<tool id="coverage_stats" name="Coverage Statistics" version="0.1.7.2">
  <description>Calculate coverage statistics for a BCF file as generated by the Variant Calling tool</description>
  <macros>
    <import>toolshed_macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <version_command>python3 -m MiModD version -q</version_command>
  <command> 
	python3 -m MiModD covstats "$ifile" --ofile "$output_vcf"
  </command>

  <inputs>
      <param name="ifile" type="data" format="bcf" label="BCF input file" help="Use the Variant Calling tool to generate input for this tool."/>
  </inputs>
  <outputs>
    <data name="output_vcf" format="tabular" label="Coverage Statistics for ${on_string}"/>
  </outputs>

<help>
.. class:: infomark

   **What it does**

The tool takes as input a BCF file produced by the *Variant Calling* tool, and calculates per-chromosome read coverage from it.

.. class:: warningmark

   The tool treats genome positions missing from the BCF input as zero coverage, so it is safe to use ONLY with BCF files produced by the *Variant Calling* tool or through other commands that keep the information for all sites.

</help>
</tool>