<tool id="flapjack_creatematrix" name="Flapjack Create Similarity Matrix" version="0.0.1">
    <description>create a similarity matrix from 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.CreateMatrix
        -g $genotypes
        -o $output
        #if $map
            -m $map
        #end if
        #if $adv_opts.show_advanced
            $adv_opts.allChromosomes
            $adv_opts.collapseHets
            -M "$adv_opts.missingData"
            -S "$adv_opts.hetSep"
            $adv_opts.transposed
            $adv_opts.decimalEnglish
        #end if
        #if $create_project
            -p $project
        #end if
    ]]></command>
    <inputs>
        <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="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
            help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>

        <!-- 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="allChromosomes" type="boolean" truevalue="-A" falsevalue="" checked="False"
                    label="Duplicate all markers onto a single 'All Chromosomes' chromosome"
                    help="Imports the data so that an additional 'All Chromosomes' chromosome is created, containing every marker in the dataset held together."/>

                <param name="collapseHets" type="boolean" truevalue="-C" falsevalue="" checked="True"
                    label="Don't distinguish between heterozygous alleles"
                    help="Ignores phase between heterozygous alleles, treating, for example, A/T the same as T/A."/>

                <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')"/>

                <param name="transposed" type="boolean" truevalue="-T" falsevalue="" checked="False"
                    label="Genotype data has been transposed"
                    help="Flapjack's default format has markers as columns. Select this to specify markers as rows instead."/>

                <param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="False"
                    label="Force English-style decimal marks"
                    help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy server's locale settings."/>

                <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>
        <!-- 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.-->

        <param name="create_project" type="boolean" label="Also create Flapjack project file"
            truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the generated similarity matrix.">
        </param>
    </inputs>

    <outputs>
        <data format="tabular" name="output" />
        <data format="flapjack" name="project">
            <filter>create_project</filter>
        </data>
    </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.

Flapjack documentation_

.. _documentation: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#creatematrix-exe-jhi-flapjack-io-creatematrix
    ]]></help>

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