Mercurial > repos > bgruening > autodock_vina_prepare_box

annotate prepare_box.xml @ 0:761762031eee draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
author bgruening
date Wed, 17 Apr 2019 09:11:01 -0400
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children 4f7c5cad3377
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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 '$__tool_directory__/calc_vina_box_params.py'
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9 --ligand '$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 ]]></command>
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16 <inputs>
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17 <param type="data" name="input1" format="mol" label="input ligand mol file"
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18 help="The input ligand (mol file)"/>
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19 <param name="bufx" type="float" value="0" label="x-axis buffer"
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20 help="the buffer in the x direction (in angs.)"/>
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21 <param name="bufy" type="float" value="0" label="y-axis buffer"
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22 help="the buffer in the y direction (in angs.)"/>
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23 <param name="bufz" type="float" value="0" label="z-axis buffer"
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24 help="the buffer in the z direction (in angs.)"/>
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25 <param name="exh" type="integer" value="0" label="exhaustiveness"
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26 help="The number of poses to return from docking job"/>
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27 </inputs>
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28 <outputs>
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29 <data name="output1" format="txt" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="input1" value="NUDT5A-x0114_2.mol" />
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34 <param name="bufx" value="1" />
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35 <param name="bufy" value="2" />
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36 <param name="bufz" value="3" />
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37 <param name="exh" value="10" />
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38 <output name="output1" file="box_params.txt" />
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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39 </test>
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40 </tests>
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41 <help><![CDATA[
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42
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43 .. class:: infomark
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44
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45 **Description:**
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46
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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47 This tool calculates a confounding box around an input ligand (mol file), and
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48 uses it to generate the input parameters for an autodock vina job.
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49
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50 The output file can be fed into the autodock vina tool as an alternative to creating the
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51 parameter file manually.
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52
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53 -----
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54 .. class:: infomark
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55
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56 **Inputs:**
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57
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58 This tool requires:
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59 * An input ligand - This should be a mol file representing the ligand you wish to dock.
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60 This should be derived from the file you use to prepare the ligand for the docking job
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61 (see prepare ligand tool).
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62
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63 * OPTIONAL Buffers for each direction (x,y,z), which defaults to 0 angstroms. This value
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64 will be added to the confounding box that the tool generates in each respective direction.
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65 We recommend that you visualise the calculated box from an initial run of this tool, and
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66 calculate the expansion needed in each direction to cover the area of the binding site
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67 you wish to explore.
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68
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69 -----
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70 .. class:: infomark
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71
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72 **Output:**
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73
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74 The output for this tool is a txt file containing the parameters needed to run an autodock
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75 vina docking calculation with the docking tool. For example:
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76
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77 size_x = 12.443000000000001
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78 size_y = 11.888
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79 size_z = 9.290999999999997
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80 center_x = -29.8395
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81 center_y = 4.364
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82 center_z = -64.5925
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83 num_modes = 9999
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84 energy_range = 9999
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85 exhaustiveness = 10
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86 cpu = 4
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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87 seed = 1
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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88
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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89 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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90
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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91 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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92
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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93 ]]></help>
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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94 <citations>
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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95 <citation type="bibtex">
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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96 @article{rdkit,
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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97 author = {Greg Landrum},
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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98 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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99 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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100 }</citation>
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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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 </tool>