Mercurial > repos > marcel > caddsuite_linux_x86_64
annotate CADDSuite/galaxyconfigs/tools/ProteinCheck.xml @ 0:bac3c274238f
Migrated tool version 0.93 from old tool shed archive to new tool shed repository
author | marcel |
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date | Tue, 07 Jun 2011 16:43:30 -0400 |
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children | 867bf9f815a0 |
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Migrated tool version 0.93 from old tool shed archive to new tool shed repository
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1 |
bac3c274238f
Migrated tool version 0.93 from old tool shed archive to new tool shed repository
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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="0.93"> |
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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" label="input pdb-file" optional="false" type="data" format="pdb"/> |
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19 <param name="bc" label="ignore broken chains" optional="true" 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. <0.7 or >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 (<1 or >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> |