Mercurial > repos > marpiech > norwich_tools_dock
diff smina.xml @ 1:dc6fb5c5d4c8 draft
planemo upload commit 489ad526806f22eefcb73e8d8efe44d648e8185e
| author | marpiech |
|---|---|
| date | Mon, 12 Sep 2016 06:00:34 -0400 |
| parents | 75f2b4087722 |
| children | 958fa7ba4715 |
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--- a/smina.xml Tue Aug 30 03:18:58 2016 -0400 +++ b/smina.xml Mon Sep 12 06:00:34 2016 -0400 @@ -1,4 +1,5 @@ -<tool id="smina" name="smina" version="0.1.0"> +<tool id="smina" name="smina" version="1.0"> + <description>Scoring and Minimization with AutoDock Vina</description> <stdio> <exit_code range="1:" /> </stdio> @@ -62,35 +63,98 @@ #if $minimize_iters --minimize_iters $minimize_iters #end if + #if $accurate_line=="true" + --accurate_line + #end if + #if $minimize_early_term=="true" + --minimize_early_term + #end if + #if $approximation + --approximation $approximation + #end if + #if $factor + --factor $factor + #end if + #if $force_cap + --force_cap $force_cap + #end if + #if $user_grid + --user_grid $user_grid + #end if + #if $user_grid_lambda + --user_grid_lambda $user_grid_lambda + #end if + #if $print_terms=="true" + --print_terms + #end if + #if $print_atom_types=="true" + --print_atom_types + #end if - --seed 1000 > $output; - cat $output > /tmp/ouput + #if $out + --out $out + #end if + #if $out_flex + --out_flex $out_flex + #end if + #if $atom_terms + --atom_terms $atom_terms + #end if + #if $atom_term_data=="true" + --atom_term_data + #end if + + #if $seed + --seed $seed + #end if + #if $exhaustiveness + --exhaustiveness $exhaustiveness + #end if + #if $num_modes + --num_modes $num_modes + #end if + #if $energy_range + --energy_range $energy_range + #end if + #if $min_rmsd_filter + --min_rmsd_filter $min_rmsd_filter + #end if + #if $addH=="false" + --addH false + #end if + + > $stand_output; + #if $out # cat $out > $out_output; #end if # + #if $out_flex # cat $out_flex > $out_flex_output; #end if # + #if $atom_terms # cat $atom_terms > $atom_terms_output; #end if # + + cat $stand_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="receptor" type="data" format="pdbqt" label="rigid part of the receptore" help="(--receptor)"/> + <param name="ligand" type="data" format="data" label="ligand(s)" help="(--ligand)"/> - <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="flex" type="data" format="pdbqt" label="flexible side chains, if any" optional="true" help="(--flex"/> + <param name="flexres" type="text" label="flexible side chains specified by comma separated list of chain:resid" optional="true" help="(--flexres)"/> + <param name="flexdist_ligand" type="data" format="data" label="Ligand to use for flexdist" optional="true" help="(--flexdist_ligand)"/> + <param name="flexdist" type="float" label="set all side chains within specified distance to flexdist_ligand to flexible" optional="true" help="(flexdist)"/> - <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="center_x" type="float" value="0" label="X coordinate of the center" help="(--center_x)"/> + <param name="center_y" type="float" value="0" label="Y coordinate of the center" help="(--center_y)"/> + <param name="center_z" type="float" value="0" label="Z coordinate of the center" help="(--center_z)"/> + <param name="size_x" type="integer" value="1" label="size in the X dimension" help="(--size_x)"/> + <param name="size_y" type="integer" value="1" label="size in the Y dimension" help="(--size_y)"/> + <param name="size_z" type="integer" value="1" label="size in the Z dimension" help="(--size_z)"/> - <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"> + <param name="autobox_ligand" type="data" format="data" label="Ligand to use for autobox" optional="true" help="(--autobox_ligand)"/> + <param name="autobox_add" type="float" label="Amount of buffer space to add to auto-generated box text(default +4 on all six sides)" optional="true" help="(autobox_add)"/> + <param name="no_lig" type="select" label="no ligand; for sampling/minimizing flexible residues (Type true if you want to use it)" help="(no_lig)"> <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"> + <param name="scoring" type="select" label="specify alternative builtin scoring function" help="(--scoring)"> <option value="default" selected="true">default</option> <option value="ad4_scoring">ad4_scoring</option> <option value="dkoes_fast">dkoes_fast</option> @@ -99,28 +163,79 @@ <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"> + <param name="custom_scoring" type="data" format="data" label="custom scoring function file" optional="true" help="(--custom_scoring)"/> + <param name="custom_atoms" type="data" format="data" label="custom atom type parameters file" optional="true" help="(--custom_atoms)"/> + <param name="score_only" type="select" label="score provided ligand pose" help="(--score_only)"> <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"> + <param name="local_only" type="select" label="local search only using autobox (you probably want to use --minimize)" help="(--local_only)"> + <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="energy minimization" help="(--minimize)"> + <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="generate random poses, attempting to avoid clashes" help="(--randomize_only)"> + <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="number iterations of steepest descent; default scales with rotors and usually isn't sufficient for convergence" optional="true" help="(--minimize_iters)"/> + <param name="accurate_line" type="select" label="use accurate line search" help="(--accurate_line)"> + <option value="false" selected="true">Don't use this option</option> + <option value="true">Use this option</option> + </param> + <param name="minimize_early_term" type="select" label="Stop minimization before convergence conditions are fully met" help="(--minimize_early_term)"> <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"> + <param name="approximation" type="select" label="approximation (linear, spline, or exact) to use" optional="true" help="(--approximation)"> + <option value="linear">linear</option> + <option value="spline">spline</option> + <option value="exact">exact</option> + </param> + <param name="factor" type="float" label="approximation factor: higher results in a finer-grained approximation" optional="true" help="(--factor)"> + <validator