view abhaddock_wrapper.xml @ 5:66d4ed17fc8d draft

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<tool id="abhaddock" name="abhaddock" version="2.0">
  <description>Using ab_haddock_format.py after ANARCI.</description>
  <command detect_errors="exit_code"><![CDATA[
    source /home/galaxy/data/_conda/bin/activate Ab-HADDOCK;
    python2.7 /home/galaxy/HADDOCK-antibody-antigen/ab_haddock_format.py '${input}' '${output}' ${chain};
    source /home/galaxy/data/_conda/bin/deactivate
  ]]></command>
  <inputs>
    <param name="input" format="pdb" type="data" label="Select your PDB file."/>
    <param name="chain" type="text" label="Chain id to use." help="Chain id to use for the HADDOCK-formatted PDB structure."/>
  </inputs>
  <outputs>
    <data name="output" format="pdb" />
  </outputs>
  <help>
<!--
usage: ab_haddock_format.py [-h] pdb out chain

Formats the antibody to fit the HADDOCK requirements with the
specified chain id and returns the list of residues belonging
to the HV loops defined according to the HADDOCK friendly format.

*** The antibody has to be numbered according to the Chothia scheme ***

Usage:
    python haddock-format.py <chothia numbered antibody> <output .pdb file> <chain_id>

Example:
    python 4G6K_ch.pdb 4G6K-HADDOCK.pdb A

Author: Francesco Ambrosetti
Email: [e-mail]

positional arguments:
  pdb         Path to the Chothia numbered antibody PDB structure
  out         Path to the output PDB file
  chain       Chain id to use for the HADDOCK-formatted PDB structure

optional arguments:
  -h, --help  show this help message and exit
-->
  </help>
</tool>