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author | earlhaminst |
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date | Tue, 08 May 2018 19:08:15 -0400 |
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<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>