<tool id="flapjack_hapmap2fj" name="HapMap to Flapjack" version="0.0.1">
    <description>convert a HapMap formatted file into a Flapjack formatted genotype file</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.HapMapToFJTabbedConverter
        -h $hapmap
        -s $separator
        -m $map
        -g $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>

        <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="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>