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comparison docking.xml @ 5:c410ffcabf9d 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 13:31:43 -0400
parents 3c8e86318a81
children 0ae768a0e5c0
comparison
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4:3c8e86318a81 5:c410ffcabf9d
1 <tool id="docking" name="Docking" version="0.1.0"> 1 <tool id="docking" name="Docking" version="0.2.0">
2 <description>Tool to running molecular docking with Autodock Vina</description> 2 <description>tool to perform protein-ligand docking with Autodock Vina</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.2">autodock-vina</requirement> 4 <requirement type="package" version="1.1.2">autodock-vina</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1" /> 7 <exit_code range="1" />
8 </stdio> 8 </stdio>
9 <command><![CDATA[ 9 <command><![CDATA[
10 vina --config "$box" --receptor "$receptor" --ligand "$ligand" --out "$file_output1" --log "$file_output2" 10 #if $config_params.config_params == 'vals':
11 vina
12 --center_x '$config_params.center_x'
13 --center_y '$config_params.center_y'
14 --center_z '$config_params.center_z'
15 --size_x '$config_params.size_x'
16 --size_y '$config_params.size_y'
17 --size_z '$config_params.size_z'
18 --exhaustiveness '$config_params.exh'
19 --num_modes 9999
20 --energy_range 9999
21 --receptor '$receptor'
22 --ligand '$ligand'
23 --out '$file_output1'
24 --log '$file_output2'
25 --cpu \${GALAXY_SLOTS:-1}
26 #if $config_params.seed.seed == 'true':
27 --seed '$config_params.seed.seed_value'
28 #end if
29 #end if
30 #if $config_params.config_params == 'file':
31 vina
32 --config '$config_params.box'
33 --receptor '$receptor'
34 --ligand '$ligand'
35 --out '$file_output1'
36 --log '$file_output2'
37 --cpu \${GALAXY_SLOTS:-1}
38
39 #end if
40
11 ]]></command> 41 ]]></command>
12 <inputs> 42 <inputs>
13 <param type="data" name="box" format="txt" label="Box configuration" help="Select a text file with the box configurations" /> 43 <param type="data" name="receptor" format="pdbqt" label="Receptor" help="Select a receptor (PDBQT format). This can be prepared using the receptor preparation tool." />
14 <param type="data" name="receptor" format="pdbqt" label="Receptor" help="Select a receptor PDBQT format. This can be prepared using the receptor preparation tool." /> 44 <param type="data" name="ligand" format="pdbqt" label="Ligand" help="Select a ligand (PDBQT format). This can be prepared using the ligand preparation tool." />
15 <param type="data" name="ligand" format="pdbqt" label="Ligand" help="Select a ligand PDBQT format. This can be prepared using the ligand preparation tool." /> 45 <conditional name="config_params">
46 <param name="config_params" type="select" label="Specify parameters">
47 <option value="file">Upload a config file to specify parameters</option>
48 <option value="vals">Specify values directly</option>
49 </param>
50 <when value="vals">
51 <param type="float" name="center_x" label="x coordinate" help="x coordinate of the binding site." value="0"/>
52 <param type="float" name="center_y" label="y coordinate" help="y coordinate of the binding site." value="0"/>
53 <param type="float" name="center_z" label="z coordinate" help="z coordinate of the binding site." value="0"/>
54 <param type="float" name="size_x" label="x size" help="Length of the binding site (Å) in the x direction." value="0"/>
55 <param type="float" name="size_y" label="y size" help="Length of the binding site (Å) in the y direction." value="0"/>
56 <param type="float" name="size_z" label="z size" help="Length of the binding site (Å) in the z direction." value="0"/>
57 <param type="integer" name="exh" label="Exhaustiveness" help="The number of poses to return from the docking job" value="10"/>
58 <conditional name="seed">
59 <param name="seed" type="boolean" label="Specify random seed for simulation reproducibility?"/>
60 <when value="true">
61 <param type="integer" name="seed_value" label="Random seed" help="Choose a seed value" value="1"/>
62 </when>
63 <when value="false"/>
64 </conditional>
65 </when>
66 <when value="file">
67 <param type="data" name="box" format="txt" label="Box configuration" help="Text file with the box configurations" />
68 </when>
69 </conditional>
16 </inputs> 70 </inputs>
17 <outputs> 71 <outputs>
18 <data name="file_output1" format="pdbqt" /> 72 <data name="file_output1" format="pdbqt" />
