view getDensityPlots.xml @ 1:413f3e610295 draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"

<tool id="gen_density_plots" name="Generate scatter plots" version="1.0+galaxy0">
  <description>for any given markers in FCS file</description>
  <requirements>
    <requirement type="package" version="1.10.0">bioconductor-flowdensity</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 --slave --vanilla '$__tool_directory__/getDensityPlots.R' '${input}' '${channels}' '${output}' '${outformat}'
  ]]>
  </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 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="testfcs1.fcs"/>
      <param name="channels" value="1,3"/>
      <param name="outformat" value="PDF"/>
      <output name="output" file="graph.pdf" compare="sim_size" delta="1000000"/>
    </test>
    <test>
      <param name="input" value="testfcs1.fcs"/>
      <param name="channels" value="i.e.:1,3,4"/>
      <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 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.

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/densityplots.png
  ]]>
  </help>
  <citations>
    <citation type="doi">10.1093/bioinformatics/btu677</citation>
    <citation type="doi">10.1186/1471-2105-10-106</citation>
  </citations>
</tool>