Mercurial > repos > gtrichard > deepstats_dscomparecurves
changeset 0:cbeae0f83ff8 draft
Uploaded
| author | gtrichard |
|---|---|
| date | Mon, 15 Jul 2019 17:54:31 -0400 |
| parents | |
| children | a2022103f2a2 |
| files | datatypes_conf.xml deepStats_macros.xml dsCompareCurves.xml |
| diffstat | 3 files changed, 217 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Mon Jul 15 17:54:31 2019 -0400 @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<datatypes> + <registration> + <datatype extension="ttf" display_in_upload="True"/> + <datatype extension="dscc" type="galaxy.datatypes.rdata" display_in_upload="True"/> + </registration> +</datatypes>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deepStats_macros.xml Mon Jul 15 17:54:31 2019 -0400 @@ -0,0 +1,17 @@ +<macros> + <token name="@THREADS@">--CPU "\${GALAXY_SLOTS:-4}"</token> + <token name="@WRAPPER_VERSION@">1.0.0</token> + <token name="@REFERENCES@">https://github.com/gtrichard/deepStats</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.3">deepstats</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.5281/zenodo.3336594</citation> + <yield /> + </citations> + </xml> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dsCompareCurves.xml Mon Jul 15 17:54:31 2019 -0400 @@ -0,0 +1,193 @@ +<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>