annotate merge_top.xml @ 19:17c12d5cb336 draft

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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date Tue, 12 Jul 2022 12:44:22 +0000
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1 <tool id="gmx_merge_topology_files" name="Merge GROMACS topologies" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>and GRO files</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">3.4.3</token>
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5 <token name="@GALAXY_VERSION@">0</token>
0
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">parmed</requirement>
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9 </requirements>
0
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10 <command detect_errors="exit_code"><![CDATA[
8
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11 python '$__tool_directory__/merge_top.py'
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12 --lig-top $lig_top
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13 --prot-top $prot_top
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14 --lig-gro $lig_gro
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15 --prot-gro $prot_gro
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16 --complex-top complex.top
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17 --complex-gro complex.gro
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18 ]]></command>
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
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19 <inputs>
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20 <param name="prot_top" type="data" format='top' label="Protein topology (TOP) file" help="Protein topology into which a ligand topology will be added."/>
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21 <param name="lig_top" type="data" format='top,itp' label="Ligand topology (TOP or ITP) file" help="Ligand topology for insertion into the protein topology. Either TOP or ITP format."/>
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22 <param name="prot_gro" type="data" format='gro' label="Protein structure (GRO) file" help="Protein structure in GRO format."/>
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23 <param name="lig_gro" type="data" format='gro' label="Ligand structure (GRO) file" help="Ligand structure in GRO format."/>
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24 </inputs>
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25 <outputs>
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26 <data name="complex_top" format="top" from_work_dir="complex.top"/>
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27 <data name="complex_gro" format="gro" from_work_dir="complex.gro"/>
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28 </outputs>
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
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29 <tests>
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30 <test>
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31 <param name="prot_top" value="topol.top" />
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32 <param name="lig_top" value="lig.itp" />
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33 <param name="prot_gro" value="newbox.gro" />
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34 <param name="lig_gro" value="lig.gro" />
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35 <output name="complex_top" file="complex.top" ftype="top" compare="diff" lines_diff="20"/>
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36 <output name="complex_gro" file="complex.gro" ftype="gro"/>
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37 </test>
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38 </tests>
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
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39 <help><![CDATA[
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f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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41 .. class:: infomark
f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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42
f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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43 **What it does**
f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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44
8
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45 This tool merges GROMACS topologies and structure (GRO) files, calculated separately for a protein and ligand, into combined topology and GRO files for the resulting complex.
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46
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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47 The tool will work best if used with the outputs of the 'acpype' and 'GROMACS initial setup' tools. If the input files are formatted unusually or incorrectly, it will probably fail.
2
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48
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49 _____
f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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50
f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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51 .. class:: infomark
f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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52
f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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53 **Input**
f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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54
8
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55 - TOP file for the protein topology
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56 - A TOP or ITP file for the ligand topology
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57 - GRO file for the protein structure
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58 - GRO file for the ligand structure
2
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59
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60 _____
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61
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62
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63 .. class:: infomark
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64
f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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65 **Output**
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66
8
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67 - TOP file for the protein-ligand complex.
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68 - GRO file for the protein-ligand complex.
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69
0
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70 ]]></help>
8
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71 <citations>
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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72 <citation type="bibtex">
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73 @misc{parmed_2020,
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74 author = {Jason Swails and other contributors},
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75 title = {ParmEd},
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76 url={https://github.com/ParmEd/ParmEd},
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77 abstract = {Parameter/topology editor and molecular simulator.},
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78 urldate = {2020-04-03},
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79 publisher = {GitHub},
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80 year = {2020},
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81 month = mar, }</citation>
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82 </citations>
0
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83 </tool>