comparison CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml @ 7:5b29b679ee6d

Uploaded Version 0.95
author marcel
date Tue, 12 Jul 2011 10:29:49 -0400
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children 9ab6da6cd36c
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6:061cbb4a9b05 7:5b29b679ee6d
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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.-->
3 <tool id="proteinprotonator" name="ProteinProtonator" version="0.95">
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>