Mercurial > repos > marpiech > norwich_docking_tools
diff galaxy-tools/smina.xml @ 0:4eb3f9cb2a51 draft
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| author | dzesikah |
|---|---|
| date | Fri, 26 Aug 2016 09:53:37 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy-tools/smina.xml Fri Aug 26 09:53:37 2016 -0400 @@ -0,0 +1,148 @@ +<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>