# HG changeset patch
# User p.lucas
# Date 1620295964 0
# Node ID a27959187855354092dda1bcd0b34031cc841354

Uploaded

diff -r 000000000000 -r a27959187855 pdbtidy_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pdbtidy_wrapper.xml	Thu May 06 10:12:44 2021 +0000
@@ -0,0 +1,39 @@
+<tool id="PDBTIDY" name="PDBTIDY" version="0">
+  <description>Using pdb_tidy tools after ab_haddock_format.py.</description>
+  <command detect_errors="exit_code"><![CDATA[
+    source /home/galaxy/data/_conda/bin/activate Ab-HADDOCK;
+    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>
+