Mercurial > repos > bgruening > deeptools_plot_profile
diff plotProfiler.xml @ 0:e4ad262c1321 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
| author | bgruening |
|---|---|
| date | Mon, 25 Jan 2016 20:27:28 -0500 |
| parents | |
| children | 466df17b2d67 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plotProfiler.xml Mon Jan 25 20:27:28 2016 -0500 @@ -0,0 +1,194 @@ +<tool id="deeptools_plot_profile" name="plotProfile" version="@WRAPPER_VERSION@.0"> + <description> + creates a profile plot for a score associated to genomic regions + </description> + <macros> + <token name="@BINARY@">plotProfile</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 $output.saveSortedRegions: + --outFileSortedRegions '$outFileSortedRegions' + #end if + #else + --plotFileFormat 'png' + #end if + + #if $scaleRegions.showScaleRegionsOpt == "yes": + --startLabel '$scaleRegions.startLabel' + --endLabel '$scaleRegions.endLabel' + #end if + + #if $advancedOpt.showAdvancedOpt == "yes": + #if $advancedOpt.averageType: + --averageType '$advancedOpt.averageType' + #end if + --plotHeight $advancedOpt.plotHeight + --plotWidth $advancedOpt.plotWidth + --plotType $advancedOpt.plotType + --regionsLabel '$advancedOpt.regionsLabel' + + #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle).strip() != "": + --plotTitle '$advancedOpt.plotTitle' + #end if + + #if str($advancedOpt.colors).strip() != "": + --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )# + #end if + + $advancedOpt.perGroup + + #if $advancedOpt.yMin: + --yMin $advancedOpt.yMin + #end if + #if $advancedOpt.yMax: + --yMax $advancedOpt.yMax + #end if + + @KMEANS_CLUSTERING@ + + #end if +]]> + </command> + <inputs> + <param argument="--matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/> + <conditional name="scaleRegions"> + <param name="showScaleRegionsOpt" type="select" label="The input matrix was computed in scale-regions mode"> + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="no" /> + <when value="yes"> + <param argument="--startLabel" type="text" value="TSS" size="10" + label="Label for the region start" + help ="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="Label shown in the plot for the region end. Default is TES (transcription end site)."/> + </when> + </conditional> + + <expand macro="input_graphic_output_settings"> + <expand macro="input_image_file_format" /> + </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"> + <param name="averageType" type="select" label="Define the type of statistic that should be used for the profile."> + <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="--plotHeight" type="integer" value="5" min="3" + label="Plot height" + help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." /> + + <param argument="--plotWidth" type="integer" value="8" min="1" + label="Plot width" + help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." /> + + <param argument="--plotType" type="select" label="Plot type" + help="The "lines" option will + plot the profile line based on the average type selected. The "fill" + option fills the region between zero and the profile curve. The filled in color is + semi-transparent. The "add standard error" + option colors the region between the profile and the standard error of the data. + As in the case of fill, a semi-transparent color is used. + The option "overlapped_lines" plots each region's value, one on top of + the other."> + <option value="lines" selected="true">lines</option> + <option value="fill">fill</option> + <option value="se">add standard error</option> + <option value="overlapped_lines">overlapped lines</option> + </param> + <param argument="--regionsLabel" type="text" value="coverage" 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 commas is required. For example, "label1, label2"."/> + + <expand macro="plotTitle" /> + <param argument="--colors" type="text" value="" size="40" + label="List of colors to use for the plotted lines" + help="Color names and html hex strings (e.g. #eeff22) are accepted. + The color names should be separated by spaces. (--colors red blue green)"> + <validator type="expression" + message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator> + </param> + + <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue="" + label="Do one plot per group" + help="When clustering is applied to the data or multiple BED files were used, + plot the groups next to each other. The default is to plot the samples next to each other." /> + + + <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"/> + <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" /> + + <expand macro="kmeans_clustering" /> + + </when> + </conditional> + </inputs> + <outputs> + <expand macro="output_image_file_format" /> + <expand macro="output_graphic_outputs" /> + </outputs> + <tests> + <test> + <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" /> + <output name="outFileName" file="profiler_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="showScaleRegionsOpt" value="yes" /> + <output name="outFileName" file="profiler_result2.png" ftype="png" compare="sim_size" delta="4000" /> + </test> + </tests> + <help> +<![CDATA[ + +**What it does** + +This tool plots the average enrichments over all genomic +regions supplied to computeMarix. It requires that computeMatrix was successfully run. +It is a very useful complement to the heatmapper, especially in cases where you want to +compare the scores for many different groups. Like heatmapper, profiler does not change the +values that were compute by computeMatrix, but you can modify the color and other display properties of the plots. + + +.. image:: $PATH_TO_IMAGES/visual_profiler_DmelPolII.png + :alt: Meta-gene profile of Rna Polymerase II + + +You can find more details on the profiler doc page: https://deeptools.readthedocs.org/en/master/content/tools/plotProfile.html + + +----- + +@REFERENCES@ +]]> + </help> + <expand macro="citations" /> +</tool>