--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/MolCombine.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,64 @@
+<?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="MolCombine" name="MolCombine" version="1.1.0">
+  <description>combine molecular files</description>
+  <macros>
+    <token name="@EXECUTABLE@">MolCombine</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>MolCombine
+
+#if $param_i1:
+  -i1 $param_i1
+#end if
+#if $param_i2:
+  -i2 $param_i2
+#end if
+#if $param_mode:
+  -mode
+  #if " " in str($param_mode):
+    "$param_mode"
+  #else
+    $param_mode
+  #end if
+#end if
+#if $param_o:
+  -o $param_o
+#end if
+#if $param_ignH:
+  -ignH $param_ignH
+#end if
+#if $param_replace_prop:
+  -replace_prop $param_replace_prop
+#end if
+#if $param_rm:
+  -rm $param_rm
+#end if
+</command>
+  <inputs>
+    <param name="param_i1" type="data" format="mol2,sdf,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input molecule file A" help="(-i1) "/>
+    <param name="param_i2" type="data" format="mol2,sdf,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input molecule file B" help="(-i2) "/>
+    <param name="param_mode" type="select" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="'intersection', 'union' or 'b_not_a'" help="(-mode) ">
+      <option value="intersection">intersection</option>
+      <option value=" union"> union</option>
+      <option value=" b_not_a"> b_not_a</option>
+    </param>
+    <param name="param_ignH" type="integer" min="0" max="1" optional="True" value="1" label="ignore hydrogens, i.e" help="(-ignH) match molecules to any protonation state"/>
+    <param name="param_replace_prop" type="integer" min="0" max="1" optional="True" value="0" label="replace properties from file 1 w/ those from file 2" help="(-replace_prop) "/>
+    <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input files when finished" help="(-rm) "/>
+  </inputs>
+  <expand macro="advanced_options"/>
+  <outputs>
+    <data name="param_o" metadata_source="param_i1" format="input"/>
+  </outputs>
+  <help>This tool generates the intersection or union of two given chemical files. Property-tags of molecules that appear in both input files are automatically merged.
+
+If you want to match molecules regardless of their protonation state, use option '-ignH'.
+
+Output of this tool is a file containing the union resp. intersection of all molecules of input A and B.
+
+</help>
+</tool>