Mercurial > repos > marcel > caddsuite_linux_x86_64
annotate CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml @ 1:867bf9f815a0
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author | g2cmnty@test-web1.g2.bx.psu.edu |
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date | Sun, 26 Jun 2011 13:45:14 -0400 |
parents | bac3c274238f |
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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.--> |
1 | 3 <tool id="proteinprotonator" name="ProteinProtonator" version="0.94"> |
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4 <description>protonate protein structures</description> |
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5 <command interpreter="bash"><![CDATA[../../ProteinProtonator |
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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( $ph ) != '' and str( $ph ) != 'None' : |
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13 -ph "$ph" |
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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 file" optional="false" type="data" format="pdb"/> |
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19 <param name="ph" label="pH-value for pH-dep. protonation" optional="true" type="text" area="true" size="1x5" value="7.0"/> |
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20 </inputs> |
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21 <outputs> |
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22 <data name="o" format="pdb" format_source="i"/> |
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23 </outputs> |
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24 <help>ProteinProtonator allows you add hydrogens to a protein structure. |
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25 |
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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. |
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27 |
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28 Output of this tool is one pdb-file containing the input protein structure with added hydrogens atoms.</help> |
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29 </tool> |