--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/LigCheck.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,63 @@
+<?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: [Checks and evaluations]-->
+<tool id="LigCheck" name="LigCheck" version="1.1.0">
+  <description>check molecules for errors</description>
+  <macros>
+    <token name="@EXECUTABLE@">LigCheck</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>LigCheck
+
+#if $param_i:
+  -i $param_i
+#end if
+#if $param_o:
+  -o $param_o
+#end if
+#if $param_ef:
+  -ef $param_ef
+#end if
+#if $param_ri:
+  -ri $param_ri
+#end if
+#if $param_ut:
+  -ut $param_ut
+#end if
+#if $param_nc:
+  -nc $param_nc
+#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 molecule file" help="(-i) "/>
+    <param name="param_ef" type="float" value="0.5" label="error fraction; print error if fraction of invalid mols is large" help="(-ef) "/>
+    <param name="param_ri" type="integer" min="0" max="1" optional="True" value="1" label="remove invalid molecules" help="(-ri) "/>
+    <param name="param_ut" type="integer" min="0" max="1" optional="True" value="0" label="check for unique topologies" help="(-ut) "/>
+    <param name="param_nc" type="integer" min="0" max="1" optional="True" value="0" label="no not check for unique conformations" help="(-nc) "/>
+    <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 checks all molecules of the given input file for errors. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+
+The following checks are done for each molecule:
+
+    * bond-lengths may not be completely senseless (i.e. &lt;0.7 or &gt;2.5 Angstroem)
+    * each 'molecule' in the input file may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments.
+    * each atom must have a valid assigned element
+    * the molecule must be protonated (since this is necessary for docking/(re-)scoring).
+    * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
+    * partial charges may not contain completely senseless values (&gt;5 or &lt;-5).
+    * each conformation should appear only once within the given file, otherwise it is rejected and not written to the output file. However, if option '-ut' is used, molecules will instead be checked for unique topologies.
+
+If option '-ri' is used, only those molecules that pass all those tests are written to the output file. If this option is not used, all molecules are written to output containing a property 'score_ligcheck' with a value of 1 if the molecule passed all tests or with a value of 0 if it did not pass them.
+
+</help>
+</tool>