Mercurial > repos > bgruening > autodock_vina_prepare_box

annotate prepare_box.xml @ 1:4f7c5cad3377 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:31:59 -0400
parents 761762031eee
children 73c2c9774c2d
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1 <tool id="prepare_box" name="Calculate the box parameters for an AutoDock Vina" version="0.1.0">
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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 '$__tool_directory__/calc_vina_box_params.py'
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9 --ligand '$input1'
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10 --config '$output1'
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11 --bufx '$bufx'
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12 --bufy '$bufy'
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13 --bufz '$bufz'
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14 --exh '$exh'
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15 #if $seed_value:
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16 --seed '$seed_value'
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17 #end if
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18 ]]></command>
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19 <inputs>
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20 <param type="data" name="input1" format="mol" label="Input ligand"
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21 help="The input ligand (mol file)"/>
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22 <param name="bufx" type="float" value="0" label="x-axis buffer"
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23 help="Buffer in the x direction (in angs.)"/>
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24 <param name="bufy" type="float" value="0" label="y-axis buffer"
1
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25 help="Buffer in the y direction (in angs.)"/>
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26 <param name="bufz" type="float" value="0" label="z-axis buffer"
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27 help="Buffer in the z direction (in angs.)"/>
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28 <param name="exh" type="integer" value="0" label="Exhaustiveness"
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29 help="Number of poses to return from docking job"/>
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30 <!-- <param name="seed" type="boolean" label="Specify random seed for simulation reproducibility?"/> -->
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31 <param type="integer" name="seed_value" optional="true" label="Random seed (optional)"
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32 help="Choose a seed value; if none is selected, a seed will be chosen randomly"/>
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33 </inputs>
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34 <outputs>
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35 <data name="output1" format="txt" />
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="input1" value="NUDT5A-x0114_2.mol" />
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40 <param name="bufx" value="1" />
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41 <param name="bufy" value="2" />
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42 <param name="bufz" value="3" />
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43 <param name="exh" value="10" />
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44 <param name="seed_value" value="1" />
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45 <output name="output1" file="box_params.txt" />
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46 </test>
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47 </tests>
1
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48 <help>
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49 <![CDATA[
0
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50
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51 .. class:: infomark
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52
1
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53 **Description**
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54
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55 This tool calculates a confounding box around an input ligand (mol file), and
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56 uses it to generate the input parameters for an autodock vina job.
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57
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58 The output file can be fed into the autodock vina tool as an alternative to creating the
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59 parameter file manually.
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60
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61 -----
1
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62
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63 .. class:: infomark
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64
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65 **Inputs:**
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66
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67 This tool requires:
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68
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69 * 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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70
1
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71 * (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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72
0
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74 -----
1
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75
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76 .. class:: infomark
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78 **Output:**
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79
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80 The output for this tool is a txt file containing the parameters needed to run an autodock
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81 vina docking calculation with the docking tool. For example: ::
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82
1
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83 size_x = 12.443000000000001
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84 size_y = 11.888
4f7c5cad3377 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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85 size_z = 9.290999999999997
4f7c5cad3377 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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86 center_x = -29.8395
4f7c5cad3377 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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87 center_y = 4.364
4f7c5cad3377 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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88 center_z = -64.5925
4f7c5cad3377 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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89 num_modes = 9999
4f7c5cad3377 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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90 energy_range = 9999
4f7c5cad3377 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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91 exhaustiveness = 10
4f7c5cad3377 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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92 cpu = 4
4f7c5cad3377 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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93 seed = 1
0
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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94
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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95 The values for num_modes, energy range, cpu and seed are set to default values here.
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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96
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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97 This file can be used as the box parameter for the docking tool.
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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98
1
4f7c5cad3377 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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99 ]]>
4f7c5cad3377 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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100 </help>
0
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101 <citations>
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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102 <citation type="bibtex">
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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103 @article{rdkit,
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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104 author = {Greg Landrum},
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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105 title = {RDKit: Open-source cheminformatics},
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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106 url ={http://www.rdkit.org}
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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107 }</citation>
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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108 </citations>
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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109 </tool>