Mercurial > repos > bgruening > autodock_vina_prepare_box

comparison 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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0:761762031eee 1:4f7c5cad3377
10 --config '$output1' 10 --config '$output1'
11 --bufx '$bufx' 11 --bufx '$bufx'
12 --bufy '$bufy' 12 --bufy '$bufy'
13 --bufz '$bufz' 13 --bufz '$bufz'
14 --exh '$exh' 14 --exh '$exh'
15 #if $seed_value:
16 --seed '$seed_value'
17 #end if
15 ]]></command> 18 ]]></command>
16 <inputs> 19 <inputs>
17 <param type="data" name="input1" format="mol" label="input ligand mol file" 20 <param type="data" name="input1" format="mol" label="Input ligand"
18 help="The input ligand (mol file)"/> 21 help="The input ligand (mol file)"/>
19 <param name="bufx" type="float" value="0" label="x-axis buffer" 22 <param name="bufx" type="float" value="0" label="x-axis buffer"
20 help="the buffer in the x direction (in angs.)"/> 23 help="Buffer in the x direction (in angs.)"/>
21 <param name="bufy" type="float" value="0" label="y-axis buffer" 24 <param name="bufy" type="float" value="0" label="y-axis buffer"
22 help="the buffer in the y direction (in angs.)"/> 25 help="Buffer in the y direction (in angs.)"/>
23 <param name="bufz" type="float" value="0" label="z-axis buffer" 26 <param name="bufz" type="float" value="0" label="z-axis buffer"
24 help="the buffer in the z direction (in angs.)"/> 27 help="Buffer in the z direction (in angs.)"/>
25 <param name="exh" type="integer" value="0" label="exhaustiveness" 28 <param name="exh" type="integer" value="0" label="Exhaustiveness"
26 help="The number of poses to return from docking job"/> 29 help="Number of poses to return from docking job"/>
30 <!-- <param name="seed" type="boolean" label="Specify random seed for simulation reproducibility?"/> -->
31 <param type="integer" name="seed_value" optional="true" label="Random seed (optional)"
32 help="Choose a seed value; if none is selected, a seed will be chosen randomly"/>
27 </inputs> 33 </inputs>
28 <outputs> 34 <outputs>
29 <data name="output1" format="txt" /> 35 <data name="output1" format="txt" />
30 </outputs> 36 </outputs>
31 <tests> 37 <tests>
33 <param name="input1" value="NUDT5A-x0114_2.mol" /> 39 <param name="input1" value="NUDT5A-x0114_2.mol" />
34 <param name="bufx" value="1" /> 40 <param name="bufx" value="1" />
35 <param name="bufy" value="2" /> 41 <param name="bufy" value="2" />
36 <param name="bufz" value="3" /> 42 <param name="bufz" value="3" />
37 <param name="exh" value="10" /> 43 <param name="exh" value="10" />
44 <param name="seed_value" value="1" />
38 <output name="output1" file="box_params.txt" /> 45 <output name="output1" file="box_params.txt" />
39 </test> 46 </test>
40 </tests> 47 </tests>
41 <help><![CDATA[ 48 <help>
49 <![CDATA[
42 50
43 .. class:: infomark 51 .. class:: infomark
44 52
45 **Description:** 53 **Description**
46 54
47 This tool calculates a confounding box around an input ligand (mol file), and 55 This tool calculates a confounding box around an input ligand (mol file), and
48 uses it to generate the input parameters for an autodock vina job. 56 uses it to generate the input parameters for an autodock vina job.
49 57
50 The output file can be fed into the autodock vina tool as an alternative to creating the 58 The output file can be fed into the autodock vina tool as an alternative to creating the
51 parameter file manually. 59 parameter file manually.
52 60
53 ----- 61 -----
62
54 .. class:: infomark 63 .. class:: infomark
55 64
56 **Inputs:** 65 **Inputs:**
57 66
58 This tool requires: 67 This tool requires:
59 * An input ligand - This should be a mol file representing the ligand you wish to dock.
60 This should be derived from the file you use to prepare the ligand for the docking job
61 (see prepare ligand tool).
62 68
63 * OPTIONAL Buffers for each direction (x,y,z), which defaults to 0 angstroms. This value 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).
64 will be added to the confounding box that the tool generates in each respective direction. 70
65 We recommend that you visualise the calculated box from an initial run of this tool, and 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.
66 calculate the expansion needed in each direction to cover the area of the binding site 72
67 you wish to explore.
68 73
69 ----- 74 -----
75
70 .. class:: infomark 76 .. class:: infomark
71 77
72 **Output:** 78 **Output:**
73 79
74 The output for this tool is a txt file containing the parameters needed to run an autodock 80 The output for this tool is a txt file containing the parameters needed to run an autodock
75 vina docking calculation with the docking tool. For example: 81 vina docking calculation with the docking tool. For example: ::
76 82
77 size_x = 12.443000000000001 83 size_x = 12.443000000000001
78 size_y = 11.888 84 size_y = 11.888
79 size_z = 9.290999999999997 85 size_z = 9.290999999999997
80 center_x = -29.8395 86 center_x = -29.8395
81 center_y = 4.364 87 center_y = 4.364
82 center_z = -64.5925 88 center_z = -64.5925
83 num_modes = 9999 89 num_modes = 9999
84 energy_range = 9999 90 energy_range = 9999
85 exhaustiveness = 10 91 exhaustiveness = 10
86 cpu = 4 92 cpu = 4
87 seed = 1 93 seed = 1
88 94
89 The values for num_modes, energy range, cpu and seed are set to default values here. 95 The values for num_modes, energy range, cpu and seed are set to default values here.
90 96
91 This file can be used as the box parameter for the docking tool. 97 This file can be used as the box parameter for the docking tool.
92 98
93 ]]></help> 99 ]]>
100 </help>
94 <citations> 101 <citations>
95 <citation type="bibtex"> 102 <citation type="bibtex">
96 @article{rdkit, 103 @article{rdkit,
97 author = {Greg Landrum}, 104 author = {Greg Landrum},
98 title = {RDKit: Open-source cheminformatics}, 105 title = {RDKit: Open-source cheminformatics},