Mercurial > repos > marpiech > norwich_docking_tools
comparison galaxy-tools/smina.xml @ 0:4eb3f9cb2a51 draft
Uploaded
| author | dzesikah |
|---|---|
| date | Fri, 26 Aug 2016 09:53:37 -0400 |
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| -1:000000000000 | 0:4eb3f9cb2a51 |
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| 1 <tool id="smina" name="smina" version="0.1.0"> | |
| 2 <requirements> | |
| 3 </requirements> | |
| 4 <stdio> | |
| 5 <exit_code range="1:" /> | |
| 6 </stdio> | |
| 7 <command> | |
| 8 <![CDATA[ | |
| 9 cat $receptor > receptor.pdbqt; | |
| 10 cat $ligand > ligand.pdbqt; | |
| 11 $__tool_directory__/tools/smina/smina.static | |
| 12 --receptor receptor.pdbqt | |
| 13 --ligand ligand.pdbqt | |
| 14 | |
| 15 #if $flex | |
| 16 --flex $flex | |
| 17 #end if | |
| 18 #if $flexres | |
| 19 --flexres $flexres | |
| 20 #end if | |
| 21 #if $flexdist_ligand | |
| 22 --flexdist_ligand $flexdist_ligand | |
| 23 #end if | |
| 24 #if $flexdist | |
| 25 --flexdist $flexdist | |
| 26 #end if | |
| 27 | |
| 28 --center_x $center_x | |
| 29 --center_y $center_y | |
| 30 --center_z $center_z | |
| 31 --size_x $size_x | |
| 32 --size_y $size_y | |
| 33 --size_z $size_z | |
| 34 | |
| 35 #if $autobox_ligand | |
| 36 --autobox_ligand $autobox_ligand | |
| 37 #end if | |
| 38 #if $autobox_add | |
| 39 --autobox_add $autobox_add | |
| 40 #end if | |
| 41 #if $no_lig=="true" | |
| 42 --no_lig | |
| 43 #end if | |
| 44 | |
| 45 --scoring $scoring | |
| 46 #if $custom_scoring | |
| 47 --custom_scoring $custom_scoring | |
| 48 #end if | |
| 49 #if $custom_atoms | |
| 50 --custom_atoms $custom_atoms | |
| 51 #end if | |
| 52 #if $score_only=="true" | |
| 53 --score_only | |
| 54 #end if | |
| 55 #if $local_only=="true" | |
| 56 --local_only | |
| 57 #end if | |
| 58 #if $minimize=="true" | |
| 59 --minimize | |
| 60 #end if | |
| 61 #if $randomize_only=="true" | |
| 62 --randomize_only | |
| 63 #end if | |
| 64 #if $minimize_iters | |
| 65 --minimize_iters $minimize_iters | |
| 66 #end if | |
| 67 | |
| 68 --seed 1000 > $output; | |
| 69 cat $output > /tmp/ouput | |
| 70 ]]> | |
| 71 </command> | |
| 72 <inputs> | |
| 73 <param name="receptor" type="data" format="pdbqt" label="receptor: rigid part of the receptore" /> | |
| 74 <param name="ligand" type="data" format="data" label="ligand: ligand(s)" /> | |
| 75 | |
| 76 <param name="flex" type="data" format="pdbqt" label="flex: flexible side chains, if any" optional="true" /> | |
| 77 <param name="flexres" type="text" label="flexres: flexible side chains specified by comma separated list of chain:resid" optional="true" /> | |
| 78 <param name="flexdist_ligand" type="data" format="data" label="flexdist_ligand: Ligand to use for flexdist" optional="true" /> | |
| 79 <param name="flexdist" type="float" label="flexdist: set all side chains within specified distance to flexdist_ligand to flexible" optional="true" /> | |
| 80 | |
| 81 <param name="center_x" type="float" value="0" label="center_x: X coordinate of the center" /> | |
| 82 <param name="center_y" type="float" value="0" label="center_y: Y coordinate of the center" /> | |
| 83 <param name="center_z" type="float" value="0" label="center_z: Z coordinate of the center" /> | |
| 84 <param name="size_x" type="integer" value="1" label="size_x: size in the X dimension" /> | |
| 85 <param name="size_y" type="integer" value="1" label="size_y: size in the Y dimension" /> | |
