--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/PDBRMSDCalculator.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,78 @@
+<?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: [Docking]-->
+<tool id="PDBRMSDCalculator" name="PDBRMSDCalculator" version="1.1.0">
+  <description>computes RMSD between protein poses </description>
+  <macros>
+    <token name="@EXECUTABLE@">PDBRMSDCalculator</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>PDBRMSDCalculator
+
+#if $param_i_pdb:
+  -i_pdb $param_i_pdb
+#end if
+#if $param_i_query:
+  -i_query $param_i_query
+#end if
+#if $param_i_type:
+  -i_type
+  #if " " in str($param_i_type):
+    "$param_i_type"
+  #else
+    $param_i_type
+  #end if
+#end if
+#if $param_o:
+  -o $param_o
+#end if
+#if $param_scope:
+  -scope
+  #if " " in str($param_scope):
+    "$param_scope"
+  #else
+    $param_scope
+  #end if
+#end if
+#if $param_rmsd_type:
+  -rmsd_type
+  #if " " in str($param_rmsd_type):
+    "$param_rmsd_type"
+  #else
+    $param_rmsd_type
+  #end if
+#end if
+</command>
+  <inputs>
+    <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) "/>
+    <param name="param_i_query" type="data" format="dcd,txt,pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="molecule(s) to compare input file" help="(-i_query) "/>
+    <param name="param_i_type" type="select" optional="True" value="pdb" label="query type (pdb, dcd, or transformation file (rigid_transformations)" help="(-i_type) ">
+      <option value="pdb">pdb</option>
+      <option value=" dcd"> dcd</option>
+      <option value=" rigid_transformations"> rigid_transformations</option>
+    </param>
+    <param name="param_scope" type="select" optional="True" value="C_ALPHA" label="atoms to be considered for scoreing a pose (C_ALPHA, BACKBONE, ALL_ATOMS)" help="(-scope) ">
+      <option value="C_ALPHA">C_ALPHA</option>
+      <option value=" BACKBONE"> BACKBONE</option>
+      <option value=" ALL_ATOMS"> ALL_ATOMS</option>
+    </param>
+    <param name="param_rmsd_type" type="select" optional="True" value="SNAPSHOT_RMSD" label="rmsd type used for clustering (SNAPSHOT_RMSD, RIGID_RMSD, CENTER_OF_MASS_DISTANCE)" help="(-rmsd_type) ">
+      <option value="SNAPSHOT_RMSD">SNAPSHOT_RMSD</option>
+      <option value=" RIGID_RMSD"> RIGID_RMSD</option>
+      <option value=" CENTER_OF_MASS_DISTANCE"> CENTER_OF_MASS_DISTANCE</option>
+    </param>
+  </inputs>
+  <expand macro="advanced_options"/>
+  <outputs>
+    <data name="param_o" format="txt"/>
+  </outputs>
+  <help>This tool computes the RMSD between proteins.
+
+Parameters are either a second input file (i_query) who's type has to be specified (i_type) and can be either a single pdb, a dcd or a transformation file. Optional parameters are the rmsd type (-rmsd_type), and the type of atoms used for scoring a pose (-scope).
+
+Output of this tool is a either the rmsd (in the pdb-pdb case) or a file (-o) containing the RMSD between the first pose and all other poses.
+
+</help>
+</tool>