<tool id="bowtie2bed" name="bowtie-to-bed">
  <description> converter and read extender</description>
  <command interpreter="perl">bowtie2bed.pl $input $out_file1 $extendLength </command>
  <inputs>
    <param name="input" format="txt" type="data" label="Bowtie map result file"/>
    <param name="extendLength" size="10" type="integer" value="200" label="Extend 3 primer (bp)"/>
  </inputs>
  <outputs>
    <data format="bed" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input" value="test.map" ftype="TXT"/>
      <param name="extendLength" value="200"/>
      <output name="out_file1" file="testmap.bed"/>
    </test>
  </tests>
  <help>


**What it does**

This tool converts bowtie output map format file to bed format, with the option to extend the 3 primer end.

- Sequence and quality information is lost after conversion
- The output contains a track name at the first row

-----

**Example**

Converting the following bowtie mapped reads::

  SRR073078.2 HWUSI-EAS465_8_1_1_524 length=36	-	chr2	112499209	AGTGTGACTGCATCTCTTCCTTCGTGGGGCTNCAGT	...
  SRR073078.3 HWUSI-EAS465_8_1_1_1054 length=36	+	chr17	75877120	CCACNCCTCCTTTCAAAACACACTGCCAGGTGCGTC	...

will result in::

  track name=/home/xuebing/Research/galaxy/galaxy-dist/database/files/000/dataset_5.dat itemRgb=On
  chr2	112499109	112499245	SRR073078.2-HWUSI-EAS465_8_1_1_524-length=36	1	-	112499209	112499245	0,255,0	
  chr17	75877120	75877256	SRR073078.3-HWUSI-EAS465_8_1_1_1054-length=36	1	+	75877120	75877156	255,0,0	

  </help>
</tool>
