<tool id="gen_density_plots_txt" name="Generate scatter plots" version="1.0">
  <description>for any given markers in a txt-converted FCS file.</description>
  <requirements>
    <requirement type="package" version="3.3.0">r</requirement>
    <requirement type="package" version="2.1.0">r-ggplot2</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 $__tool_directory__/getDensityPlots_text.R --args "${input}" "${channels}" "${outpng}" $outformat "${outpdf}"
  ]]>
  </command>
  <inputs>
    <param format="flowtext" name="input" type="data" label="txt-converted 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="PDF 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="input.flowtext"/>
      <param name="channels" value="i.e.:1,3,4"/>
      <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="input.flowtext"/>
      <param name="channels" value="1,3,5"/>
      <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 ggplot2.

-----

**Input files**

This tool takes txt-converted 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/flowtextgraph.png
  ]]>
  </help>
  <citations>
    <citation type="bibtex">@BOOK{,
      author = {Hadley Wickham},
      title = {ggplot2: Elegant Graphics for Data Analysis},
      publisher = {Springer-Verlag New York},
      year = {2009},
      isbn = {978-0-387-98140-6},
      url = {http://ggplot2.org},
    }</citation>
  </citations>
</tool>