Mercurial > repos > chemteam > ambertools_acpype

annotate acpype.xml @ 8:710301bc46fa draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit fe0c452249565047df8ac0a6f5956fe8ea0cd60d"
author chemteam
date Wed, 09 Jun 2021 09:55:04 +0000
parents 2417677038b2
children da6bd1975a71
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1 <tool id="ambertools_acpype" name="Generate MD topologies for small molecules" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>using acpype</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@GALAXY_VERSION@">0</token>
0
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6 </macros>
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7 <expand macro="requirements">
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8 <requirement type="package" version="2020.10.24.12.16">acpype</requirement>
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9 </expand>
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10 <command detect_errors="exit_code"><![CDATA[
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11 ln -s '$input1' ./input1.${input1.ext} &&
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12 acpype -i './input1.${input1.ext}'
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13 -n '$charge'
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14 -b base
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15 -m '$multiplicity'
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16 -a '$atomtype'
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17 -c '$charge_method'
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18 -o gmx
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19 ]]></command>
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20 <inputs>
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21 <param name="input1" type="data" format="pdb,mol2" label="Input file" help="Structure of the compound in pdb or mol2 format"/>
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22 <param name="charge" type="integer" value="0" label="Charge of the molecule"/>
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23 <param name="multiplicity" type="integer" value="1" label="Multiplicity" help="Default value is 1, which is correct for almost all organic molecules."/>
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24 <param name="atomtype" type="select" value="gaff" label="Force field to use for parameterization">
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25 <option value="gaff">gaff</option>
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26 <option value="amber">AMBER14SB</option>
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27 <option value="gaff2">gaff2</option>
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28 <option value="amber2">AMBER14SB + gaff2</option>
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29 </param>
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30 <param name="charge_method" type="select" value="bcc" label="Charge method">
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31 <option value="bcc">bcc (default)</option>
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32 <option value="gas">gas</option>
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33 <option value="user">charges provided by user in mol2 file</option>
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34 </param>
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35 <param name="save_gro" type="boolean" value="false" label="Save GRO file?" help="Save atomic coordinates of ligand in GRO format."/>
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36 </inputs>
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37 <outputs>
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38 <data format="itp" name="output" label="Topology" from_work_dir='base.acpype/base_GMX.itp'/>
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39 <data format="gro" name="gro_output" label="Structure file (GRO format, optional)" from_work_dir="base.acpype/base_GMX.gro">
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40 <filter>save_gro</filter>
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41 </data>
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="input1" value="JZ4.mol2"/>
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46 <param name="save_gro" value="True"/>
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47 <param name="charge_method" value="bcc"/>
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48 <output name="output">
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49 <assert_contents>
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50 <has_line line="[ atoms ]"/>
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51 <has_text text=" 15 ha 1 JZ4 H4 15 0.13"/>
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52 <has_text text=" 18 hc 1 JZ4 H7 18 0.05"/>
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53 </assert_contents>
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54 </output>
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55 <output name="gro_output" file="base_GMX.gro" lines_diff="2"/>
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56 </test>
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57 <test>
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58 <param name="input1" value="LigA_output.mol2"/>
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59 <param name="save_gro" value="false"/>
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60 <param name="charge_method" value="user"/>
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61 <output name="output" file="LigA_output.top" lines_diff="26"/>
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62 </test>
0
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63 </tests>
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64 <help><![CDATA[
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65 Tool to produce GROMACS topologies for small molecules using the acpype interface to AmberTools.
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66
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67 .. class:: infomark
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68
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69 **Input**
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70
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71 Either a mol2 file (more appropriate for small structures) or a
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72 pdb file. If you want to parameterize a large macromolecule
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73 (which is more likely to be stored in PDB format, e.g. a protein)
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74 consider using a tool such as 'GROMACS initial setup' instead.
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75
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76 .. class:: infomark
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77
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78 **Outputs**
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79
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80 GROMACS topology for the ligand, in itp format. Optional: structure file, in gro format.
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81
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82
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83 ]]></help>
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84 <expand macro="citations">
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85 <citation type="doi">doi:10.1186/1756-0500-5-367</citation>
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86 </expand>
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87 </tool>