--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/SeparateMolecules.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,44 @@
+<?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="SeperateMolecules" name="SeperateMolecules" version="1.1.0">
+  <description>Split each multi molecule entry to separate single molecule entries</description>
+  <macros>
+    <token name="@EXECUTABLE@">SeperateMolecules</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>SeperateMolecules
+
+#if $param_i:
+  -i $param_i
+#end if
+#if $param_o:
+  -o $param_o
+#end if
+#if $param_min_atoms:
+  -min_atoms $param_min_atoms
+#end if
+#if $param_all:
+  -all $param_all
+#end if
+</command>
+  <inputs>
+    <param name="param_i" type="data" format="sdf,sd,mol2,mol" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input file (mol mol2 sd sdf)" help="(-i) "/>
+    <param name="param_min_atoms" type="integer" value="0" label="only keep molecules having at least a minimal number of atoms" help="(-min_atoms) "/>
+    <param name="param_all" type="integer" min="0" max="1" optional="True" value="0" label="keep all contained molecules, but each in separated entries" help="(-all) "/>
+  </inputs>
+  <expand macro="advanced_options"/>
+  <outputs>
+    <data name="param_o" metadata_source="param_i" format="input"/>
+  </outputs>
+  <help>This tool splits each molecule entry contained in a structure file (mol, sdf, mol2) into possibly multiple molecule entries, so that the new entries contain only a single connected molecule. The results will always be written to a single structure file in the same format as the input format, or a sdf-file in the case of a mol input file. The tool works with the given bond information, which needs to be correct.
+
+Standard behaviour: only the largest molecule from each entry is retained ('largest' according to the number of atoms).
+
+Optional parameters:
+Retain all molecules contained in a molecule entry ('-all'). Alternatively the minimal number of atoms required for a molecule to be kept can be specified ('-min_atoms').
+
+</help>
+</tool>