# HG changeset patch
# User p.lucas
# Date 1620290836 0
# Node ID 40ccca3fac6df2dc625d2796d791cfa97cd1b727
# Parent  6a4d5446c12357ff99d6940471becbf91aece7ac
Uploaded wrapper

diff -r 6a4d5446c123 -r 40ccca3fac6d abhaddock_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abhaddock_wrapper.xml	Thu May 06 08:47:16 2021 +0000
@@ -0,0 +1,42 @@
+<tool id="Ab_haddock_format" name="Ab_haddock_format" version="1.0">
+  <description>Using ab_haddock_format.py after ANARCI.</description>
+  <command detect_errors="exit_code"><![CDATA[
+    conda activate Ab-HADDOCK;
+    python2.7 ab_haddock_format.py  '${input}' '${output}' '${chain}'
+    conda 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: ambrosetti.francesco@gmail.com
+
+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>
+