<tool id="lastz_dotplot_matplotlib" name="Dot Plot" version="1.0.0">
  <description>of LASTZ tabular output</description>
  <requirements>
    <requirement type="package">numpy</requirement>
    <requirement type="package">matplotlib</requirement>
  </requirements>
  <command interpreter="python">dotplot.py $input $filter $out_file1</command>
  <inputs>
    <param name="input" type="data" format="tabular" label="LASTZ tabular output"/>
    <param name="filter" type="text" value="0" label="Filter out alignments shorter than (bp)"/>
  </inputs>
  <outputs>
    <data format="pdf" name="out_file1"/>
  </outputs>
  <tests>
    <test>
      <param name="input"  value="human_vs_chicken_chr4.tabular" ftype="tabular"/>
      <param name="filter" value="100"/>
      <output name="out_file1" file="dotplot_chr4.pdf" compare="sim_size" />
    </test>
  </tests>
  <help>

**Syntax**

This tool creates a dot plot of the contents of a LASTZ tabular file resulting from the alignment of one or more sequences to a single reference sequence. 

If multiple query sequences are present, they will be sorted by size, offset from one another in the dot plot, and separated by a gray line. 

- **filter** all alignments shorter than the filter will be excluded from the analysis.

-----

**Example**

Chicken chromosome 4 was aligned against human chromosome 4 using LASTZ, specifying tabular output, no transitions, and performing gap free extension. 

Using a 100 bp filter above we get the following dotplot.

.. image:: dotplot_chr4.png
</help>
</tool>