--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter/ob_grep.xml	Tue Mar 26 14:49:44 2013 -0400
@@ -0,0 +1,68 @@
+<tool id="ctb_obgrep" name="Compound Search" version="0.1">
+    <description>an advanced molecular grep program using SMARTS</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>
+        ## The command is a Cheetah template which allows some Python based syntax.
+        ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
+        obgrep
+
+        $invert_matches
+        #if $n_times != 0:
+            -t $n_times
+        #end if
+
+        $only_name
+        $full_match
+        $number_of_matches
+        -i ${infile.ext}
+        "${smarts_pattern}"
+        "${infile}"
+        > "${outfile}" 2>&#38;1
+    </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="smarts_pattern" type="text" format="text" label="SMARTS Pattern" help="Specify a SMARTS Pattern for your search."/>
+        <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules" truevalue="-v" 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" truevalue="-n" 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" truevalue="-f" falsevalue="" checked="false" />
+        <param name="number_of_matches" type="boolean" label="Print the number of matches" truevalue="-c" falsevalue="" checked="false" />
+    </inputs>
+    <options sanitize="False"/>
+    <outputs>
+        <data name="outfile" format_source="infile" />
+    </outputs>
+    <tests>
+    <test>
+        <param name="infile" ftype="smi" value="8_mol.smi"/>
+        <param name="smarts_pattern" value="CO"/>
+        <param name="invert_matches" value="" />
+        <param name="n_times" value="0"/>
+        <param name="only_name" value="" />
+        <param name="full_match" value="" />
+        <param name="number_of_matches" value="" />
+        <output name="outfile" ftype="smi" file="obgrep_on_8_mol.smi"/>
+    </test>
+    </tests>
+    <help>
+.. class:: warningmark
+
+**What it does**
+
+The obgrep tool can be used to search for molecules inside multi-molecule database files (e.g., SMILES, SDF, etc.) or across multiple files.
+
+-----
+
+**Output format**
+
+
+**References**
+
+Rajarshi Guha, Michael T. Howard, Geoffrey R. Hutchison, Peter Murray-Rust, Henry Rzepa, Christoph Steinbeck, Joerg Kurt Wegner, Egon Willighagen. "The Blue Obelisk -- Interoperability in Chemical Informatics." J. Chem. Inf. Model. (2006) 46(3) 991-998. DOI:10.1021/ci050400b
+The Open Babel Package http://openbabel.sourceforge.net/
+
+    </help>
+</tool>