<tool id="BaseAlignCounts" name="Map coverage" version="1.0.0">
  <description>of sequencing reads</description>
  <command interpreter="sh">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -a ${chromInfo} -x $X -o $output</command>
  <inputs>
    <param name="input" type="data" format="sam,bam,bed,bedgraph" label="Sequencing reads" />
    <param name="X" type="integer" value="-1" label="In silico extension (-1 for read length)" />
  </inputs>
  <outputs>
    <data name="output" format="wig" />
  </outputs>
  
  <help>
    .. class:: warningmark
    
    This tool requires sequencing reads in SAM, BAM, or Bed format.
  </help>
</tool>
