--randomize_only" falsevalue="" label="Generate random poses, attempting to avoid clashes" />
            <param argument="--minimize_iters" type="integer" value="0" label="Number iterations of steepest descent" />
            <param argument="--accurate_line" type="boolean" truevalue="--accurate_line" falsevalue="" label="Accurate line search" />
            <param argument="--minimize_early_term" type="boolean" truevalue="--minimize_early_term" falsevalue="" label="Stop minimization before convergence conditions are fully met" />
            <param argument="--approximation" type="select" optional="true" label="Approximation">
                <option value="linear">linear</option>
                <option value="spline">spline</option>
                <option value="exact">exact</option>
            </param>
            <param argument="--factor" type="float" min="0" optional="true" label="Approximation factor: higher results in a finer-grained approximation" />
            <param argument="--force_cap" type="float" optional="true" label="Max allowed force; lower values more gently minimize clashing structures" />
            <param argument="--user_grid" type="float" optional="true" label="Autodock map file for user grid data based calculations" />
            <param argument="--user_grid_lambda" type="float" value="-1" label="Scales user_grid and functional scoring" />
            <param argument="--print_terms" type="boolean" truevalue="--print_terms" falsevalue="" label="Print all available terms with default parameterizations" />
            <param argument="--print_atom_types" type="boolean" truevalue="--print_atom_types" falsevalue="" label="Print all available atom types" />
        </section>
        <section name="misc" title="Misc">
            <param argument="--seed" type="integer" optional="true" label="Explicit random seed" />
            <param argument="--exhaustiveness" type="integer" value="8" label="Exhaustiveness of the global search" />
            <param argument="--num_modes" type="integer" min="1" value="9" label="Maximum number of binding modes to generate" />
            <param argument="--energy_range" type="float" value="3" label="Maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)" />
            <param argument="--min_rmsd_filter" type="float" value="1" label="Rmsd value used to filter final poses to remove redundancy" />
            <param argument="--addH" type="boolean" truevalue="" falsevalue="--addH false" checked="true" label="Automatically add hydrogens in ligands" />
        </section>
    </inputs>
    <outputs>
        <data name="output" format="pdbqt" from_work_dir="ligand_out.pdbqt" />
        <data name="out_flex_output" format="txt" label="smina: flexible receptor residues">
            <filter>output_sect['out_flex']</filter>
        </data>
        <data name="output_log" format="txt" label="smina: log file">
            <filter>output_sect['log']</filter>
        </data>
        <data name="atom_terms_output" format="txt" label="smima: per-atom interaction term values">
            <filter>output_sect['atom_terms']</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="receptor" value="protein.pdbqt" />
            <param name="ligand" value="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" />
            <param name="log" value="True" />
            <param name="seed" value="1000" />
            <param name="num_modes" value="5" />
            <output name="output" file="ligand_out.pdbqt" />
            <output name="output_log" file="output_smina" />
        </test>
    </tests>
    <help><![CDATA[
************
Description
************

`smina <https://sourceforge.net/projects/smina/>`_ is a fork of `AutoDock Vina <http://vina.scripps.edu/>`_ that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project.
    ]]></help>
    <citations>
        <citation type="doi">10.1021/ci300604z</citation>
    </citations>
</tool>