<tool id="IntervalToBed" name="SAM/BAM/GFF/BedGraph/BigBed/VCF to Bed" version="1.0.0">
  <description>converter</description>
  <command interpreter="bash">galaxyToolRunner.sh converters.IntervalToBed -i $input -o $output</command>
  <inputs>
      <param name="input" type="data" format="sam,bam,gff,bigbed,bedgraph,vcf" label="Input" />
  </inputs>
  <outputs>
      <data name="output" format="bed" metadata_source="input" />
  </outputs>
<help>

This tool will convert any file in SAM, BAM, GFF, BedGraph, BigBed, or VCF format to Bed format.

.. class:: warningmark
	
For SAM/BAM data, paired-end reads are converted to Bed format as the entire fragment (5' end of mate 1 to the 5' end of mate 2). Single-end reads are converted to Bed format as the read itself, with strand information. If your SAM/BAM file contains both mate alignments from a paired-end sequencing run (i.e. two entries for each fragment), you should first filter out reads from either the + or - strand with the SAM Tools -> Filter SAM tool to avoid producing redundant entries in the output Bed file.

</help>
</tool>