Mercurial > repos > bgruening > autodock_vina_prepare_box

annotate prepare_box.xml @ 6:8f766d9652a2 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 15694de1df8abe053d0fa0953262dfef419d2936"
author bgruening
date Wed, 01 Sep 2021 09:38:09 +0000
parents 668c60aa4799
children
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ad35eaa204ea "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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1 <tool id="prepare_box" name="Calculate the box parameters using RDKit" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
ad35eaa204ea "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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2 <macros>
6
8f766d9652a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 15694de1df8abe053d0fa0953262dfef419d2936"
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3 <token name="@TOOL_VERSION@">2021.03.5</token>
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ad35eaa204ea "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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4 <token name="@GALAXY_VERSION@">0</token>
ad35eaa204ea "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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5 </macros>
6
8f766d9652a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 15694de1df8abe053d0fa0953262dfef419d2936"
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6 <description>for an AutoDock Vina job from a ligand or pocket input file (confounding box)</description>
0
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7 <requirements>
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ad35eaa204ea "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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8 <requirement type="package" version="@TOOL_VERSION@">rdkit</requirement>
ad35eaa204ea "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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9 <requirement type="package" version="1.19.1">numpy</requirement>
0
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10 </requirements>
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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11 <command detect_errors="exit_code"><![CDATA[
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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12 python '$__tool_directory__/calc_vina_box_params.py'
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73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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13 --ligand '$ligand'
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14 --ftype '${ligand.ext}'
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73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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15 --config '$output'
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16 --bufx '$bufx'
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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17 --bufy '$bufy'
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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18 --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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19 #if $exh:
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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20 --exh '$exh'
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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21 #end if
1
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22 #if $seed_value:
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23 --seed '$seed_value'
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24 #end if
0
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25 ]]></command>
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26 <inputs>
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8f766d9652a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 15694de1df8abe053d0fa0953262dfef419d2936"
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27 <param type="data" name="ligand" format="mol,sdf,pdb,mol2" label="Input ligand or pocket"
8f766d9652a2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 15694de1df8abe053d0fa0953262dfef419d2936"
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28 help="The input ligand or pocket with three-dimensional coordinates (MOL, SDF, PDB and MOL formats supported)."/>
0
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29 <param name="bufx" type="float" value="0" label="x-axis buffer"
1
4f7c5cad3377 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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30 help="Buffer in the x direction (in angs.)"/>
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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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31 <param name="bufy" type="float" value="0" label="y-axis buffer"
1
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32 help="Buffer in the y direction (in angs.)"/>
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33 <param name="bufz" type="float" value="0" label="z-axis buffer"
1
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34 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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35 <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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36 help="Exhaustiveness of global search (optional, default = 8)"/>
1
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37 <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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38 help="Choose a seed value; if none is selected, a seed will be chosen randomly"/>
0
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39 </inputs>
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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40 <outputs>
2
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41 <data name="output" format="txt" />
0
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42 </outputs>
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43 <tests>
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44 <test>
3
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45 <param name="ligand" value="NUDT5A-x0114_2.mol" ftype="mol"/>
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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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46 <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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47 <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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48 <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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49 <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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50 </test>
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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51 <test>
3
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52 <param name="ligand" value="NUDT5A-x0114_2.sdf" ftype="sdf"/>
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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53 <param name="bufx" value="1" />
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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54 <param name="bufy" value="2" />
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55 <param name="bufz" value="3" />
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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56 <param name="exh" value="10" />
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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57 <param name="seed_value" value="1" />
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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58 <output name="output" file="box_params_2.txt" />
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59 </test>
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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60 <test>
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61 <param name="ligand" value="NUDT5A-x0114_2.mol2"/>
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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62 <param name="bufx" value="1" />
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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63 <param name="bufy" value="2" />
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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64 <param name="bufz" value="3" />
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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65 <output name="output" file="box_params_1.txt" />
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66 </test>
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67 <test>
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68 <param name="ligand" value="NUDT5A-x0114_2.pdb" ftype="pdb"/>
0
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69 <param name="bufx" value="1" />
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70 <param name="bufy" value="2" />
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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71 <param name="bufz" value="3" />
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72 <param name="exh" value="10" />
1
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73 <param name="seed_value" value="1" />
2
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74 <output name="output" file="box_params_2.txt" />
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75 </test>
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76 </tests>
1
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77 <help>
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78 <![CDATA[
0
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79
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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80 .. class:: infomark
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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81
1
4f7c5cad3377 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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82 **Description**
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83
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84 This tool calculates a confounding box around an input ligand or pocket and
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85 uses it to generate the input parameters for an AutoDock Vina job.
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86
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87 If you already know the coordinates of a ligand which binds to the protein, you can simply
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88 use this file as the tool input. Alternatively, you can search for pockets using the fpocket
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89 tool and use one of the output PDB files as an input.
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90
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91 The output file can be fed into the AutoDock Vina tool as an alternative to creating the
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92 parameter file manually.
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94 -----
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95
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96 .. class:: infomark
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98 **Inputs:**
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100 This tool requires:
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101
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102 * An input file (MOL, SDF, PDB or MOL2 format) representing either a ligand, or a pocket found with the fpocket tool.
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103
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104 * (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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105
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106
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107 -----
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108
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109 .. class:: infomark
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110
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111 **Output:**
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112
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113 The output for this tool is a txt file containing the parameters needed to run an autodock
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114 vina docking calculation with the docking tool. For example: ::
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115
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116 size_x = 12.443000000000001
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117 size_y = 11.888
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118 size_z = 9.290999999999997
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119 center_x = -29.8395
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120 center_y = 4.364
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121 center_z = -64.5925
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122 num_modes = 9999
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123 energy_range = 9999
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124 exhaustiveness = 10
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125 cpu = 4
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126 seed = 1
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127
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128 The values for num_modes, energy range, cpu and seed are set to default values here.
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129
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130 This file can be used as the box parameter for the docking tool.
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131
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132 ]]>
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133 </help>
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134 <citations>
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135 <citation type="bibtex">
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136 @article{rdkit,
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137 author = {Greg Landrum},
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138 title = {RDKit: Open-source cheminformatics},
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139 url ={http://www.rdkit.org}
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140 }</citation>
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141 </citations>
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142 </tool>