--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter/multi_obgrep.xml	Tue Mar 26 14:49:44 2013 -0400
@@ -0,0 +1,51 @@
+<tool id="ctb_multi_obgrep" name="Multi Compound Search" version="0.1">
+    <description>an advanced molecular grep program using SMARTS</description>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command interpreter="python">
+
+    multi_obgrep.py
+        -i $infile
+        --iformat ${infile.ext}
+        -q $query
+        -o "${outfile}"
+        $invert_matches
+        --n-times $n_times
+        $only_name
+        $full_match
+        $number_of_matches
+        --processors 10
+
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Compound File" help="Specify a compound file in SDF Format"/>
+        <param name="query" type='data' format="tabular,text" label="Query file" help="One SMARTS pattern in each line."/>
+        <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules (-v)" truevalue="--invert-matches" falsevalue="" checked="false" />
+        <param name="n_times" type="integer" value="0" label="Print a molecule only if the pattern occurs # times inside the molecule" />
+        <param name="only_name" type="boolean" label="Only print the name of the molecules (-n)" truevalue="--only-name" falsevalue="" checked="false" />
+        <param name="full_match" type="boolean" label="Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the SMARTS pattern (-f)" truevalue="--full-match" falsevalue="" checked="false" />
+        <param name="number_of_matches" type="boolean" label="Print the number of matches (-c)" truevalue="--number-of-matches" falsevalue="" checked="false" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format_source="infile" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+
+
+**What it does**
+
+Providing a query file with SMARTS pattern in each line. These tool will run obgreg in parallel and merges the results.
+
+-----
+
+**Example**
+
+
+
+    </help>
+</tool>