--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/Trajectory2RigidTransformation.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,39 @@
+<?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="Trajectory2RigidTransformation" name="Trajectory2RigidTransformation" version="1.1.0">
+  <description>converts a trajectory file into a rigid transformation file </description>
+  <macros>
+    <token name="@EXECUTABLE@">Trajectory2RigidTransformation</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>Trajectory2RigidTransformation
+
+#if $param_i_dcd:
+  -i_dcd $param_i_dcd
+#end if
+#if $param_i_pdb:
+  -i_pdb $param_i_pdb
+#end if
+#if $param_o:
+  -o $param_o
+#end if
+</command>
+  <inputs>
+    <param name="param_i_dcd" type="data" format="dcd" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input trajectory file" help="(-i_dcd) "/>
+    <param name="param_i_pdb" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input pdb-file" help="(-i_pdb) "/>
+  </inputs>
+  <expand macro="advanced_options"/>
+  <outputs>
+    <data name="param_o" format="txt"/>
+  </outputs>
+  <help>This tool converts SnapShots of a given TrajectoryFile and the reference PDBFile into a rigid transformation file.
+
+Parameters are the input SnapShots as TrajectoryFile (-i_dcd), the corresponding reference pdb file that was originally used to create the TrajectoryFile (-i_pdb) and a naming schema for the resulting transformation file (-o).
+
+Output of this tool is a file storing each given SnapShot as rigid transformation per line.
+
+</help>
+</tool>