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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Preparation]-->
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4 <tool id="AddMissingAtoms" name="AddMissingAtoms" version="1.1.0">
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5 <description>add missing atoms to protein structures</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">AddMissingAtoms</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="stdio"/>
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11 <expand macro="requirements"/>
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12 <command>AddMissingAtoms
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13
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14 #if $param_i:
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15 -i $param_i
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16 #end if
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17 #if $param_o:
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18 -o $param_o
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19 #end if
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20 #if $param_opt_hyd:
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21 -opt_hyd $param_opt_hyd
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22 #end if
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23 </command>
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24 <inputs>
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25 <param name="param_i" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input file" help="(-i) "/>
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26 <param name="param_opt_hyd" type="integer" min="0" max="1" optional="True" value="0" label="optimize the positions of hydrogens" help="(-opt_hyd) "/>
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27 </inputs>
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28 <expand macro="advanced_options"/>
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29 <outputs>
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30 <data name="param_o" format="pdb"/>
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31 </outputs>
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32 <help>AddMissingAtoms tool allows you to missing atoms, i.e. hydrogens to a protein structure.
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33
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34 Optional parameter is the optimize_hydrogens flag (-opt_hyd), which uses the AMBER force field to run a quick energy minization for all hydrogen atoms.
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35
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36 Output of this tool is one pdb-file containing the input protein structure with added atoms.
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37
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38 </help>
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39 </tool>
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