Mercurial > repos > bgruening > autodock_vina_prepare_box

comparison prepare_box.xml @ 2:73c2c9774c2d draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
author bgruening
date Wed, 02 Oct 2019 12:49:11 -0400
parents 4f7c5cad3377
children 908880455b2d
comparison
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1:4f7c5cad3377 2:73c2c9774c2d
4 <requirement type="package" version="2019.03.1.0">rdkit</requirement> 4 <requirement type="package" version="2019.03.1.0">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 '$input1' 9 --ligand '$ligand'
10 --config '$output1' 10 --config '$output'
11 --bufx '$bufx' 11 --bufx '$bufx'
12 --bufy '$bufy' 12 --bufy '$bufy'
13 --bufz '$bufz' 13 --bufz '$bufz'
14 --exh '$exh' 14 #if $exh:
15 --exh '$exh'
16 #end if
15 #if $seed_value: 17 #if $seed_value:
16 --seed '$seed_value' 18 --seed '$seed_value'
17 #end if 19 #end if
18 ]]></command> 20 ]]></command>
19 <inputs> 21 <inputs>
20 <param type="data" name="input1" format="mol" label="Input ligand" 22 <param type="data" name="ligand" format="mol" label="Input ligand"
21 help="The input ligand (mol file)"/> 23 help="The input ligand (mol file)"/>
22 <param name="bufx" type="float" value="0" label="x-axis buffer" 24 <param name="bufx" type="float" value="0" label="x-axis buffer"
23 help="Buffer in the x direction (in angs.)"/> 25 help="Buffer in the x direction (in angs.)"/>
24 <param name="bufy" type="float" value="0" label="y-axis buffer" 26 <param name="bufy" type="float" value="0" label="y-axis buffer"
25 help="Buffer in the y direction (in angs.)"/> 27 help="Buffer in the y direction (in angs.)"/>
26 <param name="bufz" type="float" value="0" label="z-axis buffer" 28 <param name="bufz" type="float" value="0" label="z-axis buffer"
27 help="Buffer in the z direction (in angs.)"/> 29 help="Buffer in the z direction (in angs.)"/>
28 <param name="exh" type="integer" value="0" label="Exhaustiveness" 30 <param name="exh" type="integer" optional="true" label="Exhaustiveness (optional)"
29 help="Number of poses to return from docking job"/> 31 help="Exhaustiveness of global search (optional, default = 8)"/>
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 <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"/> 33 help="Choose a seed value; if none is selected, a seed will be chosen randomly"/>
33 </inputs> 34 </inputs>
34 <outputs> 35 <outputs>
35 <data name="output1" format="txt" /> 36 <data name="output" format="txt" />
36 </outputs> 37 </outputs>
37 <tests> 38 <tests>
38 <test> 39 <test>
39 <param name="input1" value="NUDT5A-x0114_2.mol" /> 40 <param name="ligand" value="NUDT5A-x0114_2.mol" />
41 <param name="bufx" value="1" />
42 <param name="bufy" value="2" />
43 <param name="bufz" value="3" />
44 <output name="output" file="box_params_1.txt" />
45 </test>
46 <test>
47 <param name="ligand" value="NUDT5A-x0114_2.mol" />
40 <param name="bufx" value="1" /> 48 <param name="bufx" value="1" />
41 <param name="bufy" value="2" /> 49 <param name="bufy" value="2" />
42 <param name="bufz" value="3" /> 50 <param name="bufz" value="3" />
43 <param name="exh" value="10" /> 51 <param name="exh" value="10" />
44 <param name="seed_value" value="1" /> 52 <param name="seed_value" value="1" />
45 <output name="output1" file="box_params.txt" /> 53 <output name="output" file="box_params_2.txt" />
46 </test> 54 </test>
47 </tests> 55 </tests>
48 <help> 56 <help>
49 <![CDATA[ 57 <![CDATA[
50 58