<tool id="ggcyto_1d_density_plots" name="Generate 1D density plots" version="1.1+galaxy0">
  <description>for FCS file</description>
  <requirements>
    <requirement type="package" version="1.14.0">bioconductor-ggcyto</requirement>
    <!-- to fix https://github.com/RGLab/ggcyto/issues/64 and not able to install ggcyto 1.16.0-->
    <requirement type="package" version="3.2.1">r-ggplot2</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command><![CDATA[
     Rscript $__tool_directory__/FCS1Dplotggcyto.R '${input}' '${output}' $outformat '${transform.trans_method}'
     #if $transform.trans_method == "arcsinh"
     $transform.scaling_factor
     #else if $transform.trans_method == "logicle"
     $transform.w $transform.t $transform.m
     #end if
  ]]>
  </command>
  <inputs>
    <param format="fcs" name="input" type="data" label="FCS file"/>
    <conditional name="transform">
      <param name="trans_method" type="select" label="Apply transformation to plot:" help="by default, no transformation">
        <option value="None">no transformation please.</option>
        <option value="logicle">logicle</option>
        <option value="arcsinh">arcsinh</option>
      </param>
      <when value="arcsinh">
        <param name="scaling_factor" type="integer" min="1" max="200" value="150" label="Scaling factor b for arcsinh transform:" help="The default value is 150 for standard FCM data. The recommended value for cyTOF data is 5.">
        </param>
      </when>
      <when value="logicle">
        <param name="w" type="float" value="0.5" label="Linearization width w for logicle transform:" help="w should be positive and determines the slope of transformation at zero. The default value is 0.5.">
        </param>
        <param name="t" type="integer" value="262144" label="Top of the scale data value t for logicle transform:" help=" t should be greater than zero. Recommended values are 10000 for common 4 decade data or 262144 for a 18 bit data range. The default value is 262144.">
        </param>
        <param name="m" type="float" value="4.5" label="Full width of the transformed display m for logicle transform:" help="m is expressed in asymptotic decades and should be positive. The default value is 4.5 .">
        </param>
      </when>
    </conditional>
    <param name="outformat" type="select" label="Output Format" help="PDF will be larger files that may take some time to load.">
      <option value="PNG">PNG</option>
      <option value="PDF">PDF</option>
    </param>
  </inputs>
  <outputs>
    <data format="png" name="output" label="1D Density Plots for ${input.name} with ${transform.trans_method} in ${outformat}">
      <change_format>
        <when input="outformat" value="PDF" format="pdf" />
      </change_format>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="input" value="testfcs1.fcs"/>
      <param name="outformat" value="PDF"/>
      <param name="trans_method" value="None"/>
      <output name="output" file="graph.pdf" compare="sim_size"/>
    </test>
    <test>
      <param name="input" value="testfcs1.fcs"/>
      <param name="outformat" value="PNG"/>
      <param name="trans_method" value="logicle"/>
      <param name="w" value="0.4"/>
      <param name="m" value="4.5"/>
      <param name="t" value="10000"/>
      <output name="output" file="graph1.png" compare="sim_size"/>
    </test>
    <test>
      <param name="input" value="testfcs1.fcs"/>
      <param name="outformat" value="PNG"/>
      <param name="trans_method" value="arcsinh"/>
      <param name="scaling_factor" value="150"/>
      <output name="output" file="graph2.png" compare="sim_size"/>
    </test>
  </tests>
  <help><![CDATA[
Scatterplots of fcs sample
-------------------

This tool allows generation of density scatter plots using ggcyto.

**Input files**

This tool takes valid FCS files as input.

**Output files**

This tool generates a series of 1D density plot using ggcyto and produces a png file. A pdf file can optionally be generated.

class:: warningmark

PDF are larger files that may take some time to load. It might be faster to download the PDF output once generated to open it locally.

-----

**Transformation**

This tools currently supports 2 transformation algorithms: arcsinh and logicle, implemented using flowCore. Transformation applied are color-coded: black is no transformation, blue is arcinsh, and green is logicle.

-----

**Example**

*Output*:

.. image:: ./static/images/flowtools/testoutputggcyto.png

-----

**ggcyto reference**
Jiang M (2015). ggcyto: Visualize Cytometry data with ggplot. R package version 1.4.0, https://github.com/RGLab/ggcyto/issues.

  ]]>
  </help>
  <citations>
    <citation type="doi">10.1186/1471-2105-10-106</citation>
  </citations>
</tool>