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view galaxy_stubs/AddMissingAtoms.xml @ 2:605370bc1def draft default tip
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author | luis |
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date | Tue, 12 Jul 2016 12:33:33 -0400 |
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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="AddMissingAtoms" name="AddMissingAtoms" version="1.1.0"> <description>add missing atoms to protein structures</description> <macros> <token name="@EXECUTABLE@">AddMissingAtoms</token> <import>macros.xml</import> </macros> <expand macro="stdio"/> <expand macro="requirements"/> <command>AddMissingAtoms #if $param_i: -i $param_i #end if #if $param_o: -o $param_o #end if #if $param_opt_hyd: -opt_hyd $param_opt_hyd #end if </command> <inputs> <param name="param_i" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input file" help="(-i) "/> <param name="param_opt_hyd" type="integer" min="0" max="1" optional="True" value="0" label="optimize the positions of hydrogens" help="(-opt_hyd) "/> </inputs> <expand macro="advanced_options"/> <outputs> <data name="param_o" format="pdb"/> </outputs> <help>AddMissingAtoms tool allows you to missing atoms, i.e. hydrogens to a protein structure. Optional parameter is the optimize_hydrogens flag (-opt_hyd), which uses the AMBER force field to run a quick energy minization for all hydrogen atoms. Output of this tool is one pdb-file containing the input protein structure with added atoms. </help> </tool>