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+++ b/tools/visualization/LAJ.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,32 @@
+<tool id="laj_1" name="LAJ">
+<description>Pairwise Alignment Viewer</description>
+  <command interpreter="python">LAJ.py $maf_input $out_file1</command>
+  <inputs>
+      <param name="maf_input" type="data" format="lav" label="Alignment File" optional="False"/>
+      <param name="seq_file1" type="data" format="fasta" label="First Sequence File" optional="True"/>
+      <param name="seq_file2" type="data" format="fasta" label="Second Sequence File" optional="True"/>
+      <param name="exonfile" type="data" format="txt" label="Exon File" optional="True"/>
+      <param name="repeatfile" type="data" format="txt" label="Repeat File" optional="True"/>
+      <param name="annotationfile" type="data" format="txt" label="Annotation File" optional="True"/>
+      <param name="underlayfile" type="data" format="txt" label="Underlay File" optional="True"/>
+      <param name="highlightfile" type="data" format="txt" label="Highlight File" optional="True"/>
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="laj"/>
+  </outputs>
+<help>
+You can use this tool to view a set of LAV alignments.  You may include FASTA formatted sequences for both species.
+
+For detailed information on LAJ, click here_.
+
+.. _here: http://globin.cse.psu.edu/dist/laj/
+
+Laj is a tool for viewing and manipulating the output from pairwise alignment programs such as blastz. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and annotation links to other web sites containing additional information about particular regions.
+
+.. class:: infomark
+
+**Note:** If you save output from the applet, you will need to manually refresh your history. 
+
+  </help>
+  <code file="LAJ_code.py"/>
+</tool>
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