<tool id="IntervalLengthDistribution" name="Make histogram" version="1.0.0">
  <description>of read lengths</description>
  <command interpreter="bash">galaxyToolRunner.sh ngs.IntervalLengthDistribution -i $input $freq -o $output</command>
  <inputs>
      <param name="input" type="data" format="sam,bam,bed,bedgraph,gff" label="Reads/Intervals" />
      <param name="freq" type="boolean" checked="false" truevalue="-f" falsevalue="" label="Output normalized frequencies rather than counts" />
  </inputs>
  <outputs>
      <data format="tabular" name="output" />
  </outputs>
  <tests>
    <test>
      <param name="input" value="test.bed"/>
      <param name="freq" value="false"/>
	    <output name="output" file="intervallengthdistribution1.txt"/>
    </test>
    <test>
      <param name="input" value="test.bed"/>
      <param name="freq" value="true"/>
	    <output name="output" file="intervallengthdistribution2.txt"/>
    </test>
    <test>
      <param name="input" value="test2.bed"/>
      <param name="freq" value="false"/>
	    <output name="output" file="intervallengthdistribution3.txt"/>
    </test>
  </tests>
  
<help>
  
This tool calculates the distribution of interval lengths from a list of intervals or reads in SAM, BAM, Bed, BedGraph, or GFF format.

.. class:: warningmark

For paired-end sequencing reads, the length is the length of the fragment (5' end of read 1 to 5' end of read 2)

</help>
</tool>