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view fcs_scatterplot/getDensityPlots.xml @ 0:164cd5384f1d draft
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author | immport-devteam |
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date | Mon, 27 Feb 2017 12:52:20 -0500 |
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<tool id="gen_density_plots" name="Generate scatter plots" version="1.0"> <description>for any given markers in FCS file.</description> <requirements> <requirement type="package" version="3.3.0">r</requirement> <requirement type="package" version="1.38.2">bioconductor-flowcore</requirement> <requirement type="package" version="1.6.0">bioconductor-flowdensity</requirement> </requirements> <stdio> <exit_code range="10" level="fatal" description="Please provide a comma separated list of channels to plot" /> <exit_code range="11" level="fatal" description="Please provide numeric values for the list of channels to plot" /> </stdio> <command><![CDATA[ Rscript --slave --vanilla $__tool_directory__/getDensityPlots.R --args "${input}" "${channels}" "${outpng}" $outformat "${outpdf}" ]]> </command> <inputs> <param format="fcs" name="input" type="data" label="FCS file"/> <param name="channels" type="text" label="Markers to plot:" value="i.e.:1,3,4" help="By default, will plot FSC vs SSC if the channels are found."/> <param name="outformat" type="select" label="Output PDF?"> <option value="FALSE">No, thank you</option> <option value="TRUE">Yes, please</option> </param> </inputs> <outputs> <data format="pdf" name="outpdf" label="Scatter Plots of ${channels} from ${input.name}"> <filter>outformat=="TRUE"</filter> </data> <data format="png" name="outpng" label="Scatter Plots of ${channels} from ${input.name}"/> </outputs> <tests> <test> <param name="input" value="testfcs1.fcs"/> <param name="channels" value="1,3"/> <param name="outformat" value="TRUE"/> <output name="outpdf" file="graph.pdf" compare="sim_size"/> <output name="outpng" file="graph.png" compare="sim_size"/> </test> <test> <param name="input" value="testfcs1.fcs"/> <param name="channels" value="i.e.:1,3,4"/> <param name="outformat" value="FALSE"/> <output name="outpng" file="graph2.png" compare="sim_size"/> </test> </tests> <help><![CDATA[ This tool allows generation of density scatter plots using flowDensity. ----- **Input files** This tool takes valid FCS files as input. **Output files** This tool generates a scatter plot for each marker combination in a single png file. A pdf file can optionally be generated. ----- **Example** *Output*: .. image:: static/images/densityplots.png ]]> </help> <citations> <citation type="doi">10.1093/bioinformatics/btu677</citation> <citation type="doi">10.1186/1471-2105-10-106</citation> </citations> </tool>