annotate getDensityPlots_text.xml @ 1:754d511df1a3 draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowtext_scatterplot commit 2944aa6b74efcdb8d5cbf31abf27b352dcad9ac9"

<tool id="gen_density_plots_txt" name="Generate scatter plots" version="1.1+galaxy0" profile="18.01">
  <description>for any given markers in a txt-converted FCS file</description>
  <requirements>
    <requirement type="package" version="3.3.2">r-ggplot2</requirement>
    <requirement type="package" version="2.23_17">r-kernsmooth</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:9" level="fatal" />
    <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" />
    <exit_code range="12" level="fatal" description="Please provide more than one channel to plot" />
    <exit_code range="13:" level="fatal"/>
  </stdio>
  <command><![CDATA[
      Rscript $__tool_directory__/getDensityPlots_text.R '${input}' '${channels}' '${output}' '${outformat}'
  ]]>
  </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 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="Scatter Plots of ${channels} from ${input.name} in ${outformat}">
      <change_format>
        <when input="outformat" value="PDF" format="pdf" />
      </change_format>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="input" value="input.flowtext"/>
      <param name="channels" value="i.e.:1,3,4"/>
      <param name="outformat" value="PDF"/>
      <output name="output" file="graph.pdf" compare="sim_size" delta="2000000"/>
    </test>
    <test>
      <param name="input" value="input.flowtext"/>
      <param name="channels" value="1,3,5"/>
      <param name="outformat" value="PNG"/>
      <output name="output" file="graph2.png" compare="sim_size" delta="1000000"/>
    </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.

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.

-----

**Example**

*Output*:

.. image:: ./static/images/flowtools/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>