--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/PoseIndices2PDB.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,68 @@
+<?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: [Convert, combine and store]-->
+<tool id="PoseIndices2PDB" name="PoseIndices2PDB" version="1.1.0">
+  <description>converts pose indices into PDB files </description>
+  <macros>
+    <token name="@EXECUTABLE@">PoseIndices2PDB</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>PoseIndices2PDB
+
+#if $param_i_clust:
+  -i_clust $param_i_clust
+#end if
+#if $param_i_trans:
+  -i_trans $param_i_trans
+#end if
+#if $param_i_pdb:
+  -i_pdb $param_i_pdb
+#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_i_clust" type="data" format="txt" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input cluster index file" help="(-i_clust) "/>
+    <param name="param_i_trans" type="data" format="dcd" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input tranformation file" help="(-i_trans) "/>
+    <param name="param_i_pdb" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input reference pdb file" help="(-i_pdb) "/>
+    <expand macro="advanced_options">
+      <param name="param_o_id" type="text" size="30" value="$o.id" label="output file name prefix for 2nd to last pdb file" help="(-o_id) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param name="param_o_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last pdb file" 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 converts all pose indices from a given transformation file and the corresponding reference PDBFile into separate PDBFiles.
+
+Parameters are the input pose index file (-i_clust), the original transformation file (-i_trans), the corresponding reference pdb file (-i_pdb) and a naming schema for the resulting pdb files (-o). 
+
+Output of this tool is a set of PDBFiles representing the docking poses belonging to the given input cluster.
+
+</help>
+</tool>