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comparison acpype.xml @ 6:2417677038b2 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c440a43396b4d815ef35f45ed562e22bf37c028"
author chemteam
date Tue, 16 Feb 2021 21:55:56 +0000
parents 27ee142314a9
children 710301bc46fa
comparison
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5:27ee142314a9 6:2417677038b2
1 <tool id="ambertools_acpype" name="Generate MD topologies for small molecules" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> 1 <tool id="ambertools_acpype" name="Generate MD topologies for small molecules" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>using acpype</description> 2 <description>using acpype</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <token name="@GALAXY_VERSION@">0</token> 5 <token name="@GALAXY_VERSION@">1</token>
6 </macros> 6 </macros>
7 <expand macro="requirements"> 7 <expand macro="requirements">
8 <requirement type="package" version="2020.10.24.12.16">acpype</requirement> 8 <requirement type="package" version="2020.10.24.12.16">acpype</requirement>
9 </expand> 9 </expand>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
12 acpype -i './input1.${input1.ext}' 12 acpype -i './input1.${input1.ext}'
13 -n '$charge' 13 -n '$charge'
14 -b base 14 -b base
15 -m '$multiplicity' 15 -m '$multiplicity'
16 -a '$atomtype' 16 -a '$atomtype'
17 -c '$charge_method'
17 -o gmx 18 -o gmx
18 ]]></command> 19 ]]></command>
19 <inputs> 20 <inputs>
20 <param name="input1" type="data" format="pdb,mol2" label="Input file" help="Structure of the compound in pdb or mol2 format"/> 21 <param name="input1" type="data" format="pdb,mol2" label="Input file" help="Structure of the compound in pdb or mol2 format"/>
21 <param name="charge" type="integer" value="0" label="Charge of the molecule"/> 22 <param name="charge" type="integer" value="0" label="Charge of the molecule"/>
23 <param name="atomtype" type="select" value="gaff" label="Force field to use for parameterization"> 24 <param name="atomtype" type="select" value="gaff" label="Force field to use for parameterization">
24 <option value="gaff">gaff</option> 25 <option value="gaff">gaff</option>
25 <option value="amber">AMBER14SB</option> 26 <option value="amber">AMBER14SB</option>
26 <option value="gaff2">gaff2</option> 27 <option value="gaff2">gaff2</option>
27 <option value="amber2">AMBER14SB + gaff2</option> 28 <option value="amber2">AMBER14SB + gaff2</option>
29 </param>
30 <param name="charge_method" type="select" value="bcc" label="Charge method">
31 <option value="bcc">bcc (default)</option>
32 <option value="gas">gas</option>
33 <option value="user">charges provided by user in mol2 file</option>
28 </param> 34 </param>
29 <param name="save_gro" type="boolean" value="false" label="Save GRO file?" help="Save atomic coordinates of ligand in GRO format."/> 35 <param name="save_gro" type="boolean" value="false" label="Save GRO file?" help="Save atomic coordinates of ligand in GRO format."/>
30 </inputs> 36 </inputs>
31 <outputs> 37 <outputs>
32 <data format="itp" name="output" label="Topology" from_work_dir='base.acpype/base_GMX.itp'/> 38 <data format="itp" name="output" label="Topology" from_work_dir='base.acpype/base_GMX.itp'/>
36 </outputs> 42 </outputs>
37 <tests> 43 <tests>
38 <test> 44 <test>
39 <param name="input1" value="JZ4.mol2"/> 45 <param name="input1" value="JZ4.mol2"/>
40 <param name="save_gro" value="True"/> 46 <param name="save_gro" value="True"/>
47 <param name="charge_method" value="bcc"/>
41 <output name="output"> 48 <output name="output">
42 <assert_contents> 49 <assert_contents>
43 <has_line line="[ atoms ]"/> 50 <has_line line="[ atoms ]"/>
44 <has_text text=" 15 ha 1 JZ4 H4 15 0.13"/> 51 <has_text text=" 15 ha 1 JZ4 H4 15 0.13"/>
45 <has_text text=" 18 hc 1 JZ4 H7 18 0.05"/> 52 <has_text text=" 18 hc 1 JZ4 H7 18 0.05"/>
46 </assert_contents> 53 </assert_contents>
47 </output> 54 </output>
48 <output name="gro_output" file="base_GMX.gro" lines_diff="2"/> 55 <output name="gro_output" file="base_GMX.gro" lines_diff="2"/>
56 </test>
57 <test>
58 <param name="input1" value="LigA_output.mol2"/>
59 <param name="save_gro" value="false"/>
60 <param name="charge_method" value="user"/>
61 <output name="output" file="LigA_output.top" lines_diff="26"/>
49 </test> 62 </test>
50 </tests> 63 </tests>
51 <help><![CDATA[ 64 <help><![CDATA[
52 Tool to produce GROMACS topologies for small molecules using the acpype interface to AmberTools. 65 Tool to produce GROMACS topologies for small molecules using the acpype interface to AmberTools.
53 66