--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/DockPoseClustering.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,178 @@
+<?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="DockPoseClustering" name="DockPoseClustering" version="1.1.0">
+  <description>clusters docking poses </description>
+  <macros>
+    <token name="@EXECUTABLE@">DockPoseClustering</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>DockPoseClustering
+
+#if $param_i_pdb:
+  -i_pdb $param_i_pdb
+#end if
+#if $param_i_dcd:
+  -i_dcd $param_i_dcd
+#end if
+#if $param_i_trans:
+  -i_trans $param_i_trans
+#end if
+#if $param_o_index_list:
+  -o_index_list $param_o_index_list
+#end if
+#if $param_o_score_matrix:
+  -o_score_matrix $param_o_score_matrix
+#end if
+#if $param_o_dcd:
+  -o_dcd $param_o_dcd
+#end if
+#if $param_rmsd_cutoff:
+  -rmsd_cutoff $param_rmsd_cutoff
+#end if
+#if $param_alg:
+  -alg
+  #if " " in str($param_alg):
+    "$param_alg"
+  #else
+    $param_alg
+  #end if
+#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
+#if $param_o_red_dcd:
+  -o_red_dcd $param_o_red_dcd
+#end if
+#if $param_o_cluster_tree:
+  -o_cluster_tree $param_o_cluster_tree
+#end if
+#if $param_refine_alg:
+  -refine_alg
+  #if " " in str($param_refine_alg):
+    "$param_refine_alg"
+  #else
+    $param_refine_alg
+  #end if
+#end if
+#if $param_refine_rmsd_type:
+  -refine_rmsd_type
+  #if " " in str($param_refine_rmsd_type):
+    "$param_refine_rmsd_type"
+  #else
+    $param_refine_rmsd_type
+  #end if
+#end if
+#if $param_refine_rmsd_scope:
+  -refine_rmsd_scope
+  #if " " in str($param_refine_rmsd_scope):
+    "$param_refine_rmsd_scope"
+  #else
+    $param_refine_rmsd_scope
+  #end if
+#end if
+#if $param_use_refinement:
+  -use_refinement $param_use_refinement
+#end if
+#if $param_run_serial:
+  -run_serial $param_run_serial
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_o_dcd_id:
+  -o_dcd_id     "$adv_opts.param_o_dcd_id"
+#end if
+    #if $adv_opts.param_o_dcd_dir:
+  -o_dcd_dir     "$adv_opts.param_o_dcd_dir"
+#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_dcd" type="data" format="dcd" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input dcd-file" help="(-i_dcd) "/>
+    <param name="param_i_trans" type="data" format="txt" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="or input transformation file for rigid rmsd clustering" help="(-i_trans) "/>
+    <param name="param_rmsd_cutoff" type="float" min="0.0" max="100.0" optional="True" value="5.0" label="minimal rmsd between the final clusters (default 5.0)" help="(-rmsd_cutoff) "/>
+    <param name="param_alg" type="select" optional="True" value="CLINK_DEFAYS" label="algorithm used for clustering (CLINK_DEFAYS, CLINK_ALTHAUS, NEAREST_NEIGHBOR_CHAIN_WARD, SLINK_SIBSON, TRIVIAL_COMPLETE_LINKAGE)" help="(-alg) ">
+      <option value="CLINK_DEFAYS">CLINK_DEFAYS</option>
+      <option value=" CLINK_ALTHAUS"> CLINK_ALTHAUS</option>
+      <option value=" TRIVIAL_COMPLETE_LINKAGE"> TRIVIAL_COMPLETE_LINKAGE</option>
+      <option value=" NEAREST_NEIGHBOR_CHAIN_WARD"> NEAREST_NEIGHBOR_CHAIN_WARD</option>
+      <option value=" SLINK_SIBSON"> SLINK_SIBSON</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>
+    <param name="param_refine_alg" type="select" optional="True" value="CLINK_DEFAYS" label="algorithm used for second clustering run (CLINK_DEFAYS, NEAREST_NEIGHBOR_CHAIN_WARD, SLINK_SIBSON, TRIVIAL_COMPLETE_LINKAGE)" help="(-refine_alg) ">
+      <option value="CLINK_DEFAYS">CLINK_DEFAYS</option>
+      <option value=" CLINK_ALTHAUS"> CLINK_ALTHAUS</option>
+      <option value=" TRIVIAL_COMPLETE_LINKAGE"> TRIVIAL_COMPLETE_LINKAGE</option>
+      <option value=" NEAREST_NEIGHBOR_CHAIN_WARD"> NEAREST_NEIGHBOR_CHAIN_WARD</option>
+      <option value=" SLINK_SIBSON"> SLINK_SIBSON</option>
+    </param>
+    <param name="param_refine_rmsd_type" type="select" optional="True" value="SNAPSHOT_RMSD" label="rmsd type used for second clustering run (SNAPSHOT_RMSD, RIGID_RMSD, CENTER_OF_MASS_DISTANCE)" help="(-refine_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>
+    <param name="param_refine_rmsd_scope" type="select" optional="True" value="C_ALPHA" label="atoms to be considered for rmsd score in second clustering run (C_ALPHA, BACKBONE, ALL_ATOMS)" help="(-refine_rmsd_scope) ">
+      <option value="C_ALPHA">C_ALPHA</option>
+      <option value=" BACKBONE"> BACKBONE</option>
+      <option value=" ALL_ATOMS"> ALL_ATOMS</option>
+    </param>
+    <param name="param_use_refinement" type="integer" min="0" max="1" optional="True" value="0" label="Apply a second clustering run with different options (-refine_alg &lt;string&gt;, -refine_rmsd_type &lt;string&gt;, and -refine_rmsd_scope &lt;string&gt;)" help="(-use_refinement) "/>
+    <param name="param_run_serial" type="integer" min="0" max="1" optional="True" value="0" label="force serial excecution, even if parallel execution would be supported by the algorithm" help="(-run_serial) "/>
+    <expand macro="advanced_options">
+      <param name="param_o_dcd_id" type="text" size="30" value="$o_dcd.id" label="output id" help="(-o_dcd_id) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param name="param_o_dcd_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last cluster dcd file (if needed)" help="(-o_dcd_dir) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_o_index_list" format="txt"/>
+    <data name="param_o_score_matrix" format="txt"/>
+    <data name="param_o_dcd" format="dcd"/>
+    <data name="param_o_red_dcd" format="dcd"/>
+    <data name="param_o_cluster_tree" format="dat"/>
+  </outputs>
+  <help>This tool computes clusters of docking poses given as conformation set or a list of rigid transformations.
+
+Parameters are either the input ConformationSet (-i_dcd) and one corresponding pdb file (-i_pdb), or a transformation file (-i_trans). Output can be a cluster index list (-o_index_list), a cluster scoring matrix (-o_score_matrix), or dcd files per cluster (-o_dcd). Optional parameters are the algorithm (-alg), the minimal rmsd between the final clusters (-rmsd_cutoff), the rmsd type (-rmsd_type), and the type of atoms used for scoring a pose (-scope). The optional parameter -o_red_dcd sets the output file for the reduced cluster set (one representative per cluster). The optional parameter -o_cluster_tree specifies the output file for storing the cluster tree.
+
+Output of this tool depends in the choice of the output parameters.
+
+</help>
+</tool>