--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter/ob_remSmall.xml	Tue Mar 26 14:49:44 2013 -0400
@@ -0,0 +1,56 @@
+<tool id="ctb_remSmall" name="Remove small molecules" version="1.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+    obabel
+      -i"${infile.ext}"
+      "${infile}"
+      -ocopy
+      -O "${outfile}"
+      --filter "atoms > $cutoff"
+      -e
+      2>&#38;1
+    </command>
+    <inputs>
+        <param name="infile" format="sdf,mol,mol2,cml,inchi,smi" type="data" label="Molecular input file" />
+        <param name="cutoff" size="3" type="integer" value="5" label="Specify the cut-off value (only molecules with more than this number of atoms will pass the filter)" />
+    </inputs>
+    <outputs>
+        <data format_source="infile" name="outfile" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="smi" value="3_mol.smi" />
+            <param name="cutoff" value="5" />
+            <output name="outfile" ftype="smi" file="obremsmall_on_3_mol.smi" />
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**What does this tool do?**
+
+  This tool filters a library of compounds and removes small molecules.
+
+-----
+
+.. class:: warningmark
+
+**Tip:** some libraries may contain molecules without 1D/3D descriptor. These molecules may provoke the crashing of any other tool. As a general rule, the user is strongly adviced to run this tool before proceeding to any further step.
+
+-----
+
+.. class:: infomark
+
+**Output format:** is the same as the input file format.
+
+-----
+
+**This tool uses OpenBabel:** The Open Babel Package, version 2.3.0 http://openbabel.sourceforge.net/
+
+    </help>
+</tool>