Mercurial > repos > bgruening > autodock_vina_prepare_box

annotate prepare_box.xml @ 3:908880455b2d draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
author bgruening
date Fri, 18 Oct 2019 04:57:34 -0400
parents 73c2c9774c2d
children ad35eaa204ea
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3
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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1 <tool id="prepare_box" name="Calculate the box parameters for an AutoDock Vina" version="0.1.1">
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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2 <description>job from a ligand input file (confounding box)</description>
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3 <requirements>
3
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4 <requirement type="package" version="2019.03.1">rdkit</requirement>
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5 <requirement type="package" version="1.16.2">numpy</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 python '$__tool_directory__/calc_vina_box_params.py'
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73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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9 --ligand '$ligand'
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10 --ftype '${ligand.ext}'
2
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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11 --config '$output'
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12 --bufx '$bufx'
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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13 --bufy '$bufy'
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14 --bufz '$bufz'
2
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15 #if $exh:
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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16 --exh '$exh'
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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17 #end if
1
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18 #if $seed_value:
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19 --seed '$seed_value'
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20 #end if
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21 ]]></command>
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22 <inputs>
3
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23 <param type="data" name="ligand" format="mol,sdf,pdb,mol2" label="Input ligand"
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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24 help="The input ligand with three-dimensional coordinates (MOL, SDF, PDB and MOL formats supported)."/>
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25 <param name="bufx" type="float" value="0" label="x-axis buffer"
1
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26 help="Buffer in the x direction (in angs.)"/>
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27 <param name="bufy" type="float" value="0" label="y-axis buffer"
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28 help="Buffer in the y direction (in angs.)"/>
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29 <param name="bufz" type="float" value="0" label="z-axis buffer"
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30 help="Buffer in the z direction (in angs.)"/>
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31 <param name="exh" type="integer" optional="true" label="Exhaustiveness (optional)"
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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32 help="Exhaustiveness of global search (optional, default = 8)"/>
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33 <param type="integer" name="seed_value" optional="true" label="Random seed (optional)"
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34 help="Choose a seed value; if none is selected, a seed will be chosen randomly"/>
0
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35 </inputs>
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36 <outputs>
2
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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37 <data name="output" format="txt" />
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38 </outputs>
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39 <tests>
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40 <test>
3
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41 <param name="ligand" value="NUDT5A-x0114_2.mol" ftype="mol"/>
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42 <param name="bufx" value="1" />
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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43 <param name="bufy" value="2" />
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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44 <param name="bufz" value="3" />
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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45 <output name="output" file="box_params_1.txt" />
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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46 </test>
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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47 <test>
3
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48 <param name="ligand" value="NUDT5A-x0114_2.sdf" ftype="sdf"/>
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49 <param name="bufx" value="1" />
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50 <param name="bufy" value="2" />
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51 <param name="bufz" value="3" />
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52 <param name="exh" value="10" />
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53 <param name="seed_value" value="1" />
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54 <output name="output" file="box_params_2.txt" />
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55 </test>
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56 <test>
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57 <param name="ligand" value="NUDT5A-x0114_2.mol2"/>
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58 <param name="bufx" value="1" />
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59 <param name="bufy" value="2" />
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60 <param name="bufz" value="3" />
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61 <output name="output" file="box_params_1.txt" />
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62 </test>
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63 <test>
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64 <param name="ligand" value="NUDT5A-x0114_2.pdb" ftype="pdb"/>
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65 <param name="bufx" value="1" />
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66 <param name="bufy" value="2" />
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67 <param name="bufz" value="3" />
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68 <param name="exh" value="10" />
1
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69 <param name="seed_value" value="1" />
2
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70 <output name="output" file="box_params_2.txt" />
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71 </test>
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72 </tests>
1
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73 <help>
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74 <![CDATA[
0
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75
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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76 .. class:: infomark
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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77
1
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78 **Description**
0
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79
3
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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80 This tool calculates a confounding box around an input ligand and
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81 uses it to generate the input parameters for an autodock vina job.
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82
3
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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83 The output file can be fed into the AutoDock Vina tool as an alternative to creating the
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84 parameter file manually.
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85
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86 -----
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87
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88 .. class:: infomark
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89
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90 **Inputs:**
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91
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92 This tool requires:
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93
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908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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94 * An input ligand - This should be a file (MOL, SDF, PDB or MOL2 format) representing the ligand you wish to dock.
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95
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96 * (OPTIONAL) Buffers for each direction (x,y,z), which defaults to 0 Å. This value will be added to the confounding box that the tool generates in each respective direction. We recommend that you visualise the calculated box from an initial run of this tool, and calculate the expansion needed in each direction to cover the area of the binding site you wish to explore.
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97
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98
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99 -----
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100
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101 .. class:: infomark
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102
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103 **Output:**
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104
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105 The output for this tool is a txt file containing the parameters needed to run an autodock
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106 vina docking calculation with the docking tool. For example: ::
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107
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108 size_x = 12.443000000000001
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109 size_y = 11.888
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110 size_z = 9.290999999999997
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111 center_x = -29.8395
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112 center_y = 4.364
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113 center_z = -64.5925
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114 num_modes = 9999
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115 energy_range = 9999
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116 exhaustiveness = 10
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117 cpu = 4
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118 seed = 1
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119
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120 The values for num_modes, energy range, cpu and seed are set to default values here.
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121
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122 This file can be used as the box parameter for the docking tool.
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123
1
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124 ]]>
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125 </help>
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126 <citations>
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127 <citation type="bibtex">
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128 @article{rdkit,
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129 author = {Greg Landrum},
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130 title = {RDKit: Open-source cheminformatics},
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131 url ={http://www.rdkit.org}
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132 }</citation>
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133 </citations>
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134 </tool>