comparison plotHeatmap.xml @ 1:6a247ae015cc draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920

0:e1bb51933e7f

<tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@WRAPPER_VERSION@.0">
    <description>creates a heatmap for a score associated to genomic regions</description>
    <macros>
        <token name="@BINARY@">plotHeatmap</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements"/>

                --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

                    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 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>
        </conditional>
    </inputs>

            <output name="outFileName" file="heatmapper_result2.png" ftype="png" compare="sim_size" delta="4000" />
        </test>
    </tests>
    <help>
<![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 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


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


-----

@REFERENCES@
]]>

1:6a247ae015cc

<tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@WRAPPER_VERSION@.0">
    <description>creates a heatmap for score distributions across genomic regions</description>
    <macros>
        <token name="@BINARY@">plotHeatmap</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements"/>

                --whatToShow '$advancedOpt.whatToShow'

                --startLabel '$advancedOpt.startLabel'
                --endLabel '$advancedOpt.endLabel'

                --refPointLabel '$advancedOpt.referencePointLabel'

                #if $advancedOpt.samplesLabel and str($advancedOpt.samplesLabel).strip() != "":
                    --samplesLabel $advancedOpt.samplesLabel
                #end if

                #if $advancedOpt.regionsLabel and str($advancedOpt.regionsLabel).strip() != "":
                    --regionsLabel $advancedOpt.regionsLabel
                #end if

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

                    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="--samplesLabel" type="text" size="30"
                    label="Labels for the samples (each bigwig) plotted"
                    help="The default is to use the file name of the sample. The sample labels should be separated by
                    spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;">
                    <sanitizer>
                        <valid initial="string.printable">
                        </valid>
                    </sanitizer>
                </param>
                <param argument="--regionsLabel" type="text" 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 space is required.
                          If a label itself contains a space, then quotes are needed.
                          For example, label_1, &quot;label 2&quot;" />

                <expand macro="plotTitle" />
                <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
                    label="Make one plot per group of regions"
                    help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions."/>

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

            <output name="outFileName" file="heatmapper_result2.png" ftype="png" compare="sim_size" delta="4000" />
        </test>
    </tests>
    <help>
<![CDATA[

What it does
--------------

``plotHeatmap`` visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
Like ``plotProfile``, it requires that computeMatrix was run first to calculate the values.

We have implemented a 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.

**TIP:** *If your data is rather sparse and the resulting heatmap is too black, change the "Missing data color" to white (via "Advanced options").*

The most powerful option is probably the **k-means/hierarchical clustering** where you can sort your regions into groups of regions with similar score distributions.

**NOTE:** *The clustering will only work if you supplied a single BED file to computeMatrix. plotHeatmap cannot cluster regions within pre-defined groups. Moreover, k-means will be much faster than hierarchical clustering.*

Output
--------------

This is a heatmap based on two bigWig files generated with default settings and k-means clustering.

.. image:: $PATH_TO_IMAGES/plotHeatmap_example.png
   :width: 600
   :height: 694

.. image:: $PATH_TO_IMAGES/plotHeatmap_example02.png
    :width: 600
    :height: 694

In addition to the image, ``plotHeatmap`` can also generate the values underlying both the heatmap.

See the following table for the optional output options:

+-----------------------------------+--------------------+-----------------+-----------------+
|  **optional output type**         |  **computeMatrix** | **plotHeatmap** | **plotProfile** |
+-----------------------------------+--------------------+-----------------+-----------------+
| values underlying the heatmap     |  yes               | yes             | no              |
+-----------------------------------+--------------------+-----------------+-----------------+
| values underlying the profile     | no                 | no              | yes             |
+-----------------------------------+--------------------+-----------------+-----------------+
| sorted and/or filtered regions    | yes                | yes             | yes             |
+-----------------------------------+--------------------+-----------------+-----------------+

**More examples** can be found in our `Gallery <http://deeptools.readthedocs.org/en/latest/content/example_gallery.html#normalized-chip-seq-signals-and-peak-regions>`_.

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@REFERENCES@
]]>