annotate merge_top.xml @ 13:534ff13ea227 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit bf18581ac3de6b65bdc0a988e6f844cea6e77975"
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date Wed, 27 Oct 2021 08:01:32 +0000
parents 9389cd867cf2
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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>
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
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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
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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."/>
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."/>
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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"/>
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"/>
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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"/>
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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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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40
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
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
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48
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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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
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
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59
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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61
f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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62
f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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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**
f2faba46d680 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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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">
06ea4e040d45 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
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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
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
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83 </tool>