Mercurial > repos > bgruening > autodock_vina_prepare_box

comparison prepare_box.xml @ 3:908880455b2d draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
author bgruening
date Fri, 18 Oct 2019 04:57:34 -0400
parents 73c2c9774c2d
children ad35eaa204ea
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2:73c2c9774c2d 3:908880455b2d
1 <tool id="prepare_box" name="Calculate the box parameters for an AutoDock Vina" version="0.1.0"> 1 <tool id="prepare_box" name="Calculate the box parameters for an AutoDock Vina" version="0.1.1">
2 <description>job from an input mol file (confounding box)</description> 2 <description>job from a ligand input file (confounding box)</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2019.03.1.0">rdkit</requirement> 4 <requirement type="package" version="2019.03.1">rdkit</requirement>
5 <requirement type="package" version="1.16.2">numpy</requirement> 5 <requirement type="package" version="1.16.2">numpy</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 python '$__tool_directory__/calc_vina_box_params.py' 8 python '$__tool_directory__/calc_vina_box_params.py'
9 --ligand '$ligand' 9 --ligand '$ligand'
10 --ftype '${ligand.ext}'
10 --config '$output' 11 --config '$output'
11 --bufx '$bufx' 12 --bufx '$bufx'
12 --bufy '$bufy' 13 --bufy '$bufy'
13 --bufz '$bufz' 14 --bufz '$bufz'
14 #if $exh: 15 #if $exh:
17 #if $seed_value: 18 #if $seed_value:
18 --seed '$seed_value' 19 --seed '$seed_value'
19 #end if 20 #end if
20 ]]></command> 21 ]]></command>
21 <inputs> 22 <inputs>
22 <param type="data" name="ligand" format="mol" label="Input ligand" 23 <param type="data" name="ligand" format="mol,sdf,pdb,mol2" label="Input ligand"
23 help="The input ligand (mol file)"/> 24 help="The input ligand with three-dimensional coordinates (MOL, SDF, PDB and MOL formats supported)."/>
24 <param name="bufx" type="float" value="0" label="x-axis buffer" 25 <param name="bufx" type="float" value="0" label="x-axis buffer"
25 help="Buffer in the x direction (in angs.)"/> 26 help="Buffer in the x direction (in angs.)"/>
26 <param name="bufy" type="float" value="0" label="y-axis buffer" 27 <param name="bufy" type="float" value="0" label="y-axis buffer"
27 help="Buffer in the y direction (in angs.)"/> 28 help="Buffer in the y direction (in angs.)"/>
28 <param name="bufz" type="float" value="0" label="z-axis buffer" 29 <param name="bufz" type="float" value="0" label="z-axis buffer"
35 <outputs> 36 <outputs>
36 <data name="output" format="txt" /> 37 <data name="output" format="txt" />
37 </outputs> 38 </outputs>
38 <tests> 39 <tests>
39 <test> 40 <test>
40 <param name="ligand" value="NUDT5A-x0114_2.mol" /> 41 <param name="ligand" value="NUDT5A-x0114_2.mol" ftype="mol"/>
41 <param name="bufx" value="1" /> 42 <param name="bufx" value="1" />
42 <param name="bufy" value="2" /> 43 <param name="bufy" value="2" />
43 <param name="bufz" value="3" /> 44 <param name="bufz" value="3" />
44 <output name="output" file="box_params_1.txt" /> 45 <output name="output" file="box_params_1.txt" />
45 </test> 46 </test>
46 <test> 47 <test>
47 <param name="ligand" value="NUDT5A-x0114_2.mol" /> 48 <param name="ligand" value="NUDT5A-x0114_2.sdf" ftype="sdf"/>
49 <param name="bufx" value="1" />
50 <param name="bufy" value="2" />
51 <param name="bufz" value="3" />
52 <param name="exh" value="10" />
53 <param name="seed_value" value="1" />
54 <output name="output" file="box_params_2.txt" />
55 </test>
56 <test>
57 <param name="ligand" value="NUDT5A-x0114_2.mol2"/>
58 <param name="bufx" value="1" />
59 <param name="bufy" value="2" />
60 <param name="bufz" value="3" />
61 <output name="output" file="box_params_1.txt" />
62 </test>
63 <test>
64 <param name="ligand" value="NUDT5A-x0114_2.pdb" ftype="pdb"/>
48 <param name="bufx" value="1" /> 65 <param name="bufx" value="1" />
49 <param name="bufy" value="2" /> 66 <param name="bufy" value="2" />
50 <param name="bufz" value="3" /> 67 <param name="bufz" value="3" />
51 <param name="exh" value="10" /> 68 <param name="exh" value="10" />
52 <param name="seed_value" value="1" /> 69 <param name="seed_value" value="1" />
58 75
59 .. class:: infomark 76 .. class:: infomark
60 77
61 **Description** 78 **Description**
62 79
63 This tool calculates a confounding box around an input ligand (mol file), and 80 This tool calculates a confounding box around an input ligand and
64 uses it to generate the input parameters for an autodock vina job. 81 uses it to generate the input parameters for an autodock vina job.
65 82
66 The output file can be fed into the autodock vina tool as an alternative to creating the 83 The output file can be fed into the AutoDock Vina tool as an alternative to creating the
67 parameter file manually. 84 parameter file manually.
68 85
69 ----- 86 -----
70 87
71 .. class:: infomark 88 .. class:: infomark
72 89
73 **Inputs:** 90 **Inputs:**
74 91
75 This tool requires: 92 This tool requires:
76 93
77 * 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). 94 * An input ligand - This should be a file (MOL, SDF, PDB or MOL2 format) representing the ligand you wish to dock.
78 95
79 * (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. 96 * (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.
80 97
81 98
82 ----- 99 -----