<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>