--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/Converter.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,96 @@
+<?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="Converter" name="Converter" version="1.1.0">
+  <description>interconvert molecular file-formats</description>
+  <macros>
+    <token name="@EXECUTABLE@">Converter</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>Converter
+
+#if $param_i:
+  -i $param_i
+#end if
+#if $param_if:
+  -if
+  #if " " in str($param_if):
+    "$param_if"
+  #else
+    $param_if
+  #end if
+#end if
+#if $param_o:
+  -o $param_o
+#end if
+#if $param_of:
+  -of
+  #if " " in str($param_of):
+    "$param_of"
+  #else
+    $param_of
+  #end if
+#end if
+#if $param_rm:
+  -rm $param_rm
+#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 filename" help="(-i) "/>
+    <param name="param_if" type="select" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input format" help="(-if) ">
+      <option value="mol2">mol2</option>
+      <option value=" sdf"> sdf</option>
+      <option value=" drf"> drf</option>
+      <option value=" pdb"> pdb</option>
+      <option value=" ac"> ac</option>
+      <option value=" ent"> ent</option>
+      <option value=" brk"> brk</option>
+      <option value=" hin"> hin</option>
+      <option value=" mol"> mol</option>
+      <option value=" xyz"> xyz</option>
+      <option value=" mol2.gz"> mol2.gz</option>
+      <option value=" sdf.gz"> sdf.gz</option>
+      <option value=" drf.gz"> drf.gz</option>
+      <option value=" pdb.gz"> pdb.gz</option>
+      <option value=" ac.gz"> ac.gz</option>
+      <option value=" ent.gz"> ent.gz</option>
+      <option value=" brk.gz"> brk.gz</option>
+      <option value=" hin.gz"> hin.gz</option>
+      <option value=" mol.gz"> mol.gz</option>
+      <option value=" xyz.gz"> xyz.gz</option>
+    </param>
+    <param name="param_of" type="select" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="output format" help="(-of) ">
+      <option value="mol2">mol2</option>
+      <option value=" sdf"> sdf</option>
+      <option value=" drf"> drf</option>
+      <option value=" pdb"> pdb</option>
+      <option value=" ac"> ac</option>
+      <option value=" ent"> ent</option>
+      <option value=" brk"> brk</option>
+      <option value=" hin"> hin</option>
+      <option value=" mol"> mol</option>
+      <option value=" xyz"> xyz</option>
+      <option value=" mol2.gz"> mol2.gz</option>
+      <option value=" sdf.gz"> sdf.gz</option>
+      <option value=" drf.gz"> drf.gz</option>
+      <option value=" pdb.gz"> pdb.gz</option>
+      <option value=" ac.gz"> ac.gz</option>
+      <option value=" ent.gz"> ent.gz</option>
+      <option value=" brk.gz"> brk.gz</option>
+      <option value=" hin.gz"> hin.gz</option>
+      <option value=" mol.gz"> mol.gz</option>
+      <option value=" xyz.gz"> xyz.gz</option>
+    </param>
+    <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>This tool can be used to convert between different molecular file-formats.
+Supported formats are mol2,sdf,drf,pdb,ac,ent,brk,hin,mol,xyz,mol2.gz,sdf.gz,drf.gz,pdb.gz,ac.gz,ent.gz,brk.gz,hin.gz,mol.gz,xyz.gz. File extensions of input and output filenames are ignored.
+
+</help>
+</tool>