# HG changeset patch
# User p.lucas
# Date 1620306402 0
# Node ID ed93b303798ce4af6ca55e9371e60cab58ef9cb3

Uploaded

diff -r 000000000000 -r ed93b303798c pdbselaltloc_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pdbselaltloc_wrapper.xml	Thu May 06 13:06:42 2021 +0000
@@ -0,0 +1,40 @@
+<tool id="PDBSELALTLOC" name="SELALTLOC" version="0">
+  <description>Using pdb_selaltloc tool.</description>
+  <command detect_errors="exit_code"><![CDATA[
+    source /home/galaxy/data/_conda/bin/activate pdbtools;
+    pdb_selaltloc '${input}' > '${output}';
+    source /home/galaxy/data/_conda/bin/deactivate
+  ]]></command>
+  <inputs>
+    <param name="input" format="pdb" type="data" label="Select your PDB file."/>
+    <param name="opt" format="text" label="Specific altloc label to select."/>
+  </inputs>
+  <outputs>
+    <data name="output" format="pdb" />
+  </outputs>
+  <help>
+Selects altloc labels for the entire PDB file.
+
+By default, selects the label with the highest occupancy value for each atom,
+but the user can define a specific altloc label to select.
+
+Selecting by highest occupancy removes all altloc labels for all atoms. If the
+user provides an option (e.g. -A), only atoms with conformers with an altloc A
+are processed by the script. If you select -A and an atom has conformers with
+altlocs B and C, both B and C will be kept in the output.
+
+Usage:
+    python pdb_selaltloc.py [-<option>] <pdb file>
+
+Example:
+    python pdb_selaltloc.py 1CTF.pdb  # picks locations with highest occupancy
+    python pdb_selaltloc.py -A 1CTF.pdb  # picks alternate locations labelled 'A'
+
+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>
+