type="in_range" min="0"/> + </param> + <param name="force_cap" type="float" label="max allowed force; lower values more gently minimize clashing structures" optional="true" help="(--force_cap)"/> + <param name="user_grid" type="float" label="Autodock map file for user grid data based calculations" optional="true" help="(--user_grid)"/> + <param name="user_grid_lambda" type="float" label="Scales user_grid and functional scoring" optional="true" help="(--user_grid)"/> + <param name="print_terms" type="select" label="Print all available terms with default parameterizations" help="(--print_terms)"> + <option value="false" selected="true">Don't use this option</option> + <option value="true">Use this option</option> + </param> + <param name="print_atom_types" type="select" label="Print all available atom types" help="(--print_atom_types)"> <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"> + + <param name="out" type="text" label="output file name, format taken from file extension" optional="true" help="(--out)"/> + <param name="out_flex" type="text" label="output file for flexible receptor residues" optional="true" help="(--out_flex)"/> + <param name="atom_terms" type="text" label="output file for flexible receptor residues" optional="true" help="(--atom_terms)"/> + <param name="atom_term_data" type="select" label="embedded per-atom interaction terms in output sd data" help="(--atom_term_data)"> <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" /> + + <param name="seed" type="float" label="explicit random seed" optional="true" help="(--seed)"/> + <param name="exhaustiveness" type="integer" label="exhaustiveness of the global search (roughly proportional to time)" optional="true" help="(--exhaustiveness)"/> + <param name="num_modes" type="integer" label="exhaustiveness of the global search (roughly proportional to time)" optional="true" help="(--num_modes)"> + <validator type="in_range" min="1"/> + </param> + <param name="energy_range" type="float" label="maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)" optional="true" help="(--energy_range)"/> + <param name="min_rmsd_filter" type="float" label="rmsd value used to filter final poses to remove redundancy" optional="true" help="(--min_rmsd_filter)"/> + <param name="addH" type="select" label="automatically add hydrogens in ligands (on by default)" help="(--addH)"> + <option value="false" >Don't use this option</option> + <option value="true" selected="true">Use this option</option> + </param> + </inputs> <outputs> - <data name="output" format="data" /> + <data name="stand_output" format="data" /> + <data name="out_output" format="data" /> + <data name="out_flex_output" format="data" /> + <data name="atom_terms_output" format="data" /> </outputs> <tests> <test> @@ -132,15 +247,95 @@ <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" /> + <output name="stand_output" > + <assert_contents> + <has_text_matching expression="Using random seed" /> + </assert_contents> + </output> </test> </tests> <help> - "Smina help" + <![CDATA[ +************ +Description +************ + +A fork of AutoDock Vina 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 +****** + + **Input** + + --receptor arg rigid part of the receptor (PDBQT) + --flex arg flexible side chains, if any (PDBQT) + --ligand arg ligand(s) + --flexres arg flexible side chains specified by comma separated list of chain:resid + --flexdist_ligand arg Ligand to use for flexdist + --flexdist arg set all side chains within + specified distance to flexdist_ligand to flexible + + **Search space** + + --center_x arg X coordinate of the center + --center_y arg Y coordinate of the center + --center_z arg Z coordinate of the center + --size_x arg size in the X dimension (Angstroms) + --size_y arg size in the Y dimension (Angstroms) + --size_z arg size in the Z dimension (Angstroms) + --autobox_ligand arg Ligand to use for autobox + --autobox_add arg Amount of buffer space to add + to auto-generated box (default +4 on all six sides) + --no_lig no ligand; for + sampling/minimizing flexible residues + + **Scoring and minimization options** + + --scoring arg specify alternative + builtin scoring function + --custom_scoring arg custom scoring function file + --custom_atoms arg custom atom type parameters file + --score_only score provided ligand pose + --local_only local search only using autobox (you probably want to use --minimize) + --minimize energy minimization + --randomize_only generate random poses, attempting to avoid clashes + --minimize_iters arg number iterations of steepest descent; + default scales with rotors and usually isn't + sufficient for convergence + --accurate_line use accurate line search + --minimize_early_term Stop minimization before convergence conditions are fully met. + --approximation arg approximation (linear, spline, or exact) to use + --factor arg approximation factor: higher results in a finer-grained approximation + --force_cap arg max allowed force; lower values more gently minimize clashing structures + --user_grid arg Autodock map file for user grid data based calculations + --user_grid_lambda arg Scales user_grid and functional scoring + --print_terms Print all available terms with default parameterizations + --print_atom_types Print all available atom types + + **Output** + + --out arg output file name, format taken from file extension + --out_flex arg output file for flexible receptor residues + --atom_terms arg optionally write per-atom interaction term values + --atom_term_data embedded per-atom + interaction terms in output sd data + + **Misc** + + --seed arg explicit random seed + --exhaustiveness arg exhaustiveness of the global search (roughly proportional to time) + --num_modes arg maximum number of binding modes to generate + --energy_range arg maximum energy difference between the best binding mode and the worst one displayed (kcal/mol) + --min_rmsd_filter arg rmsd value used to filter final poses to remove redundancy + --addH arg automatically add hydrogens + in ligands (on by default) + + ]]> </help> <citations> <citation type="bibtex"> - @misc{renameTODO, author = {LastTODO, FirstTODO}, year = {TODO}, title = {TODO}, url = {https://sourceforge.net/projects/smina/}, } + @misc{url = {https://sourceforge.net/projects/smina/}, } </citation> </citations> </tool>