Mercurial > repos > marcel > caddsuite_mac10_6
comparison CADDSuite-1.5/galaxyconfigs/tools/ProteinCheck.xml @ 7:bfab27640f5e draft
CADDSuite version 1.5
| author | Marcel Schumann <schumann.marcel@gmail.com> |
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| date | Tue, 24 Jul 2012 11:13:59 -0400 |
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| 6:decca54699e3 | 7:bfab27640f5e |
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| 1 | |
| 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.--> | |
| 3 <tool id="proteincheck" name="ProteinCheck" version="1.5"> | |
| 4 <description>quality check for proteins structures</description> | |
| 5 <command interpreter="bash"><![CDATA[../../ProteinCheck | |
| 6 #if str( $i ) != '' and str( $i ) != 'None' : | |
| 7 -i "$i" | |
| 8 #end if | |
| 9 #if str( $o ) != '' and str( $o ) != 'None' : | |
| 10 -o "$o" | |
| 11 #end if | |
| 12 #if str( $bc ) != '' and str( $bc ) != 'None' : | |
| 13 -bc | |
| 14 #end if | |
| 15 | tail -n 5 | |
| 16 ]]></command> | |
| 17 <inputs> | |
| 18 <param name="i" optional="false" label="input pdb-file" type="data" format="pdb"/> | |
| 19 <param name="bc" optional="true" label="ignore broken chains" type="boolean" truevalue="true" falsevalue=""/> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <data name="o" format="pdf"/> | |
| 23 </outputs> | |
| 24 <help>Check a given protein structure for the following errors: | |
| 25 * bond-lengths may not be completely senseless (i.e. <0.7 or >2.5 Angstroem) | |
| 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. | |
| 27 * each atom must have a valid assigned element | |
| 28 * the protein must be protonated (since this is necessary for docking/(re-)scoring). | |
| 29 * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring) | |
| 30 * there may be no senseless temperature factors (<1 or >100) | |
| 31 * there may be no sterical clashes between atoms | |
| 32 | |
| 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> | |
| 34 </tool> |