<tool id="flapjack_hapmap2fj" name="HapMap to Flapjack" version="0.0.1">

<!--System.out.println("Usage: hapmap2flapjack <options>\n"
			+ " where valid options are:\n"
			+ "   -separator=<s or t>            (required separator used in input file)\n"
			+ "   -hapmap=<hapmap_file>          (required input file)\n"
			+ "   -map=<map_file>                (required output file)\n"
			+ "   -genotypes=<genotype_file>     (required output file)\n");-->

  <description>convert an HapMap formatted file into a Flapjack-formatted genotype file</description>
  <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.HapMapToFJTabbedConverter 
	  -hapmap=$hapmap
	  -separator=$separator 
	  -map=$map
	  -genotypes=$genotypes
  </command>
  <inputs>
    <param format="txt" name="hapmap" type="data" label="Source file"
		help="HapMap Formatted File"/>
	<param name="separator" type="boolean" label="File is tab-separated"
		truevalue="-t" falsevalue="-s">
	</param>
	<param name="memory" type="select" label="Memory"
		help="How much memory to use; larger files may require more memory">
	  <option selected="true" value="64m">64MB</option>
	  <option value="128m">128MB</option>
	  <option value="256m">256MB</option>
	</param>
  </inputs>
  <outputs>
	<data format="fjmap" name="map" />
    <data format="fjgenotype" name="genotypes" />
  </outputs>
  
  <stdio>
    <exit_code range="1:" />
  </stdio>

  <help><![CDATA[
.. class:: infomark

**What it does**

Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
allowing for rapid navigation and comparisons between lines, markers and chromosomes.

This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
See Flapjack's documentation_ for more details on the various Flapjack data formats.

.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 



  ]]></help>
  <citations>
    <citation type="doi">10.1093/bioinformatics/btq580</citation>
  </citations>
</tool>