view tools/filters/lav_to_bed.xml @ 0:9071e359b9a3

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<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>