Mercurial > repos > marcel > caddsuite_linux_x86_64
view CADDSuite-1.5/galaxyconfigs/tools/ProteinProtonator.xml @ 16:1a24aef40d01 draft
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author | marcel |
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date | Tue, 24 Jul 2012 11:10:07 -0400 |
parents | ac342506cd4e |
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<!--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.--> <tool id="proteinprotonator" name="ProteinProtonator" version="1.5"> <description>protonate protein structures</description> <command interpreter="bash"><![CDATA[../../ProteinProtonator #if str( $i ) != '' and str( $i ) != 'None' : -i "$i" #end if #if str( $o ) != '' and str( $o ) != 'None' : -o "$o" #end if #if str( $ph ) != '' and str( $ph ) != 'None' : -ph "$ph" #end if | tail -n 5 ]]></command> <inputs> <param name="i" optional="false" label="input file" type="data" format="pdb"/> <param name="ph" optional="true" label="Optional: pH-value for pH-dep. protonation" type="text" area="true" size="1x5" value="7.0"/> </inputs> <outputs> <data name="o" format="pdb" format_source="i"/> </outputs> <help>ProteinProtonator allows you add hydrogens to a protein structure. 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. Output of this tool is one pdb-file containing the input protein structure with added hydrogens atoms.</help> </tool>