annotate heatmapper.xml @ 27:bf1b1dcdd67b draft

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<tool id="deeptools_heatmapper" name="heatmapper" version="1.0.5">
    <description>creates a heatmap for a score associated to genomic regions</description>
    <expand macro="requirements"/>
    <expand macro="stdio" />
    <macros>
        <token name="@BINARY@">heatmapper</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <command>
        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 $advancedOpt.zMin:
                --zMin $advancedOpt.zMin
            #end if
            #if $advancedOpt.zMax:
                --zMax $advancedOpt.zMax
            #end if

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

            $advancedOpt.onePlotPerGroup

            @kmeans_clusterin@

        #end if
    </command>
    <inputs>
        <param name="matrixFile" 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">
                <param name="sortRegions" type="select" label="Sort regions"
                    help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
                    <option value="no">no ordering</option>
                    <option value="descend" selected="true">descending order</option>
                    <option value="ascend">ascending order</option>
                </param>

                <param name="sortUsing" type="select" label="Method used for sorting" help="For each row the method is computed." >
                    <option value="mean" selected="true">mean</option>
                    <option value="median">median</option>
                    <option value="min">min</option>
                    <option value="max">max</option>
                    <option value="sum">sum</option>
                    <option value="region_length">region length</option>
                </param>

                <param name="averageTypeSummaryPlot" type="select" label="Type of statistic that should be plotted in the summary image above the heatmap">
                    <option value="mean" selected="true">mean</option>
                    <option value="median">median</option>
                    <option value="min">min</option>
                    <option value="max">max</option>
                    <option value="sum">sum</option>
                    <option value="std">std</option>
                </param>

                <param name="missingDataColor" type="text" label="Missing data color" value="black" optional="true" help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default. By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0). Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html. Alternatively colors can be specified using the #rrggbb notation." />

                <expand macro="colormap" />

                <param name="zMin" type="float" value="" size="3" label="Minimum value for the heatmap intensities. Leave empty for automatic values" optional="true"/>
                <param name="zMax" type="float" value="" size="3" label="Maximum value for the heatmap intensities. Leave empty for automatic values" optional="true"/>
                <param name="yMin" type="float" value="" size="3" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>
                <param name="yMax" type="float" value="" size="3" label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>

                <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;." />
                <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. Default is TES (transcription end site)."/>

                <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." />
                <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.">
                    <sanitizer>
                        <valid initial="string.printable">
                        </valid>
                    </sanitizer>
                </param>
                <param name="plotTitle" type="text" value="" size="30" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title." />
                <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."/>

                <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="master.mat.gz" ftype="bgzip" />
            <output name="outFileName" file="master.png" ftype="png" compare="sim_size" delta="100" />
        </test>
    </tests>
    <help>

**What it does**

The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
Like profiler, it requires that computeMatrix was run first to calculate the values.
 
We implemented vast optional parameters to optimize the visual output and we encourage you to play around with the min/max values displayed in the heatmap as well as 
with the different coloring options. The most powerful option is the k-means clustering where you simply need to indicate the number of 
groups with similar read distributions that you expect and the algorithm will do the sorting for you.

Do check the examples on our help page with step-by-step protocols: https://github.com/fidelram/deepTools/wiki/Example-workflows


.. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png
   :alt: Heatmap of RNA Polymerase II ChIP-seq


You can find more details on the tool itself on the heatmapper wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper


-----

@REFERENCES@

    </help>
</tool>