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1 <tool id="ABHADDOCK" name="ABHADDOCK" version="1">
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2 <description>Using ab_haddock_format.py after ANARCI.</description>
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3 <command detect_errors="exit_code"><![CDATA[
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4 source /home/galaxy/data/_conda/bin/activate Ab-HADDOCK;
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5 python2.7 /home/galaxy/HADDOCK-antibody-antigen/ab_haddock_format.py '${input}' '${output1}' ${chain} > '${output2}';
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6 source /home/galaxy/data/_conda/bin/deactivate
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7 ]]></command>
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8 <inputs>
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9 <param name="input" format="pdb" type="data" label="Select your PDB file."/>
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10 <param name="chain" type="text" label="Chain id to use." help="Chain id to use for the HADDOCK-formatted PDB structure."/>
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11 </inputs>
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12 <outputs>
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13 <data name="output1" format="pdb" />
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14 <data name="output2" format="txt" />
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15 </outputs>
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16 <help>
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17 usage: ab_haddock_format.py [-h] pdb out chain
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18
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19 Formats the antibody to fit the HADDOCK requirements with the
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20 specified chain id and returns the list of residues belonging
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21 to the HV loops defined according to the HADDOCK friendly format.
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22
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23 *** The antibody has to be numbered according to the Chothia scheme ***
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24
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25 Usage:
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26 python haddock-format.py 'chothia numbered antibody' 'output .pdb file' 'chain_id'
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27
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28 Example:
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29 python 4G6K_ch.pdb 4G6K-HADDOCK.pdb A
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30
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31 Author: Francesco Ambrosetti
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32 Email: ambrosetti.francesco@gmail.com
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33
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34 positional arguments:
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35 pdb Path to the Chothia numbered antibody PDB structure
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36 out Path to the output PDB file
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37 chain Chain id to use for the HADDOCK-formatted PDB structure
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38
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39 optional arguments:
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40 -h, --help show this help message and exit
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41 </help>
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42 </tool>
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43
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