<tool id="flapjack_fj2hdf5" name="Flapjack to HDF5" version="0.0.1">
  <description>convert a Flapjack-formatted genotype file into HDF5</description>
  <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.FJTabbedToHdf5Converter -genotypes=$input_genotypes -hdf5=$output_hdf5</command>
  <inputs>
    <param format="csv,tabular,txt" name="input_genotypes" type="data" label="Source file"
		help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
	<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="h5" name="output_hdf5" />
  </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>