--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/regVariation/getIndels_2way.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,59 @@
+<tool id="getIndels_2way" name="Fetch Indels">
+  <description> from pairwise alignments</description>
+  <command interpreter="python">
+  	getIndels.py $input1 $out_file1
+  </command>
+  <inputs>
+    <page>
+    	<param format="maf" name="input1" type="data" label="Select data"/>
+    </page>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out_file1" metadata_source="input1"/>
+  </outputs>
+  <requirements>
+    <requirement type="python-module">numpy</requirement>
+  </requirements>
+  <tests>
+    <test>
+      <param name="input1" value="6.maf"/>
+      <output name="out_file1" file="6_indels.tabular"/>
+    </test>
+  </tests>
+ <help> 
+
+.. class:: infomark
+
+**What it does**
+
+This tool estimates the number of indels for every alignment block of the MAF file. 
+
+-----
+
+.. class:: warningmark
+
+**Note**
+
+Any block/s not containing exactly 2 species will be omitted. 
+
+-----
+
+**Example**
+
+- For the following alignment block::
+
+   a score=7233.0
+   s hg18.chr1     100 35 + 247249719 AT--GACTGAGGACTTAGTTTAAGATGTTCCTACT
+   s rheMac2.chr11 200 31 + 134511895 ATAAG-CGGACGACTTAGTTTAAGATGTTCC---- 
+
+- running this tool will return::
+
+   #Block   Source	      Seq1_Start	Seq1_End  Seq2_Start	Seq2_End	Indel_length
+   1	   hg18.chr1            101	         102	     202	     204	      2
+   1	   rheMac2.chr11	103	         104	     204	     205	      1
+   1	   rheMac2.chr11	129	         133	     229	     230	      4
+   
+</help>  
+
+
+</tool>