| 86 <param name="size_z" type="integer" value="1" label="size_z: size in the Z dimension" /> | |
| 87 | |
| 88 <param name="autobox_ligand" type="data" format="data" label="autobox_ligand: Ligand to use for autobox" optional="true" /> | |
| 89 <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" /> | |
| 90 <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"> | |
| 91 <option value="false" selected="true">Don't use this option</option> | |
| 92 <option value="true">Use this option</option> | |
| 93 </param> | |
| 94 | |
| 95 <param name="scoring" type="select" label="scoring: specify alternative builtin scoring function" optional="true"> | |
| 96 <option value="default" selected="true">default</option> | |
| 97 <option value="ad4_scoring">ad4_scoring</option> | |
| 98 <option value="dkoes_fast">dkoes_fast</option> | |
| 99 <option value="dkoes_scoring">dkoes_scoring</option> | |
| 100 <option value="dkoes_scoring_old">dkoes_scoring_old</option> | |
| 101 <option value="vina">vina</option> | |
| 102 <option value="vinardo">vinardo</option> | |
| 103 </param> | |
| 104 <param name="custom_scoring" type="data" format="data" label="custom_scoring: custom scoring function file" optional="true" /> | |
| 105 <param name="custom_atoms" type="data" format="data" label="custom_atoms: custom atom type parameters file" optional="true" /> | |
| 106 <param name="score_only" type="select" label="score_only: score provided ligand pose" optional="true"> | |
| 107 <option value="false" selected="true">Don't use this option</option> | |
| 108 <option value="true">Use this option</option> | |
| 109 </param> | |
| 110 <param name="local_only" type="select" label="local_only: local search only using autobox (you probably want to use --minimize)" optional="true"> | |
| 111 <option value="false" selected="true">Don't use this option</option> | |
| 112 <option value="true">Use this option</option> | |
| 113 </param> | |
| 114 <param name="minimize" type="select" label="minimize: energy minimization" optional="true"> | |
| 115 <option value="false" selected="true">Don't use this option</option> | |
| 116 <option value="true">Use this option</option> | |
| 117 </param> | |
| 118 <param name="randomize_only" type="select" label="randomize_only: generate random poses, attempting to avoid clashes" optional="true"> | |
| 119 <option value="false" selected="true">Don't use this option</option> | |
| 120 <option value="true">Use this option</option> | |
| 121 </param> | |
| 122 <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" /> | |
| 123 </inputs> | |
| 124 <outputs> | |
| 125 <data name="output" format="data" /> | |
| 126 </outputs> | |
| 127 <tests> | |
| 128 <test> | |
| 129 <param name="receptor" value="smina/protein.pdbqt" /> | |
| 130 <param name="ligand" value="smina/ligand.pdbqt" /> | |
| 131 <param name="center_x" value="11" /> | |
| 132 <param name="center_y" value="90.5" /> | |
| 133 <param name="center_z" value="57.5" /> | |
| 134 <param name="size_x" value="22" /> | |
| 135 <param name="size_y" value="24" /> | |
| 136 <param name="size_z" value="28" /> | |
| 137 <output name="output" file="smina/output_smina" /> | |
| 138 </test> | |
| 139 </tests> | |
| 140 <help> | |
| 141 "Smina help" | |
| 142 </help> | |
| 143 <citations> | |
| 144 <citation type="bibtex"> | |
| 145 @misc{renameTODO, author = {LastTODO, FirstTODO}, year = {TODO}, title = {TODO}, url = {https://sourceforge.net/projects/smina/}, } | |
| 146 </citation> | |
| 147 </citations> | |
| 148 </tool> |