<tool id="deeptools_plotCorrelation" name="plotCorrelation" version="@WRAPPER_VERSION@.0">
    <description>creates a heatmap for a score associated to genomic regions</description>
    <macros>
        <token name="@BINARY@">heatmapper</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command>
<![CDATA[
        heatmapper

        --matrixFile $matrixFile
        --outFileName $outFileName

        #if $output.showOutputSettings == "yes"
            --plotFileFormat $output.outFileFormat
            #if $outFileNameData:
                --outFileNameData '$outFileNameData'
            #end if

            #if $outFileNameMatrix:
                --outFileNameMatrix '$outFileNameMatrix'
            #end if

            #if $outFileSortedRegions:
                --outFileSortedRegions '$outFileSortedRegions'
            #end if
        #else
            --plotFileFormat 'png'
        #end if

        #if $advancedOpt.showAdvancedOpt == "yes"
            #if $advancedOpt.sortRegions:
                --sortRegions '$advancedOpt.sortRegions'
            #end if
      
            #if $advancedOpt.sortUsing:
                --sortUsing '$advancedOpt.sortUsing'
            #end if

            #if $advancedOpt.averageTypeSummaryPlot:
                --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
            #end if

            #if str($advancedOpt.missingDataColor.value) != "None":
                --missingDataColor '$advancedOpt.missingDataColor'
            #end if

            --colorMap '$advancedOpt.colorMap'

            #if str($advancedOpt.zMin).strip() != "":
                --zMin $advancedOpt.zMin
            #end if
            #if $advancedOpt.zMax:
                --zMax $advancedOpt.zMax
            #end if

            #if str($advancedOpt.yMin).strip() != "":
                --yMin $advancedOpt.yMin
            #end if
            #if $advancedOpt.yMax:
                --yMax $advancedOpt.yMax
            #end if

            --xAxisLabel '$advancedOpt.xAxisLabel'
            --yAxisLabel '$advancedOpt.yAxisLabel'

            --heatmapWidth $advancedOpt.heatmapWidth
            --heatmapHeight $advancedOpt.heatmapHeight

            --whatToShow '$advancedOpt.whatToShow'

            --startLabel '$advancedOpt.startLabel' 
            --endLabel '$advancedOpt.endLabel'
            --refPointLabel '$advancedOpt.referencePointLabel'
            --regionsLabel '$advancedOpt.regionsLabel'

            #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
                --plotTitle '$advancedOpt.plotTitle'
            #end if

            $advancedOpt.onePlotPerGroup

            @KMEANS_CLUSTERING@

        #end if
]]>
    </command>
    <inputs>
        <param name="corData" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>

        <expand macro="input_graphic_output_settings">
            <expand macro="input_image_file_format" />
            <expand macro="input_save_matrix_values" />
        </expand>

        <conditional name="advancedOpt" >
            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">

                <expand macro="colormap" />

                <param name="zMin" type="float" value="" size="3"
                    label="Minimum value for the heatmap intensities. Leave empty for automatic values"/>
                <param name="zMax" type="float" value="" size="3"
                    label="Maximum value for the heatmap intensities. Leave empty for automatic values"/>

                <param name="yMin" type="float" value="" size="3"
                    label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/>
                <param name="yMax" type="float" value="" size="3"
                    label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values"/>
                <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200"
                    label="Description for the x-axis label" />
                <param name="yAxisLabel" type="text" value="genes" size="30"
                    label="Description for the y-axis label for the top panel" />

                <param name="heatmapWidth" type="float" value="7.5" min="1" max="100"
                    label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
                <param name="heatmapHeight" type="float" value="25" min="3" max="100"
                    label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/>

                <param name="whatToShow" type="select" label="What to show"
                    help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar.">
                    <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
                    <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
                    <option value="heatmap only">heatmap only</option>
                    <option value="heatmap and colorbar">heatmap and colorbar</option>
                    <option value="colorbar only">colorbar only</option>
                </param>

                <param name="startLabel" type="text" value="TSS" size="10"
                    label="Label for the region start"
                    help ="[only for scale-regions mode] Label shown in the plot for the start of the region.
                    Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;. (--startLabel)" />
                <param name="endLabel" type="text" value="TES" size="10"
                    label="Label for the region end"
                    help="[only for scale-regions mode] Label shown in the plot for the region end. (--endLabel)"/>

                <param name="referencePointLabel" type="text" value="TSS" size="10"
                    label="Reference point label"
                    help ="[only for scale-regions mode] Label shown in the plot for the reference-point.
                    Default is the same as the reference point selected (e.g. TSS),
                    but could be anything, e.g. &quot;peak start&quot; etc (--referencePointLabel)" />
                <param name="regionsLabel" type="text" value="genes" size="30" 
                    label="Labels for the regions plotted in the heatmap" 
                    help="If more than one region is being plotted a list of labels
                    separated by comma and limited by quotes, is required. For example, label1, label2. (--regionsLabel)">
                    <sanitizer>
                        <valid initial="string.printable">
                        </valid>
                    </sanitizer>
                </param>

                <expand macro="plotTitle" />
                <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
                    label="Do one plot per group"
                    help="When computeMatrix was used on more than one group of genes,
                    the average plots for all the groups will be drawn in one panel by default.
                    If this option is set, each group will get its own plot, stacked on top of each other. (--onePlotPerGroup)"/>

                <expand macro="kmeans_clustering" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <expand macro="output_image_file_format" />
        <expand macro="output_graphic_outputs" />
        <expand macro="output_save_matrix_values" />
    </outputs>
    <tests>
        <test>
            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="bgzip" />
            <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Tool for visualizing a correlation using either bamCorrelate or
bigwigCorrelate. Pearson or Spearman methods are available to compute correlation
coefficients. Results can be saved into a heat map image or as multiple
scatter plots. Further output files are optional.

-----

@REFERENCES@
]]>
    </help>
    <expand macro="citations" />
</tool>