annotate fcs_scatterplot/getDensityPlots.xml @ 0:164cd5384f1d draft

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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>