comparison plotHeatmap.xml @ 8:8ed7e3b6a16c draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69

7:aaf01404686f

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

                #if $advancedOpt.averageTypeSummaryPlot:

                --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
]]>

                    <option value="max">max</option>
                    <option value="sum">sum</option>
                    <option value="std">std</option>
                </param>

                <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color" 
                    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." />

                <param argument="--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 argument="--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;." />

                    help="Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site)."/>

                <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="--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>

<![CDATA[
**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@

8:8ed7e3b6a16c

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

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

                #if $advancedOpt.averageTypeSummaryPlot:

                --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.perGroup

                @KMEANS_CLUSTERING@

            #end if
]]>

                    <option value="max">max</option>
                    <option value="sum">sum</option>
                    <option value="std">std</option>
                </param>

                <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color"
                    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." />

                <param argument="--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 and colorbar">heatmap and colorbar</option>
                </param>

                <param argument="--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;." />

                    help="Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site)."/>

                <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>
        </conditional>
    </inputs>

<![CDATA[
**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


You can find more details on the tool on the plotHeatmap doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/plotHeatmap.html


-----

@REFERENCES@