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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Docking]-->
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4 <tool id="GridBuilder" name="GridBuilder" version="1.1.0">
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5 <description>create score-grids for docking</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">GridBuilder</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="stdio"/>
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11 <expand macro="requirements"/>
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12 <command>GridBuilder
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13
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14 #if $param_rec:
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15 -rec $param_rec
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16 #end if
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17 #if $param_rl:
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18 -rl $param_rl
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19 #end if
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20 #if $param_grd:
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21 -grd $param_grd
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22 #end if
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23 #if $param_pocket:
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24 -pocket $param_pocket
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25 #end if
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26 #if $adv_opts.adv_opts_selector=='advanced':
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27 #if $adv_opts.param_ScoringFunction_filename:
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28 -ScoringFunction:filename $adv_opts.param_ScoringFunction_filename
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29 #end if
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30 #if $adv_opts.param_ScoringFunction_electrostatic_cuton:
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31 -ScoringFunction:electrostatic_cuton $adv_opts.param_ScoringFunction_electrostatic_cuton
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32 #end if
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33 #if $adv_opts.param_ScoringFunction_electrostatic_cutoff:
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34 -ScoringFunction:electrostatic_cutoff $adv_opts.param_ScoringFunction_electrostatic_cutoff
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35 #end if
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36 #if $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap:
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37 -ScoringFunction:allowed_intermolecular_overlap $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap
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38 #end if
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39 #if $adv_opts.param_ScoringFunction_ignore_H_clashes:
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40 -ScoringFunction:ignore_H_clashes
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41 #end if
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42 #if $adv_opts.param_ScoringFunction_atom_types:
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43 -ScoringFunction:atom_types "$adv_opts.param_ScoringFunction_atom_types"
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44 #end if
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45 #if $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap:
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46 -ScoringFunction:allowed_intramolecular_overlap $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap
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47 #end if
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48 #if $adv_opts.param_ScoringFunction_burial_depth_scale:
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49 -ScoringFunction:burial_depth_scale $adv_opts.param_ScoringFunction_burial_depth_scale
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50 #end if
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51 #if $adv_opts.param_ScoringFunction_vdw_cutoff:
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52 -ScoringFunction:vdw_cutoff $adv_opts.param_ScoringFunction_vdw_cutoff
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53 #end if
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54 #if $adv_opts.param_ScoringFunction_nonbonded_cutoff:
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55 -ScoringFunction:nonbonded_cutoff $adv_opts.param_ScoringFunction_nonbonded_cutoff
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56 #end if
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57 #if $adv_opts.param_ScoringFunction_hashgrid_size:
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58 -ScoringFunction:hashgrid_size $adv_opts.param_ScoringFunction_hashgrid_size
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59 #end if
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60 #if $adv_opts.param_ScoringFunction_vdw_cuton:
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61 -ScoringFunction:vdw_cuton $adv_opts.param_ScoringFunction_vdw_cuton
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62 #end if
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63 #if $adv_opts.param_ScoringFunction_hashgrid_resolution:
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64 -ScoringFunction:hashgrid_resolution $adv_opts.param_ScoringFunction_hashgrid_resolution
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65 #end if
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66 #end if
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67 </command>
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68 <inputs>
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69 <param name="param_rec" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="receptor pdb-file" help="(-rec) "/>
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70 <param name="param_rl" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="reference-ligand" help="(-rl) "/>
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71 <param name="param_pocket" type="data" format="ini" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="configuration file" help="(-pocket) "/>
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72 <expand macro="advanced_options">
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73 <param name="param_ScoringFunction_filename" type="data" format="ini" optional="True" value="Amber/amber96-docking.ini" label="file with electrostatics and vdW parameters" help="(-filename) "/>
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74 <param name="param_ScoringFunction_electrostatic_cuton" type="float" value="17.0" label="electrostatic cuton" help="(-electrostatic_cuton) "/>
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75 <param name="param_ScoringFunction_electrostatic_cutoff" type="float" value="20.0" label="electrostatic cutoff" help="(-electrostatic_cutoff) "/>
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76 <param name="param_ScoringFunction_allowed_intermolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intermolecular atom-overlap" help="(-allowed_intermolecular_overlap) "/>
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77 <param name="param_ScoringFunction_ignore_H_clashes" type="boolean" truevalue="-ScoringFunction:ignore_H_clashes" falsevalue="" checked="true" optional="True" label="ignore clashes involving hydrogens" help="(-ignore_H_clashes) "/>
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78 <param name="param_ScoringFunction_atom_types" type="text" size="30" value="C, H, N, O, P, S, Cl, F, I" label="elements for which grids should be precalculated" help="(-atom_types) ">
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79 <sanitizer>
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80 <valid initial="string.printable">
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81 <remove value="'"/>
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82 <remove value="""/>
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83 </valid>
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84 </sanitizer>
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85 </param>
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86 <param name="param_ScoringFunction_allowed_intramolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intramolecular atom-overlap" help="(-allowed_intramolecular_overlap) "/>
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87 <param name="param_ScoringFunction_burial_depth_scale" type="float" min="1.0" max="5.0" optional="True" value="1.0" label="relative-depth-of-burial scale" help="(-burial_depth_scale) "/>
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88 <param name="param_ScoringFunction_vdw_cutoff" type="float" value="20.0" label="vdw cutoff" help="(-vdw_cutoff) "/>
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89 <param name="param_ScoringFunction_nonbonded_cutoff" type="float" value="20.0" label="nonbonded cutoff" help="(-nonbonded_cutoff) "/>
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90 <param name="param_ScoringFunction_hashgrid_size" type="integer" value="10" label="hashgrid size (num of boxes)" help="(-hashgrid_size) "/>
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91 <param name="param_ScoringFunction_vdw_cuton" type="float" value="17.0" label="vdw cuton" help="(-vdw_cuton) "/>
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92 <param name="param_ScoringFunction_hashgrid_resolution" type="integer" min="1" max="5" optional="True" value="3" label="hashgrid resolution" help="(-hashgrid_resolution) "/>
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93 </expand>
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94 </inputs>
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95 <outputs>
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96 <data name="param_grd" format="bngrd"/>
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97 </outputs>
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98 <help>This tool precalculates a score-grid for a binding pocket of a given receptor.
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99
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100 As input we need:
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101 * a file containing a protonated protein in pdb-format
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102 * a file containing a reference ligand.
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103 This reference ligand should be located in the binding pocket,
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104 so that a grid can be precalculated around it.
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105 Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
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106
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107 Output of this tool is a file containing the score-grids that can be used by docking-/scoring-tools (e.g. IMeedyDock).
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108
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109 </help>
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110 </tool>
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