Mercurial > repos > bgruening > deeptools_plot_heatmap
diff plotHeatmap.xml @ 1:6a247ae015cc draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
| author | bgruening |
|---|---|
| date | Mon, 15 Feb 2016 10:26:54 -0500 |
| parents | e1bb51933e7f |
| children | ca218dae7902 |
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--- a/plotHeatmap.xml Mon Jan 25 20:16:56 2016 -0500 +++ b/plotHeatmap.xml Mon Feb 15 10:26:54 2016 -0500 @@ -1,218 +1,258 @@ -<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"/> - <command> -<![CDATA[ - @BINARY@ - --matrixFile "$matrixFile" - --outFileName "$outFileName" - - #if $output.showOutputSettings == "yes" - --plotFileFormat "$output.outFileFormat" - - #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.perGroup - - @KMEANS_CLUSTERING@ - - #end if -]]> - </command> - <inputs> - <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool" help=""/> - - <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="sortRegions" /> - <expand macro="sortUsing" /> - <param argument="--averageTypeSummaryPlot" type="select" - label="Type of statistic that should be plotted in the summary image above the heatmap" - help=""> - <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 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." /> - - <expand macro="colorMap" /> - - <param argument="--zMin" type="float" value="" size="3" optional="True" - label="Minimum value for the heatmap intensities. Leave empty for automatic values" help=""/> - <param argument="--zMax" type="float" value="" size="3" optional="True" - label="Maximum value for the heatmap intensities. Leave empty for automatic values" help=""/> - <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="--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. "peak start"." /> - <param argument="--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 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. "peak start" 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> - <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="deeptools_compute_matrix_archive" /> - <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="4000" /> - </test> - <test> - <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" /> - <param name="showAdvancedOpt" value="yes" /> - <param name="whatToShow" value="heatmap and colorbar" /> - <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:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png - :alt: Heatmap of RNA Polymerase II ChIP-seq - - -You can find more details on the tool on the plotHeatmap doc page: https://deeptools.readthedocs.org/en/master/content/tools/plotHeatmap.html - - ------ - -@REFERENCES@ -]]> - </help> - <expand macro="citations" /> -</tool> +<tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@WRAPPER_VERSION@.0"> + <description>creates a heatmap for score distributions across genomic regions</description> + <macros> + <token name="@BINARY@">plotHeatmap</token> + <import>deepTools_macros.xml</import> + </macros> + <expand macro="requirements"/> + <command> +<![CDATA[ + @BINARY@ + --matrixFile "$matrixFile" + --outFileName "$outFileName" + + #if $output.showOutputSettings == "yes" + --plotFileFormat "$output.outFileFormat" + + #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' + + #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 + + $advancedOpt.perGroup + + @KMEANS_CLUSTERING@ + + #end if +]]> + </command> + <inputs> + <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool" help=""/> + + <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="sortRegions" /> + <expand macro="sortUsing" /> + <param argument="--averageTypeSummaryPlot" type="select" + label="Type of statistic that should be plotted in the summary image above the heatmap" + help=""> + <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 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." /> + + <expand macro="colorMap" /> + + <param argument="--zMin" type="float" value="" size="3" optional="True" + label="Minimum value for the heatmap intensities. Leave empty for automatic values" help=""/> + <param argument="--zMax" type="float" value="" size="3" optional="True" + label="Maximum value for the heatmap intensities. Leave empty for automatic values" help=""/> + <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="--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. "peak start"." /> + <param argument="--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 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. "peak start" 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 "label 2""> + <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, "label 2"" /> + + <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> + <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="deeptools_compute_matrix_archive" /> + <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="4000" /> + </test> + <test> + <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" /> + <param name="showAdvancedOpt" value="yes" /> + <param name="whatToShow" value="heatmap and colorbar" /> + <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>`_. + +----- + +@REFERENCES@ +]]> + </help> + <expand macro="citations" /> +</tool>