--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/MolFilter.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,84 @@
+<?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="MolFilter" name="MolFilter" version="0.9">
+  <description>filter molecule files            </description>
+  <macros>
+    <token name="@EXECUTABLE@">MolFilter</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>MolFilter
+
+#if $param_i:
+  -i $param_i
+#end if
+#if $param_min_logP:
+  -min_logP $param_min_logP
+#end if
+#if $param_max_logP:
+  -max_logP $param_max_logP
+#end if
+#if $param_min_MW:
+  -min_MW $param_min_MW
+#end if
+#if $param_max_MW:
+  -max_MW $param_max_MW
+#end if
+#if $param_q:
+  -q $param_q
+#end if
+#if $param_min_sim:
+  -min_sim $param_min_sim
+#end if
+#if $param_max_sim:
+  -max_sim $param_max_sim
+#end if
+#if $param_smarts:
+  -smarts     "$param_smarts"
+#end if
+#if $param_smarts_file:
+  -smarts_file $param_smarts_file
+#end if
+#if $param_o:
+  -o $param_o
+#end if
+#if $param_quiet:
+  -quiet $param_quiet
+#end if
+#if $param_rm:
+  -rm $param_rm
+#end if
+</command>
+  <inputs>
+    <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input molecule-file" help="(-i) "/>
+    <param name="param_min_logP" type="float" value="0.0" label="minimal logP value" help="(-min_logP) "/>
+    <param name="param_max_logP" type="float" value="20.0" label="maximal logP value" help="(-max_logP) "/>
+    <param name="param_min_MW" type="float" value="0.0" label="minimal molecular weight" help="(-min_MW) "/>
+    <param name="param_max_MW" type="float" value="10000000000.0" label="maximal molecular weight" help="(-max_MW) "/>
+    <param name="param_q" type="data" format="txt" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="query molecules for similarity searching" help="(-q) "/>
+    <param name="param_min_sim" type="float" value="0.0" label="minimal average similarity" help="(-min_sim) "/>
+    <param name="param_max_sim" type="float" value="1.0" label="maximal similarity" help="(-max_sim) "/>
+    <param name="param_smarts" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="SMARTS pattern" help="(-smarts) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_smarts_file" type="data" format="txt" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="SMARTS pattern" help="(-smarts_file) "/>
+    <param name="param_quiet" type="integer" min="0" max="1" optional="True" value="0" label="by quiet, i.e. do not show progress information" help="(-quiet) "/>
+    <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/>
+  </inputs>
+  <expand macro="advanced_options"/>
+  <outputs>
+    <data name="param_o" metadata_source="param_i" format="input"/>
+  </outputs>
+  <help>MolFilter can filter molecules from a molecule input file according to SMARTS expressions, logP, molecular weight, or similarity to query molecule(s).
+
+Output of this tool is a molecule file that contains all compounds that fulfilled the specified search criteria.
+
+</help>
+</tool>