<tool id="RollingReadLength" name="Compute mean fragment length" version="1.1.0">
  <description>over each locus</description>
  <command interpreter="bash">galaxyToolRunner.sh ngs.RollingReadLength -i $input -a ${chromInfo} -o $output</command>
  <inputs>
      <param format="sam,bam,bed,bedgraph" name="input" type="data" label="Mapped reads" />
  </inputs>
  <outputs>
      <data format="wig" name="output" />
  </outputs>
  
<help>
  
This tool will compute the mean length of all fragments overlapping a given locus, and can be used to identify sites with exceptionally long or short reads.
  
.. class:: warningmark

This tool requires paired-end SAM, BAM, Bed, or BedGraph formatted data. Using single-end data will result in a constant read length.

</help>
</tool>