--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/PartialChargesCopy.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,36 @@
+<?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: [Preparation]-->
+<tool id="PartialChargesCopy" name="PartialChargesCopy" version="1.1.0">
+  <description>transfer part. charges between files</description>
+  <macros>
+    <token name="@EXECUTABLE@">PartialChargesCopy</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>PartialChargesCopy
+
+#if $param_i:
+  -i $param_i
+#end if
+#if $param_chr:
+  -chr $param_chr
+#end if
+#if $param_o:
+  -o $param_o
+#end if
+</command>
+  <inputs>
+    <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input molecule file" help="(-i) "/>
+    <param name="param_chr" type="data" format="mol2,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="file containing the same molecules as the input file, but with (different) partial charges" help="(-chr) "/>
+  </inputs>
+  <expand macro="advanced_options"/>
+  <outputs>
+    <data name="param_o" metadata_source="param_chr" format="input"/>
+  </outputs>
+  <help>This tool copies partial charges from a given file to the conformations read from a different file.
+This can be useful when computing partial charges with external tools, most of which write output as mol2-files *without* support for storing molecular properties. By use of this tool we can thus assign the computed partial charges to the original molecules, thus retaining all properties.
+
+</help>
+</tool>