<tool id="flapjack_createproject" name="Flapjack CreateProject" version="0.0.1">
    <description>create a Flapjack project file from Flapjack formatted input files.</description>
    <command><![CDATA[
        python $__tool_directory__/FlapjackProject.py
        -j $__tool_directory__/lib/flapjack.jar
        -g $genotypes
        -s $traits
        #if $map
            -m $map
        #end if
        #if $name
            -n $name
        #end if
        #if $qtls
            -q $qtls
        #end if
        #if $adv_opts.show_advanced
            -M "$adv_opts.missingData"
            -S "$adv_opts.hetSep"
        #end if
    ]]>
    </command>
    <inputs>
        <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
            help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>

        <param format="fjphenotype" name="traits" type="data" label="Flapjack phenotype file"
            help="Flapjack-formatted (tab-delimited text) input file of phenotype data"/>

        <param format="fjmap" name="map" type="data" label="Flapjack map file"
            help="Flapjack-formatted (tab-delimited text) input file of map data"
            optional="true"/>

        <param format="fjqtl" name="qtls" type="data" label="Flapjack QTL file"
            help="Flapjack-formatted (tab-delimited text) input file of QTL data"
            optional="true"/>

        <!-- WARNING: Below is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.-->
        <conditional name="adv_opts">
            <param name="show_advanced" type="boolean"
               label="Enable advanced options"
               truevalue="show" falsevalue="">
            </param>
            <when value="show">
                <param name="missingData" type="text" value="-"
                    label="Missing data string"
                    help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/>

                <param name="hetSep" type="text" value="/"
                    label="Heterozygous allele separator string"
                    help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/>
            </when>
        </conditional>
        <!-- WARNING: Above is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.-->
    </inputs>

    <outputs>
        <data name="output" format="flapjack" />
    </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 creates a Flapjack project file from the supplied tab-delimitted flapjack input files.
See Flapjack's documentation_ for more details on the various Flapjack data formats.
More information on the CreateProject tool can be found here_

.. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html
.. _here: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#createproject-exe-jhi-flapjack-io-createproject
    ]]></help>

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