<tool id="flapjack_hdf52fj" name="HDF5 to Flapjack Tabbed Genotype Format" version="0.0.1">

  <description>convert an HDF5 formatted genotype file into a Flapjack-formatted genotype file</description>
  <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.Hdf5ToFJTabbedConverter 
	  -hdf5=$hdf5 
	  -lines=$lines
	  -markers=$markers
	  -missing_filter=$missing_filter
	  -heterozygous_filter=$heterozygous_filter
	  -genotypes=$genotypes
  </command>
  <inputs>
    <param format="h5" name="hdf5" type="data" label="Source file"
		help="Flapjack's flavour of HDF5 for storing genotype data."/>
	<param format="txt" name="lines" type="data" label="Source file"
		help="A list of lines desired in the output. One line name per line on each line of the file."/>
	<param format="txt" name="markers" type="data" label="Source file"
		help="A list of markers desired in the output. One line name per marker on each line of the file."/>
	<param name="missing_filter" type="boolean" label="Filter out missing markers"
		truevalue="true" falsevalue="false">
	</param>
	<param name="heterozygous_filter" type="boolean" label="Filter out heterozygous markers"
		truevalue="true" falsevalue="false">
	</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="fjgenotype" name="genotypes" />
  </outputs>

  <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>