Mercurial > repos > bgruening > autodock_vina_prepare_box

annotate prepare_box.xml @ 2:73c2c9774c2d draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
author bgruening
date Wed, 02 Oct 2019 12:49:11 -0400
parents 4f7c5cad3377
children 908880455b2d
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761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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1 <tool id="prepare_box" name="Calculate the box parameters for an AutoDock Vina" version="0.1.0">
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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2 <description>job from an input mol file (confounding box)</description>
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3 <requirements>
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4 <requirement type="package" version="2019.03.1.0">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'
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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10 --config '$output'
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11 --bufx '$bufx'
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12 --bufy '$bufy'
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13 --bufz '$bufz'
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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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14 #if $exh:
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15 --exh '$exh'
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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16 #end if
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17 #if $seed_value:
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18 --seed '$seed_value'
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19 #end if
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20 ]]></command>
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21 <inputs>
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22 <param type="data" name="ligand" format="mol" label="Input ligand"
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761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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23 help="The input ligand (mol file)"/>
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24 <param name="bufx" type="float" value="0" label="x-axis buffer"
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25 help="Buffer in the x direction (in angs.)"/>
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26 <param name="bufy" type="float" value="0" label="y-axis buffer"
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27 help="Buffer in the y direction (in angs.)"/>
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28 <param name="bufz" type="float" value="0" label="z-axis buffer"
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29 help="Buffer in the z direction (in angs.)"/>
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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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30 <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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31 help="Exhaustiveness of global search (optional, default = 8)"/>
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32 <param type="integer" name="seed_value" optional="true" label="Random seed (optional)"
4f7c5cad3377 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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33 help="Choose a seed value; if none is selected, a seed will be chosen randomly"/>
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34 </inputs>
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35 <outputs>
2
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36 <data name="output" format="txt" />
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37 </outputs>
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38 <tests>
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39 <test>
2
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40 <param name="ligand" value="NUDT5A-x0114_2.mol" />
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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41 <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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42 <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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43 <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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44 <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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45 </test>
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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46 <test>
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47 <param name="ligand" value="NUDT5A-x0114_2.mol" />
0
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48 <param name="bufx" value="1" />
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49 <param name="bufy" value="2" />
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50 <param name="bufz" value="3" />
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51 <param name="exh" value="10" />
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52 <param name="seed_value" value="1" />
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53 <output name="output" file="box_params_2.txt" />
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54 </test>
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55 </tests>
1
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56 <help>
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57 <![CDATA[
0
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58
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59 .. class:: infomark
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60
1
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61 **Description**
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62
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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63 This tool calculates a confounding box around an input ligand (mol file), and
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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64 uses it to generate the input parameters for an autodock vina job.
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65
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66 The output file can be fed into the autodock vina tool as an alternative to creating the
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67 parameter file manually.
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68
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69 -----
1
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70
0
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71 .. class:: infomark
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73 **Inputs:**
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75 This tool requires:
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77 * An input ligand - This should be a mol file representing the ligand you wish to dock. This should be derived from the file you use to prepare the ligand for the docking job (see prepare ligand tool).
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78
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79 * (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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82 -----
1
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83
0
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84 .. class:: infomark
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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85
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86 **Output:**
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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87
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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88 The output for this tool is a txt file containing the parameters needed to run an autodock
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89 vina docking calculation with the docking tool. For example: ::
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761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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90
1
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91 size_x = 12.443000000000001
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92 size_y = 11.888
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93 size_z = 9.290999999999997
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94 center_x = -29.8395
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95 center_y = 4.364
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96 center_z = -64.5925
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97 num_modes = 9999
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98 energy_range = 9999
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99 exhaustiveness = 10
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100 cpu = 4
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101 seed = 1
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102
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103 The values for num_modes, energy range, cpu and seed are set to default values here.
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104
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105 This file can be used as the box parameter for the docking tool.
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106
1
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107 ]]>
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108 </help>
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109 <citations>
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110 <citation type="bibtex">
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111 @article{rdkit,
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112 author = {Greg Landrum},
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113 title = {RDKit: Open-source cheminformatics},
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114 url ={http://www.rdkit.org}
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115 }</citation>
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116 </citations>
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117 </tool>