--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/ExtractProteinChains.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,67 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+<!--Proposed Tool Section: [Preparation]-->
+<tool id="ExtractProteinChains" name="ExtractProteinChains" version="1.1.0">
+  <description>separate all chains of a pdb file into separate pdb files</description>
+  <macros>
+    <token name="@EXECUTABLE@">ExtractProteinChains</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>ExtractProteinChains
+
+#if $param_pdb:
+  -pdb $param_pdb
+#end if
+#if $param_chain_id:
+  -chain_id     "$param_chain_id"
+#end if
+#if $param_o:
+  -o $param_o
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_o_id:
+  -o_id     "$adv_opts.param_o_id"
+#end if
+    #if $adv_opts.param_o_dir:
+  -o_dir     "$adv_opts.param_o_dir"
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_pdb" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input pdb file" help="(-pdb) "/>
+    <param name="param_chain_id" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="chain to extract" help="(-chain_id) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <expand macro="advanced_options">
+      <param name="param_o_id" type="text" size="30" value="$o.id" label="output id" help="(-o_id) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param name="param_o_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last solution" help="(-o_dir) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_o" format="pdb"/>
+  </outputs>
+  <help>This tool splits a pdb file into its chains.
+
+</help>
+</tool>