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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: [Checks and evaluations]-->
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4 <tool id="ProteinCheck" name="ProteinCheck" version="1.1.0">
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5 <description>quality check for proteins structures</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">ProteinCheck</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>ProteinCheck
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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_bc:
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21 -bc $param_bc
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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 pdb-file" help="(-i) "/>
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26 <param name="param_bc" type="integer" min="0" max="1" optional="True" value="0" label="ignore broken chains" help="(-bc) "/>
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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="pdf"/>
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31 </outputs>
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32 <help>Check a given protein structure for the following errors:
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33 * bond-lengths may not be completely senseless (i.e. <0.7 or >2.5 Angstroem)
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34 * each chain may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments. This test is skipped if the above box is checked.
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35 * each atom must have a valid assigned element
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36 * the protein must be protonated (since this is necessary for docking/(re-)scoring).
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37 * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
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38 * there may be no senseless temperature factors (<1 or >100)
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39 * there may be no sterical clashes between atoms
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40
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41 A protein structure quality report, containing the results of those tests and a secondary structure prediction, a Ramachandran plot and a temperature factor plot will be generated and saved as a pdf-file.
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42
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43 </help>
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44 </tool>
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