comparison plotHeatmap.xml @ 9:f509604dbf06 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7

8:8ed7e3b6a16c

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

                <param argument="--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 argument="--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 argument="--referencePointLabel" type="text" value="TSS" size="10"
                    label="Reference point label"
                    help ="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 argument="--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>
                <expand macro="plotTitle" />
                <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
                    label="Do one plot per group"
                    help="When clustering is applied to the data, or the computematrix was performed on file containing
                    groups separated by &quot;#&quot;, plot the groups next to each other. The default is to plot
                    the samples next to each other. If this option is set, each group (or cluster) will get its own plot,
                    with different samples stacked on top of each other."/>

                <expand macro="kmeans_clustering" />
            </when>

**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/hirarchichal 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.


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

9:f509604dbf06

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

                <param argument="--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 argument="--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 argument="--referencePointLabel" type="text" value="TSS" size="10"
                    label="Reference point label"
                    help ="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 argument="--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 then a list of labels separated by comma is required. For example, label1, label2.">
                    <sanitizer>
                        <valid initial="string.printable">
                        </valid>
                    </sanitizer>
                </param>
                <expand macro="plotTitle" />
                <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
                    label="Do one plot per group"
                    help="When clustering is applied to the data, or the computematrix was performed on multiple BED files,
                    plot the groups next to each other. The default is to plot
                    the samples next to each other. If this option is set, each group (or cluster) will get its own plot,
                    with different samples stacked on top of each other."/>

                <expand macro="kmeans_clustering" />
            </when>

**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 have implemented number of 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/hierarchical 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.


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