Mercurial > repos > marcel > caddsuite_linux_x86_64
comparison CADDSuite-1.0.1/galaxyconfigs/tools/ProteinProtonator.xml @ 9:2cff9609f2c7
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| author | marcel |
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| date | Tue, 15 Nov 2011 10:40:26 -0500 |
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| 8:9ab6da6cd36c | 9:2cff9609f2c7 |
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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="proteinprotonator" name="ProteinProtonator" version="1.0.1"> | |
| 4 <description>protonate protein structures</description> | |
| 5 <command interpreter="bash"><![CDATA[../../ProteinProtonator | |
| 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( $ph ) != '' and str( $ph ) != 'None' : | |
| 13 -ph "$ph" | |
| 14 #end if | |
| 15 | tail -n 5 | |
| 16 ]]></command> | |
| 17 <inputs> | |
| 18 <param name="i" optional="false" label="input file" type="data" format="pdb"/> | |
| 19 <param name="ph" optional="true" label="Optional: pH-value for pH-dep. protonation" type="text" area="true" size="1x5" value="7.0"/> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <data name="o" format="pdb" format_source="i"/> | |
| 23 </outputs> | |
| 24 <help>ProteinProtonator allows you add hydrogens to a protein structure. | |
| 25 | |
| 26 Note that all hydrogen atoms already present in the input file will be ignored. If desired, you can specify a specific pH value, for which protonation is to be done; otherwise a neutral pH will be assumed. | |
| 27 | |
| 28 Output of this tool is one pdb-file containing the input protein structure with added hydrogens atoms.</help> | |
| 29 </tool> |