--- a/find_in_reference.xml	Wed Feb 05 08:12:47 2014 -0500
+++ b/find_in_reference.xml	Wed Aug 13 15:01:33 2014 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="find_in_reference" name="find in reference" version="0.0.1">
+<tool id="find_in_reference" name="find in reference" version="0.0.2">
   <description>filter peptides that are present in proteins</description>
   <command interpreter="python">find_in_reference.py  --input "$input" 
   --reference "$reference" 
@@ -7,7 +7,7 @@
     --input_column $column.input_column
     --reference_column $column.reference_column
   #end if
-  $case_insensitive
+  $case_insensitive $reverse_find
   #if 'novel' in $outputs.__str__ or not 'found' in $outputs.__str__:
     --output "$novel"
   #end if
@@ -43,6 +43,7 @@
       </when>
     </conditional>
     <param name="case_insensitive" type="boolean" truevalue="--case_insensitive" falsevalue="" checked="false" label="Ignore case when comparing"/>
+    <param name="reverse_find" type="boolean" truevalue="--reverse_find" falsevalue="" checked="false" label="reverse search: find the reference in the input" />
     <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
       <option value="novel" selected="true">lines with no match in reference</option>
       <option value="found">lines with match in reference</option>
@@ -100,6 +101,13 @@
       <param name="reference" value="human_proteins.tabular" ftype="tabular" dbkey="hg19"/>
       <output name="novel" file="novel_peptides.tabular"/>
     </test>
+    <test>
+      <param name="input" value="human_proteins.tabular" ftype="tabular" dbkey="hg19"/>
+      <param name="reference" value="human_peptides.tabular" ftype="tabular" dbkey="hg19"/>
+      <param name="reverse_find" value="True"/>
+      <param name="outputs" value="found"/>
+      <output name="found" file="found_proteins.tabular"/>
+    </test>
   </tests>
   <help>
 **Find in Reference**