Mercurial > repos > marpiech > norwich_tools_dock
diff smina.xml @ 2:958fa7ba4715 draft
planemo upload commit 489ad526806f22eefcb73e8d8efe44d648e8185e-dirty
| author | marpiech |
|---|---|
| date | Wed, 14 Sep 2016 09:47:48 -0400 |
| parents | dc6fb5c5d4c8 |
| children | 8c2e85bb2ce9 |
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--- a/smina.xml Mon Sep 12 06:00:34 2016 -0400 +++ b/smina.xml Wed Sep 14 09:47:48 2016 -0400 @@ -5,237 +5,254 @@ </stdio> <command> <![CDATA[ - cat $receptor > receptor.pdbqt; - cat $ligand > ligand.pdbqt; + cat $input.receptor > receptor.pdbqt; + cat $input.ligand > ligand.pdbqt; $__tool_directory__/tools/smina/smina.static --receptor receptor.pdbqt --ligand ligand.pdbqt - #if $flex - --flex $flex + #if $input.flex + --flex $input.flex #end if - #if $flexres - --flexres $flexres + #if $input.flexres + --flexres $input.flexres #end if - #if $flexdist_ligand - --flexdist_ligand $flexdist_ligand + #if $input.flexdist_ligand + --flexdist_ligand $input.flexdist_ligand #end if - #if $flexdist - --flexdist $flexdist + #if $input.flexdist + --flexdist $input.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 + --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 $autobox_ligand - --autobox_ligand $autobox_ligand + #if $search_space.autobox_ligand + --autobox_ligand $search_space.autobox_ligand #end if - #if $autobox_add - --autobox_add $autobox_add + #if $search_space.autobox_add + --autobox_add $search_space.autobox_add #end if - #if $no_lig=="true" + #if $search_space.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 - #if $accurate_line=="true" - --accurate_line - #end if - #if $minimize_early_term=="true" - --minimize_early_term + --out ligand_out.pdbqt + #if $output_sect.out_flex=="true" + --out_flex output_flex + #end if + #if $output_sect.log=="true" + --log output_log #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 + #if $output_sect.atom_terms=="true" + --atom_terms output_atom_terms #end if - #if $print_terms=="true" - --print_terms - #end if - #if $print_atom_types=="true" - --print_atom_types - #end if - - #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" + #if $output_sect.atom_term_data=="true" --atom_term_data #end if - #if $seed - --seed $seed + --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 + #if $scoring_and_minimization.score_only=="true" + --score_only + #end if + #if $scoring_and_minimization.local_only=="true" + --local_only #end if - #if $exhaustiveness - --exhaustiveness $exhaustiveness + #if $scoring_and_minimization.minimize=="true" + --minimize + #end if + #if $scoring_and_minimization.randomize_only=="true" + --randomize_only + #end if + --minimize_iters $scoring_and_minimization.minimize_iters + #if $scoring_and_minimization.accurate_line=="true" + --accurate_line + #end if + #if $scoring_and_minimization.minimize_early_term=="true" + --minimize_early_term + #end if + #if $scoring_and_minimization.approximation + --approximation $scoring_and_minimization.approximation #end if - #if $num_modes - --num_modes $num_modes + #if $scoring_and_minimization.factor + --factor $scoring_and_minimization.factor + #end if + #if $scoring_and_minimization.force_cap + --force_cap $scoring_and_minimization.force_cap + #end if + #if $scoring_and_minimization.user_grid + --user_grid $scoring_and_minimization.user_grid + #end if + --user_grid_lambda $scoring_and_minimization.user_grid_lambda + #if $scoring_and_minimization.print_terms=="true" + --print_terms #end if - #if $energy_range - --energy_range $energy_range + #if $scoring_and_minimization.print_atom_types=="true" + --print_atom_types + #end if + + #if $misc.cpu + --cpu $misc.cpu #end if - #if $min_rmsd_filter - --min_rmsd_filter $min_rmsd_filter + #if $misc.seed + --seed $misc.seed #end if - #if $addH=="false" + --exhaustiveness $misc.exhaustiveness + --num_modes $misc.num_modes + --energy_range $misc.energy_range + --min_rmsd_filter $misc.min_rmsd_filter + #if $misc.addH=="false" --addH false #end if + ; + #if $output_sect.out_flex=="true" # + cat output_flex > $out_flex_output; + #end if # + #if $output_sect.log=="true" # + cat output_log > $output_log; + #end if # + #if $output_sect.atom_terms=="true" # + cat output_atom_terms > $atom_terms_output; + #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 + cat ligand_out.pdbqt > $output ]]> </command> <inputs> - <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="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="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)"/> + <section name="input" title="Input" expanded="True"> + <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="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)"/> + </section> + <section name="search_space" title="Search space" expanded="True"> + <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="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="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> - <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 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 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">Do not use this option</option> + <option value="true">Use this option</option> + </param> + </section> + <section name="output_sect" title="Output" > + <param