/tools/filters/lav_to_bed.xml

<tool id="lav_to_bed1" name="LAV to BED">

  <description>Converts a LAV formatted file to BED format</description>

  <command interpreter="python">lav_to_bed.py $lav_file $bed_file1 $bed_file2</command>

  <inputs>

    <param name="lav_file" type="data" format="lav" label="LAV File" optional="False"/>

  </inputs>

  <outputs>

    <data name="bed_file1" format="bed"/>

    <data name="bed_file2" format="bed"/>

  </outputs>

  <tests>

    <test>

      <param name="lav_file" value="2.lav" ftype="lav" />

      <output name="bed_file2" file="lav_to_bed_out_1.bed" />

      <output name="bed_file2" file="lav_to_bed_out_2.bed" />

    </test>

  </tests>

  <help>



**Syntax**



This tool converts a LAV formatted file to the BED format.



- **LAV format** LAV is an alignment format developed by Webb Miller's group at Penn State University. It is the primary output format for BLASTZ.



- **BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser.



-----



**Example**



- Convert LAV format::



    #:lav

    s {

      &quot;/galaxy/data/hg16/seq/chr19.nib&quot; 1 63811651 0 1

      &quot;/galaxy/data/mm5/seq/chr11.nib&quot; 1 121648857 0 1

    }

    h {

      &quot;> hg16.chr19&quot;

      &quot;> mm5.chr11 (reverse complement)&quot;

    }

    a {

      s 3500

      b 3001012 70568380

      e 3001075 70568443

      l 3001012 70568380 3001075 70568443 81

    }

    a {

      s 3900

      b 3008279 70573976

      e 3008357 70574054

      l 3008279 70573976 3008357 70574054 78

    }

    #:eof



- To two BED formatted files::



    chr19	3001011	3001075	hg16_0	0	+

    chr19	3008278	3008357	hg16_1	0	+

    

 **and**::

    

    chr11	70568379	70568443	mm5_0	0	+

    chr11	70573975	70574054	mm5_1	0	+

  </help>

  <code file="lav_to_bed_code.py"/>

</tool>