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comparison galaxy_stubs/AddMissingAtoms.xml @ 2:605370bc1def draft default tip

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author luis
date Tue, 12 Jul 2016 12:33:33 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Preparation]-->
4 <tool id="AddMissingAtoms" name="AddMissingAtoms" version="1.1.0">
5 <description>add missing atoms to protein structures</description>
6 <macros>
7 <token name="@EXECUTABLE@">AddMissingAtoms</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>AddMissingAtoms
13
14 #if $param_i:
15 -i $param_i
16 #end if
17 #if $param_o:
18 -o $param_o
19 #end if
20 #if $param_opt_hyd:
21 -opt_hyd $param_opt_hyd
22 #end if
23 </command>
24 <inputs>
25 <param name="param_i" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input file" help="(-i) "/>
26 <param name="param_opt_hyd" type="integer" min="0" max="1" optional="True" value="0" label="optimize the positions of hydrogens" help="(-opt_hyd) "/>
27 </inputs>
28 <expand macro="advanced_options"/>
29 <outputs>
30 <data name="param_o" format="pdb"/>
31 </outputs>
32 <help>AddMissingAtoms tool allows you to missing atoms, i.e. hydrogens to a protein structure.
33
34 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.
35
36 Output of this tool is one pdb-file containing the input protein structure with added atoms.
37
38 </help>
39 </tool>