Mercurial > repos > marpiech > norwich_tools
view smina.xml @ 0:bc03dbb6eb37 draft
planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
| author | marpiech |
|---|---|
| date | Mon, 29 Aug 2016 03:38:13 -0400 |
| parents | |
| children | 16673005d799 |
line wrap: on
line source
<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>