view galaxy_stubs/ProteinProtonator.xml @ 2:605370bc1def draft default tip

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<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Preparation]-->
<tool id="ProteinProtonator" name="ProteinProtonator" version="1.1.0">
  <description>protonate protein structures</description>
  <macros>
    <token name="@EXECUTABLE@">ProteinProtonator</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>ProteinProtonator

#if $param_i:
  -i $param_i
#end if
#if $param_o:
  -o $param_o
#end if
#if $param_ph:
  -ph $param_ph
#end if
</command>
  <inputs>
    <param name="param_i" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input file" help="(-i) "/>
    <param name="param_ph" type="float" value="7.0" label="pH-value for pH-dep. protonation" help="(-ph) "/>
  </inputs>
  <expand macro="advanced_options"/>
  <outputs>
    <data name="param_o" format="pdb"/>
  </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>