<tool id="join_nucmer" name="join_nucmer" version="">
  <description>Join multiple mummer output files in a phenetic matrix</description>
  <command>
 <![CDATA[
	perl $__tool_directory__/join_nucmer.pl $output_file ${" ".join(map(str, $input_file))}
  ]]>
  </command>

  <inputs>
    <param name="input_file" format="tsv" type="data" multiple="true" label="show-snps tabular output" help="join mutiple nucmer output files" />
  </inputs>

  <outputs>
    <data format="tsv" name="output_file" label="${tool.name} on ${on_string} consolidated variants file" />
  </outputs>
  <stdio>
    <exit_code range="1:" level="fatal" />
  </stdio>
  <help>
	**What it does?**

	This tool is used to merge variant calls, in nucmer format, into a single tabular file. The output file will have as may columns as
	the number of genomes provided in input. And as many rows as the number of variants observed in the genomes. For every genome assembly and
	variant a simple binary code 1= present, 0=absent will be used to indicate whether that genome carries a specific variant.
	This table should be provided to the FunAnn tool to obtain the functional annotation of the variants.
	
  </help>

  <tests>
    <test>
    </test>
  </tests>

</tool>