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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
author bgruening
date Thu, 16 Apr 2020 08:25:04 -0400
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89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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1 <macros>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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2 <token name="@VERSION@">0.1.1</token>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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3 <xml name="requirements">
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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4 <requirements>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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5 <requirement type="package" version="3.7">python</requirement>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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6 <requirement type="package" version="0.25.2">yank</requirement>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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7 <requirement type="package" version="1.6">pdbfixer</requirement>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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8 <requirement type="package" version="0.6.0">openforcefield</requirement>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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9 <requirement type="package" version="3.2.0">parmed</requirement>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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10 <requirement type="package" version="@VERSION@">openduck</requirement>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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11 </requirements>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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12 </xml>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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13 <xml name="interaction_params">
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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14 <section name="ia" title="Parameters for the protein-ligand interaction" expanded="true">
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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15 <param argument="chain_sel" type="text" label="Chain ID for selection" help="E.g. 'A', 'B', etc.">
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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16 <validator type="regex" message="Invalid chain ID">^[A-Z]$</validator>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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17 </param>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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18 <param argument="res_sel" type="text" label="Three letter residue code for selection" help="E.g. 'ASP', 'TYR', etc.">
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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19 <validator type="regex" message="Invalid chain ID">^[A-Z]{3}$</validator>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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20 </param>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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21 <param argument="resid_sel" type="text" label="Residue ID for selection" help="Position of residue in sequence, e.g. 163">
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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22 <validator type="regex" message="Invalid chain ID">^[0-9]+$</validator>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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23 </param>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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24 <param argument="atom_sel" type="text" label="Atom to select within the chosen residue" help="E.g. 'OD2'">
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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25 <validator type="regex" message="Invalid chain ID">^[A-Z0-9]+$</validator>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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26 </param>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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27 </section>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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28 </xml>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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29 <xml name="tar_param">
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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30 <param argument="return_tar" type="boolean" checked="true" label="Return a tar file?" help="Return a tar file containing all files produced during the simulations."/>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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31 </xml>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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32 <xml name="tar_output">
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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33 <data name="tar" format="tar" from_work_dir="allfiles.tar.gz" label="${tool.name} tarball">
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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34 <filter>return_tar</filter>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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35 </data>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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36 </xml>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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37 <xml name="citations">
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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38 <citations>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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39 <citation type="doi">10.1038/nchem.2660</citation>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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40 <citation type="bibtex">
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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41 @misc{Bradley2019,
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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42 author = {Bradley, Anthony},
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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43 title = {OpenDUck source code},
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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44 year = {2019},
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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45 publisher = {GitHub},
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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46 journal = {GitHub repository},
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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47 howpublished = {URL: https://github.com/xchem/duck},
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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48 commit = {b98bb78284e9c92837ac1e69fc2f06306ab1e28c}
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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49 }
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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50 </citation>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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51 </citations>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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52 </xml>
89c3bd4f50a3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
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53 </macros>