19 <data name="file_output2" format="txt" /> 73 <data name="file_output2" format="txt" />
20 </outputs> 74 </outputs>
21 <tests> 75 <tests>
22 <test> 76 <test>
23 <param name="box" value="config_complexo_dm.txt"/>
24 <param name="receptor" value="3u1i_for_DM.pdbqt"/> 77 <param name="receptor" value="3u1i_for_DM.pdbqt"/>
25 <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/> 78 <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/>
79 <param name="config_params" value="vals"/>
80 <param name="center_x" value="70.92" />
81 <param name="center_y" value="70.57" />
82 <param name="center_z" value="36.86" />
83 <param name="size_x" value="20.00" />
84 <param name="size_y" value="18.40" />
85 <param name="size_z" value="23.60" />
86 <param name="seed" value="true" />
87 <param name="seed_value" value="1" />
88 <param name="exhaustivenesss" value="10" />
89 <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/>
90 <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/>
91 </test>
92 <test>
93 <param name="receptor" value="3u1i_for_DM.pdbqt"/>
94 <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/>
95 <param name="config_params" value="file"/>
96 <param name="box" value="config_complexo_dm.txt"/>
26 <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/> 97 <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/>
27 <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/> 98 <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/>
28 </test> 99 </test>
29 </tests> 100 </tests>
30 <help><![CDATA[ 101 <help><![CDATA[
31 **What it does?** 102
32 103 This tool performs protein-ligand docking using the Autodock Vina program.
33 This tool performs molecular docking with Autodock Vina program.
34 104
35 **Inputs** 105 **Inputs**
36 106
37 Three inputs are required for use this tools. The first is a text file with the box configurations, this file looks like the following example:: 107 The first two inputs required are files (in the pdbqt format) describing the receptor and ligand respectively. These files are produced by the receptor and ligand preparation tools.
38 108
39 size_x = 20.00 109 In addition, parameters for docking must be defined. The Cartesian coordinates of the center of the binding site should be provided, along with the size of the binding site along each dimension. Effectively, this defines a cuboidal volume in which docking is performed. Alternatively, a config file can be uploaded containing this information - such a file can be generated from the box parameter calculation file.
40 size_y = 18.40
41 size_z = 23.60
42 center_x = 70.92
43 center_y = 70.57
44 center_z = 36.86
45 num_modes = 9999
46 energy_range = 9999
47 exhaustiveness = 10
48 cpu = 4
49 seed = 1
50
51 Where the parameters size_x, size_y, size_z, center_x, center_y and center_z are coordinates of the binding site.
52 The parameters num_modes, energy_range, exhaustiveness, cpu and seed are autodock vina configurations to execute the algorithm.
53
54 The second input is a receptor file (pdbqt) what is a output of the prepare receptor tool.
55 The last input is a ligand file (pdbqt) what is a output of the prepare ligand tool.
56 110
57 **Outputs** 111 **Outputs**
58 112
59 Two outputs are generated by this tool. The first is a pdbqt file with the molecule structure resulting of the molecular docking, this file looks like the following example:: 113 Two outputs are generated by this tool. The first is another pdbqt file containing the molecular structure resulting from docking, such as the following example::
60 114
61 MODEL 1 115 MODEL 1
62 REMARK VINA RESULT: -0.0 0.000 0.000 116 REMARK VINA RESULT: -0.0 0.000 0.000
63 REMARK 9 active torsions: 117 REMARK 9 active torsions:
64 REMARK status: ('A' for Active; 'I' for Inactive) 118 REMARK status: ('A' for Active; 'I' for Inactive)
115 ENDBRANCH 17 22 169 ENDBRANCH 17 22
116 ENDBRANCH 2 14 170 ENDBRANCH 2 14
117 TORSDOF 9 171 TORSDOF 9
118 ENDMDL 172 ENDMDL
119 173
120 The last is a log file with the binding affinity scores, this file looks like the following example:: 174 The second output is a log file containing the binding affinity scores, like the following::
121 175
122 ----------------------------------------------------------------- 176 -----------------------------------------------------------------
123 If you used AutoDock Vina in your work, please cite: 177 If you used AutoDock Vina in your work, please cite:
124 178
125 O. Trott, A. J. Olson, 179 O. Trott, A. J. Olson,