<tool id="flapjack_fj2hdf5" name="Flapjack to HDF5" version="0.0.1">
    <description>convert a Flapjack formatted genotype file into HDF5</description>
    <command><![CDATA[
        java
        #if $adv_opts.show_advanced
            -Xmx$adv_opts.memory
        #end if
        -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.FJTabbedToHdf5Converter
        -g $genotypes
        -h $output
    ]]></command>
    <inputs>
        <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
            help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>

        <conditional name="adv_opts">
            <param name="show_advanced" type="boolean"
                label="Enable advanced options"
                truevalue="show" falsevalue="">
            </param>
            <when value="show">
                <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>
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data format="h5" name="output" />
    </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: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html
    ]]></help>

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