<tool id="PDBTIDY" name="PDBTIDY" version="1">
  <description>Using pdb_tidy tools after ab_haddock_format.py.</description>
  <command detect_errors="exit_code"><![CDATA[
    source /home/galaxy/data/_conda/bin/activate pdbtools;
    pdb_tidy '${input}' > '${output}';
    source /home/galaxy/data/_conda/bin/deactivate
  ]]></command>
  <inputs>
    <param name="input" format="pdb" type="data" label="Select your PDB file."/>
  </inputs>
  <outputs>
    <data name="output" format="pdb" />
  </outputs>
  <help>
Modifies the file to adhere (as much as possible) to the format specifications.
Expects a sorted file - REMARK/ATOM/HETATM/END - so use pdb_sort in case you are
not sure.

This includes:
    - Adding TER statements after chain breaks/changes
    - Truncating/Padding all lines to 80 characters
    - Adds END statement at the end of the file

Will remove all original TER/END statements from the file.

Usage:
    python pdb_tidy.py 'pdb file'

Example:
    python pdb_tidy.py 1CTF.pdb

This program is part of the 'pdb-tools' suite of utilities and should not be
distributed isolatedly. The 'pdb-tools' were created to quickly manipulate PDB
files using the terminal, and can be used sequentially, with one tool streaming
data to another. They are based on old FORTRAN77 code that was taking too much
effort to maintain and compile. RIP.
  </help>
</tool>