name="out_flex" type="select" label="Write flexible receptor residues" help="(--out_flex)"> + <option value="false" selected="true" >No </option> + <option value="true" >Yes </option> + </param> + <param name="log" type="select" label="Write log file" help="(--log)"> + <option value="false" selected="true" >No </option> + <option value="true" >Yes </option> + </param> + <param name="atom_terms" type="select" label="Write per-atom interaction term values" help="(--atom_terms)"> + <option value="false" selected="true" >No </option> + <option value="true" >Yes </option> + </param> + <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">Do not use this option</option> + <option value="true">Use this option</option> + </param> + </section> + <section name="scoring_and_minimization" title="Scoring and minimization options" > + <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> + <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="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="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="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="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> - + <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">Do not use this option</option> + <option value="true">Use this option</option> + </param> + <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">Do not 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">Do not 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">Do not use this option</option> + <option value="true">Use this option</option> + </param> + <param name="minimize_iters" type="integer" value="0" label="number iterations of steepest descent; default scales with rotors and usually isn't sufficient for convergence" help="(--minimize_iters)"/> + <param name="accurate_line" type="select" label="use accurate line search" help="(--accurate_line)"> + <option value="false" selected="true">Do not 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">Do not use this option</option> + <option value="true">Use this option</option> + </param> + <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" value="-1" label="Scales user_grid and functional scoring" help="(--user_grid_lambda)"/> + <param name="print_terms" type="select" label="Print all available terms with default parameterizations" help="(--print_terms)"> + <option value="false" selected="true">Do not 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">Do not use this option</option> + <option value="true">Use this option</option> + </param> + </section> + <section name="misc" title="Misc" > + <param name="cpu" type="integer" label="the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1)" optional="true" help="(--cpu)"/> + <param name="seed" type="float" label="explicit random seed" optional="true" help="(--seed)"/> + <param name="exhaustiveness" type="integer" value="8" label="exhaustiveness of the global search (roughly proportional to time)" help="(--exhaustiveness)"/> + <param name="num_modes" type="integer" value="9" label="exhaustiveness of the global search (roughly proportional to time)" help="(--num_modes)"> + <validator type="in_range" min="1"/> + </param> + <param name="energy_range" type="float" value="3" label="maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)" help="(--energy_range)"/> + <param name="min_rmsd_filter" type="float" value="1" label="rmsd value used to filter final poses to remove redundancy" help="(--min_rmsd_filter)"/> + <param name="addH" type="select" label="automatically add hydrogens in ligands (on by default)" help="(--addH)"> + <option value="false" >Do not use this option</option> + <option value="true" selected="true">Use this option</option> + </param> + </section> </inputs> <outputs> - <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" /> + <data name="output" format="txt" /> + <data name="out_flex_output" format="txt" label="smina: flexible receptor residues"> + <filter>output_sect['out_flex']=="true"</filter> + </data> + <data name="output_log" format="txt" label="smina: log file"> + <filter>output_sect['log']=="true"</filter> + </data> + <data name="atom_terms_output" format="txt" label="smima: per-atom interaction term values"> + <filter>output_sect['atom_terms']=="true"</filter> + </data> </outputs> <tests> <test> @@ -249,7 +266,7 @@ <param name="size_z" value="28" /> <output name="stand_output" > <assert_contents> - <has_text_matching expression="Using random seed" /> + <has_text_matching expression="END" /> </assert_contents> </output> </test> @@ -335,7 +352,20 @@ </help> <citations> <citation type="bibtex"> - @misc{url = {https://sourceforge.net/projects/smina/}, } + @article{Koes2013, + doi = {10.1021/ci300604z}, + url = {http://dx.doi.org/10.1021/ci300604z}, + year = {2013}, + month = {aug}, + publisher = {American Chemical Society ({ACS})}, + volume = {53}, + number = {8}, + pages = {1893--1904}, + author = {David Ryan Koes and Matthew P. Baumgartner and Carlos J. Camacho}, + title = {Lessons Learned in Empirical Scoring with smina from the {CSAR} 2011 Benchmarking Exercise}, + journal = {Journal of Chemical Information and Modeling} + } + @misc{url = {https://sourceforge.net/projects/smina/}} </citation> </citations> </tool>