Mercurial > repos > gtrichard > deepstats_dscomparecurves
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author | gtrichard |
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date | Mon, 15 Jul 2019 17:54:31 -0400 |
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children | a2022103f2a2 |
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<tool id="deepstats_compare_curves" name="dsCompareCurves" version="@WRAPPER_VERSION@.0" profile="18.01"> <description> compares multiple bigwigs over multiple region sets with bootstraps and Wilcoxon rank-sum test using deepTools computeMatrix output </description> <macros> <token name="@BINARY@">dsCompareCurves</token> <import>deepStats_macros.xml</import> </macros> <expand macro="requirements" /> <command> <![CDATA[ @BINARY@ --input '$input' --output 'output' --comparison '$comparison' --signalName '$signalName' --scoreLabels '$nameLabels.scoreLabels' --regionLabels '$nameLabels.regionLabels' #if $scaleRegions.showScaleRegionsOpt == "yes": --firstRegionName '$scaleRegions.firstRegionName' --secondRegionName '$scaleRegions.secondRegionName' #else --firstRegionName '$scaleRegions.firstRegionName' #end if --bootstraps '$statsOptions.bootstraps' --bootstrapsCI '$statsOptions.bootstrapsCI' --wilcoxThreshold '$statsOptions.wilcoxThreshold' --bootPlotShareY '$plotOptions.bootPlotShareY' --bootPlotRatio '$plotOptions.bootPlotRatio' --bootPlotWidth '$plotOptions.bootPlotWidth' --bootPlotHeight '$plotOptions.bootPlotHeight' --wilcoxPlotWidth '$plotOptions.wilcoxPlotWidth' --wilcoxPlotHeight '$plotOptions.wilcoxPlotHeight' --CPU '$advancedOptions.CPU' #if $fontOptions.showFontOptions == "yes": --font '$fontOptions.font_file' #end if #if $colorsOptions.showColorsOptions == "yes": --bootPlotColors '$colorsOptions.bootPlotColors' #end if ]]> </command> <inputs> <param argument="--input" format="tabular" type="data" label="deepTools computeMatrix output file."/> <param argument="--comparison" type="select" label="What do you want to compare?"> <option value="scores" selected="true">scores</option> <option value="regions">regions</option> </param> <param argument="--signalName" type="text" value= "Normalized ATAC-seq counts" label="Name of the genomic signal" help="Name given to the signal on the plots, \n can be added for linebreaks."/> <conditional name="scaleRegions"> <param name="showScaleRegionsOpt" type="select" label="Which mode was used in deepTools computeMatrix?"> <option value="reference-point" selected="true">reference-point</option> <option value="scale-regions">scale-regions</option> </param> <when value="scale-regions"> <param argument="--firstRegionName" 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="--secondRegionName" type="text" value="TES" size="10" label="Label for the region end" help ="Label shown in the plot for the end of the region. Default is TES (transcription end site), but could be changed to anything, e.g. "peak end"." /> </when> <when value="reference-point"> <param argument="--firstRegionName" type="text" value="TSS" 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"." /> </when> </conditional> <section name="nameLabels" title="Customize score and region labels" expanded="false"> <param argument="--scoreLabels" optional="true" type="text" value= "" label="Name of the scores" help="For plot display. It must be provided as text seperated by semi-colons, i.e. 'Score A;Score B;Score C' as in the example."> <sanitizer> <valid initial="string.printable"/> </sanitizer> </param> <param argument="--regionLabels" optional="true" type="text" value= "" label="Name of the regions" help="For plot display. It must be provided as text seperated by semi-colons, i.e. 'Regions A;Regions B;Regions C' as in the example."> <sanitizer> <valid initial="string.printable"/> </sanitizer> </param> </section> <section name="statsOptions" title="Statistics options" expanded="false"> <param argument="--bootstraps" type="integer" value="1000" label="--bootstraps" help="Number of bootstraps to perform. Default is 1000, increasing this number will increase the computing time."/> <param argument="--bootstrapsCI" type="float" value="0.95" label="--bootstrapsCI" help="Bootstraps confidence interval. Default is 0.95, increasing this will make the analysis more stringent by increasing the min and max of the shadowed area on the bootstrap plot."/> <param argument="--wilcoxThreshold" type="float" value="0.05" label="--wilcoxThreshold" help="Threshold used to define significant bins on the Wilcoxon rank-sum test plot (grey box). Default is 0.05"/> </section> <section name="plotOptions" title="Plotting options" expanded="false"> <param argument="--bootPlotShareY" type="select" label="--bootPlotShareY"> <option value="TRUE" selected="true">TRUE</option> <option value="FALSE">FALSE</option> </param> <param argument="--bootPlotRatio" type="float" value="0.85" label="--bootPlotRatio" help="Changes the aspect ratio of the plot. A value inferior to 1 results in a wide plot, a value above 1 results in a narrow plot. Default: 0.85."/> <param argument="--bootPlotWidth" type="float" value="5.2" label="--bootPlotWidth" help="How large the bootstraps plot should be."/> <param argument="--bootPlotHeight" type="float" value="3.7" label="--bootPlotHeight" help="How tall the bootstraps plot should be."/> <param argument="--wilcoxPlotWidth" type="float" value="4.6" label="--wilcoxPlotWidth" help="How large the Wilcoxon rank-sum test plot should be."/> <param argument="--wilcoxPlotHeight" type="float" value="4.6" label="--wilcoxPlotHeight" help="How tall the Wilcoxon rank-sum test plot should be."/> </section> <section name="advancedOptions" title="Computing options" expanded="false"> <param argument="--CPU" type="integer" value="4" label="--CPU" help="Number of CPU to use."/> </section> <conditional name="fontOptions"> <param name="showFontOptions" type="select" label="Customize font?"> <option value="No" selected="true">No</option> <option value="Yes">Yes</option> </param> <when value="No"/> <when value="Yes"> <param argument="--font" type="file" format="ttf" value=" " label="--font" optional="true" help="Font used for plotting, given a TTF file. Default is usually Helvetica."/> </when> </conditional> <conditional name="colorsOptions"> <param name="showColorsOptions" type="select" label="Customize colors?"> <option value="No" selected="true">No</option> <option value="Yes">Yes</option> </param> <when value="No"/> <when value="Yes"> <param argument="--bootPlotColors" type="file" format="tabular" value=" " label="--bootPlotColors" help="Change the bootstraps plot color palette to a user-provided one. The file must be tab-delimited and contain for each line two HTML color codes ( #3366CC #769EF2 ). The first column corresponds to the mean color, the second column corresponds to the color of the bootstrap confidence interval shadowed area. The default color scale contains 6 colors that are color blind friendly using the dichromat R package."/> </when> </conditional> </inputs> <outputs> <data format="pdf" name="pdf1" label="${tool.name} on ${on_string}: Bootstrap Plot" from_work_dir="output_bootstraps.pdf"/> <data format="pdf" name="pdf2" label="${tool.name} on ${on_string}: Wilcox Plot" from_work_dir="output_wilcoxon.pdf"/> </outputs> <tests> <test> </test> </tests> <help> <![CDATA[ This tool assesses if multiple genomics signals ( ChIP-seq, ATAC-seq... ) are significantly different or not between conditions ( control, KO1, KO2, etc ). `dsCompareCurves` uses bootstraps and corrected Wilcoxon Rank-sum tests to do so. The input of this tool corresponds to the output of deepTools `computeMatrix --outFileNameMatrix`. If multiple region sets have been used in deepTools, one plot and tab-delimited table will be produced for each set of regions. @REFERENCES@ ]]> </help> <expand macro="citations" /> </tool>