<macros>
    <token name="@VERSION@">1.0.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">bioconductor-iwtomics</requirement>
        </requirements>
    </xml>
    
    <xml name="alignment-s">
        <conditional name="conditionalscale">
            <param name="alignment" type="select" label="Region alignment" help="">
                <option value="center">Center - Alignment on the central position</option>
                <option value="left">Left - Alignment on the starting position</option>
                <option value="right">Right - Alignment on the ending position</option>
                <option value="scale">Scale - Scaling all regions to the same length</option>
            </param>
            <when value="center">
                <!-- fill gaps -->
                <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
            </when>
            <when value="left">
                <!-- fill gaps -->
                <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
            </when>
            <when value="right">
                <!-- fill gaps -->
                <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
            </when>
            <when value="scale">
                <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
            </when>
        </conditional>
    </xml>

    <xml name="alignment">
        <param name="alignment" type="select" label="Region alignment" help="">
            <option value="center">Center - Alignment on the central position</option>
            <option value="left">Left - Alignment on the starting position</option>
            <option value="right">Right - Alignment on the ending position</option>
        </param>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1080/10485252.2017.1306627</citation>
            <citation type="doi">10.1093/bioinformatics/bty090</citation>
        </citations>
    </xml>

    <xml name="plot-params">
        <!-- average -->
        <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" />
        <!-- average -->
        <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" />
        <!-- conditional plot type -->
        <conditional name="conditionalplottype">
            <!-- plot type -->
            <param name="plottype" type="select" label="Plot type">
                <option value="boxplot">Pointwise quantile curves (boxplot)</option>
                <option value="curves">Curves (aligned)</option>
            </param>
            <when value="boxplot">
                <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
                    <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
                    <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
                    <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
                    <repeat name="probabilities" title="Probabilities">
                        <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
                    </repeat>
                </section>
            </when>
            <when value="curves" />
        </conditional>
    </xml>

    <xml name="plot-sum">
        <section name="plotsum" title="Summary plot" expanded="True">
            <!-- conditional group by -->
            <conditional name="conditionalgroupby">
                <!-- group by -->
                <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
                    <option value="none">No plot</option>
                    <option value="test">Group by test</option>
                    <option value="feature">Group by feature</option>
                </param>
                <when value="none" />
                <when value="test">
                    <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
                    <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
                </when>
                <when value="feature">
                    <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
                    <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
                </when>
            </conditional>
        </section>
    </xml>
</macros>