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annotate CADDSuite-1.5/galaxyconfigs/tools/ProteinCheck.xml @ 15:ac342506cd4e draft

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CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:08:49 -0400
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1
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2 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
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3 <tool id="proteincheck" name="ProteinCheck" version="1.5">
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4 <description>quality check for proteins structures</description>
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5 <command interpreter="bash"><![CDATA[../../ProteinCheck
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6 #if str( $i ) != '' and str( $i ) != 'None' :
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7 -i "$i"
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8 #end if
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9 #if str( $o ) != '' and str( $o ) != 'None' :
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10 -o "$o"
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11 #end if
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12 #if str( $bc ) != '' and str( $bc ) != 'None' :
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13 -bc
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14 #end if
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15 | tail -n 5
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16 ]]></command>
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17 <inputs>
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18 <param name="i" optional="false" label="input pdb-file" type="data" format="pdb"/>
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19 <param name="bc" optional="true" label="ignore broken chains" type="boolean" truevalue="true" falsevalue=""/>
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20 </inputs>
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21 <outputs>
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22 <data name="o" format="pdf"/>
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23 </outputs>
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24 <help>Check a given protein structure for the following errors:
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25 * bond-lengths may not be completely senseless (i.e. &lt;0.7 or &gt;2.5 Angstroem)
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26 * 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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27 * each atom must have a valid assigned element
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28 * the protein must be protonated (since this is necessary for docking/(re-)scoring).
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29 * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
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30 * there may be no senseless temperature factors (&lt;1 or &gt;100)
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31 * there may be no sterical clashes between atoms
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32
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33 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.</help>
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34 </tool>