Mercurial > repos > chemteam > gmx_merge_topology_files

annotate merge_top.xml @ 19:17c12d5cb336 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
author chemteam
date Tue, 12 Jul 2022 12:44:22 +0000
parents 9389cd867cf2
children
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ced8ec975548 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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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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06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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2 <description>and GRO files</description>
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33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
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3 <macros>
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9389cd867cf2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"
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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
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
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6 </macros>
8
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7 <requirements>
10
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8 <requirement type="package" version="@TOOL_VERSION@">parmed</requirement>
8
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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'
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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12 --lig-top $lig_top
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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13 --prot-top $prot_top
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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14 --lig-gro $lig_gro
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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15 --prot-gro $prot_gro
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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16 --complex-top complex.top
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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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."/>
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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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."/>
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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22 <param name="prot_gro" type="data" format='gro' label="Protein structure (GRO) file" help="Protein structure in GRO format."/>
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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23 <param name="lig_gro" type="data" format='gro' label="Ligand structure (GRO) file" help="Ligand structure in GRO format."/>
0
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
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24 </inputs>
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
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25 <outputs>
8
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26 <data name="complex_top" format="top" from_work_dir="complex.top"/>
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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27 <data name="complex_gro" format="gro" from_work_dir="complex.gro"/>
0
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
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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>
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
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30 <test>
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31 <param name="prot_top" value="topol.top" />
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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32 <param name="lig_top" value="lig.itp" />
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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33 <param name="prot_gro" value="newbox.gro" />
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34 <param name="lig_gro" value="lig.gro" />
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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35 <output name="complex_top" file="complex.top" ftype="top" compare="diff" lines_diff="20"/>
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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36 <output name="complex_gro" file="complex.gro" ftype="gro"/>
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33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
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37 </test>
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
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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[
2
f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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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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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
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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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.
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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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
f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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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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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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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
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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55 - TOP file for the protein topology
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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56 - A TOP or ITP file for the ligand topology
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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57 - GRO file for the protein structure
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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58 - GRO file for the ligand structure
2
f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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60 _____
f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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63 .. class:: infomark
f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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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**
f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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66
8
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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67 - TOP file for the protein-ligand complex.
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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68 - GRO file for the protein-ligand complex.
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69
0
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
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70 ]]></help>
8
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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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">
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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73 @misc{parmed_2020,
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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74 author = {Jason Swails and other contributors},
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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75 title = {ParmEd},
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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76 url={https://github.com/ParmEd/ParmEd},
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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77 abstract = {Parameter/topology editor and molecular simulator.},
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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78 urldate = {2020-04-03},
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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79 publisher = {GitHub},
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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80 year = {2020},
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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81 month = mar, }</citation>
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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82 </citations>
0
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
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83 </tool>