--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/filters/compare.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,79 @@
+<tool id="comp1" name="Compare two Datasets" version="1.0.2">
+  <description>to find common or distinct rows</description>
+  <command interpreter="python">joinWrapper.py $input1 $input2 $field1 $field2 $mode $out_file1</command>
+  <inputs>
+    <param format="tabular" name="input1" type="data" label="Compare"/>
+    <param name="field1" label="Using column" type="data_column" data_ref="input1">
+        <validator type="no_options" message="Invalid column choice. Please try again after editing metadata of your input dataset by clicking on the pencil icon next to it."/>
+    </param>
+    <param format="tabular" name="input2" type="data" label="against" />
+    <param name="field2" label="and column" type="data_column" data_ref="input2">
+            <validator type="no_options" message="Invalid column choice. Please try again after editing metadata of your input dataset by clicking on the pencil icon next to it."/>
+    </param>
+    <param name="mode" type="select" label="To find" help="See examples below for explanation of these options">
+      <option value="N">Matching rows of 1st dataset</option>
+      <option value="V">Non Matching rows of 1st dataset</option>
+    </param>
+  </inputs>
+  <outputs>
+     <data format="input" name="out_file1" metadata_source="input1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="1.bed"/>
+      <param name="input2" value="2.bed"/>
+      <param name="field1" value="2"/>
+      <param name="field2" value="2"/>
+      <param name="mode" value="N"/>
+      <output name="out_file1" file="fs-compare.dat"/>
+    </test>
+    <!--test case with duplicated key values-->
+    <test>
+      <param name="input1" value="1.bed"/>
+      <param name="input2" value="3.bed"/>
+      <param name="field1" value="1"/>
+      <param name="field2" value="1"/>
+      <param name="mode" value="V"/>
+      <output name="out_file1" file="fs-compare-2.dat"/>
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
+
+-----
+
+**Syntax**
+
+This tool finds lines in one dataset that HAVE or DO NOT HAVE a common field with another dataset.
+
+-----
+
+**Example**
+
+If this is **First dataset**::
+
+  chr1 10 20 geneA 
+  chr1 50 80 geneB
+  chr5 10 40 geneL
+
+and this is **Second dataset**::
+
+  geneA tumor-suppressor
+  geneB Foxp2
+  geneC Gnas1
+  geneE INK4a
+
+Finding lines of the **First dataset** whose 4th column matches the 1st column of the **Second dataset** yields::
+
+  chr1 10 20 geneA 
+  chr1 50 80 geneB
+
+Conversely, using option **Non Matching rows of First dataset** on the same fields will yield::
+
+  chr5 10 40 geneL
+
+</help>
+</tool>