Mercurial > repos > bgruening > deeptools_plot_heatmap
diff plotHeatmap.xml @ 0:e1bb51933e7f draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
| author | bgruening |
|---|---|
| date | Mon, 25 Jan 2016 20:16:56 -0500 |
| parents | |
| children | 6a247ae015cc |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plotHeatmap.xml Mon Jan 25 20:16:56 2016 -0500 @@ -0,0 +1,218 @@ +<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>