Mercurial > repos > bgruening > autodock_vina_prepare_box

comparison prepare_box.xml @ 0:761762031eee draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children 4f7c5cad3377
comparison
equal deleted inserted replaced
-1:000000000000 0:761762031eee
1 <tool id="prepare_box" name="Calculate the box parameters for an AutoDock Vina" version="0.1.0">
2 <description>job from an input mol file (confounding box)</description>
3 <requirements>
4 <requirement type="package" version="2019.03.1.0">rdkit</requirement>
5 <requirement type="package" version="1.16.2">numpy</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8 python '$__tool_directory__/calc_vina_box_params.py'
9 --ligand '$input1'
10 --config '$output1'
11 --bufx '$bufx'
12 --bufy '$bufy'
13 --bufz '$bufz'
14 --exh '$exh'
15 ]]></command>
16 <inputs>
17 <param type="data" name="input1" format="mol" label="input ligand mol file"
18 help="The input ligand (mol file)"/>
19 <param name="bufx" type="float" value="0" label="x-axis buffer"
20 help="the buffer in the x direction (in angs.)"/>
21 <param name="bufy" type="float" value="0" label="y-axis buffer"
22 help="the buffer in the y direction (in angs.)"/>
23 <param name="bufz" type="float" value="0" label="z-axis buffer"
24 help="the buffer in the z direction (in angs.)"/>
25 <param name="exh" type="integer" value="0" label="exhaustiveness"
26 help="The number of poses to return from docking job"/>
27 </inputs>
28 <outputs>
29 <data name="output1" format="txt" />
30 </outputs>
31 <tests>
32 <test>
33 <param name="input1" value="NUDT5A-x0114_2.mol" />
34 <param name="bufx" value="1" />
35 <param name="bufy" value="2" />
36 <param name="bufz" value="3" />
37 <param name="exh" value="10" />
38 <output name="output1" file="box_params.txt" />
39 </test>
40 </tests>
41 <help><![CDATA[
42
43 .. class:: infomark
44
45 **Description:**
46
47 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.
49
50 The output file can be fed into the autodock vina tool as an alternative to creating the
51 parameter file manually.
52
53 -----
54 .. class:: infomark
55
56 **Inputs:**
57
58 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
63 * OPTIONAL Buffers for each direction (x,y,z), which defaults to 0 angstroms. This value
64 will be added to the confounding box that the tool generates in each respective direction.
65 We recommend that you visualise the calculated box from an initial run of this tool, and
66 calculate the expansion needed in each direction to cover the area of the binding site
67 you wish to explore.
68
69 -----
70 .. class:: infomark
71
72 **Output:**
73
74 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:
76
77 size_x = 12.443000000000001
78 size_y = 11.888
79 size_z = 9.290999999999997
80 center_x = -29.8395
81 center_y = 4.364
82 center_z = -64.5925
83 num_modes = 9999
84 energy_range = 9999
85 exhaustiveness = 10
86 cpu = 4
87 seed = 1
88
89 The values for num_modes, energy range, cpu and seed are set to default values here.
90
91 This file can be used as the box parameter for the docking tool.
92
93 ]]></help>
94 <citations>
95 <citation type="bibtex">
96 @article{rdkit,
97 author = {Greg Landrum},
98 title = {RDKit: Open-source cheminformatics},
99 url ={http://www.rdkit.org}
100 }</citation>
101 </citations>
102 </tool>