--- a/ob_grep.xml	Mon Sep 03 16:40:06 2018 -0400
+++ b/ob_grep.xml	Tue May 07 13:33:55 2019 -0400
@@ -1,5 +1,5 @@
-<tool id="openbabel_obgrep" name="Compound Search" version="@VERSION@.0">
-    <description>an advanced molecular grep program using SMARTS</description>
+<tool id="openbabel_obgrep" name="Compound search" version="@VERSION@.0">
+    <description>- an advanced molecular search program using SMARTS</description>
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
@@ -7,28 +7,55 @@
     <expand macro="requirements"/>
     <command>
 <![CDATA[
-        obgrep
-            $invert_matches
-            #if $n_times:
-                -t $n_times
-            #end if
-            $only_name
-            $full_match
-            $number_of_matches
-            -i '${infile.ext}'
-            '${smarts_pattern}'
-            '${infile}'
-            > '${outfile}'
+
+        #if $input_type.inp == 'single':
+            obgrep
+                $invert_matches
+                #if $n_times:
+                    -t $n_times
+                #end if
+                $only_name
+                $full_match
+                $number_of_matches
+                -i '${infile.ext}'
+                '${input_type.smarts_pattern}'
+                '${infile}'
+                > '${outfile}'
+        #else if $input_type.inp == 'multi':
+            python '$__tool_directory__/multi_obgrep.py'
+                -i $infile
+                --iformat ${infile.ext}
+                -q '${input_type.query}'
+                -o '${outfile}'
+                $invert_matches
+                --n-times $n_times
+                $only_name
+                $full_match
+                $number_of_matches
+                --processors "\${GALAXY_SLOTS:-12}"
+        #end if
+
 ]]>
     </command>
     <inputs>
         <expand macro="infile_all_types"/>
-        <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="" min="1" optional="True"
-            label="Print a molecule only if the pattern occurs # times inside the molecule" />
+        <conditional name="input_type">
+            <param name="inp" type="select" label="Input">
+                <option value="single">Enter a single SMARTS pattern</option>
+                <option value="multi">Upload one or more SMARTS patterns in a text file</option>
+            </param>
+            <when value="single">
+                <param name="smarts_pattern" type="text" format="text" label="SMARTS Pattern" help="Specify a SMARTS Pattern for your search."/>
+            </when>
+            <when value="multi">
+                <param name="query" type='data' format="tabular,text" label="Query file" help="One SMARTS pattern in each line."/>
+            </when>
+        </conditional>
+        <param name="invert_matches" type="boolean" label="Perform an inverted search, i.e. print non-matching molecules" truevalue="-v" falsevalue="" checked="false" />
+        <param name="n_times" type="integer" value="0" min="0" optional="True"
+            label="Print a molecule only if the pattern occurs this often 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="full_match" type="boolean" label="Full match" help="Print matching molecules only when the number of heavy atoms equals 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"/>
@@ -38,6 +65,7 @@
     <tests>
         <test>
             <param name="infile" ftype="smi" value="8_mol.smi"/>
+            <param name="inp" value="single"/>
             <param name="smarts_pattern" value="CO"/>
             <param name="invert_matches" value="False" />
             <param name="only_name" value="False" />
@@ -45,6 +73,12 @@
             <param name="number_of_matches" value="False" />
             <output name="outfile" ftype="smi" file="obgrep_on_8_mol.smi"/>
         </test>
+        <test>
+            <param name="infile" ftype="smi" value="2_mol.smi"/>
+            <param name="inp" value="multi"/>
+            <param name="query" value="pattern.smarts" />
+            <output name="outfile" ftype="smi" file="ob_multi_obgrep.smi" />
+        </test>
     </tests>
     <help>
 <![CDATA[
@@ -53,9 +87,9 @@
 
 **What this tool does**
 
-Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files.
-It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_.
+Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files. Not all SMARTS features from the original implementation in the Daylight Toolkit are supported by OpenBabel; please have a look here_.
 
+The search query can be submitted either as a single SMARTS pattern or as a file containing multiple SMARTS patterns.
 
 .. _Obgrep: http://openbabel.org/wiki/Obgrep
 .. _here: http://openbabel.org/wiki/SMARTS