<tool id="get_cell_ontology" name="Explore cell ontology" version="1.0">
  <description>given a phenotype using flowCL.</description>
  <requirements>
    <requirement type="package" version="2.8">jinja2</requirement>
    <requirement type="package" version="3.2.3">r</requirement>
    <requirement type="package" version="1.11.1">bioconductor-flowcl</requirement>
  </requirements>
 <stdio>
    <exit_code range="2" level="fatal" description="There was a problem running flowCL. You might want to check your marker names - See stderr for more details." />
    <exit_code range="3:" level="fatal" description="See stderr for more details." />
  </stdio>
  <command><![CDATA[
      python $__tool_directory__/getOntology.py -o "${html_file}" -d "${html_file.files_path}" -t $__tool_directory__ -m "${marker1}" -y "${type1}"
      #for $mrkrs in $Markers
        -m "${mrkrs.markername}"
        -y "${mrkrs.markertype}"
      #end for
  ]]>
  </command>
  <inputs>
    <param name="marker1" type="text" label="First marker"/>
    <param name="type1" type="select" label="First marker type">
      <option value="+">+</option>
      <option value="-">-</option>
      <option value="lo">lo</option>
      <option value="lo">low</option>
      <option value="lo">dim</option>
      <option value="lo">--</option>
      <option value="hi">hi</option>
      <option value="hi">high</option>
      <option value="hi">bri</option>
      <option value="hi">bright</option>
      <option value="hi">++</option>
    </param>
    <repeat name="Markers" title="Marker">
      <param name="markername" type="text" label="Add marker"/>
      <param name="markertype" type="select" label="Marker type">
        <option value="+">+</option>
        <option value="-">-</option>
        <option value="lo">lo</option>
        <option value="lo">low</option>
        <option value="lo">dim</option>
        <option value="lo">--</option>
        <option value="hi">hi</option>
        <option value="hi">high</option>
        <option value="hi">bri</option>
        <option value="hi">bright</option>
        <option value="hi">++</option>
      </param>
    </repeat>
  </inputs>
  <outputs>
    <data format="html" name="html_file" label="flowCL run"/>
  </outputs>
  <tests>
    <test>
      <param name="marker1" value="CD4"/>
      <param name="type1" value="+"/>
      <output name="html_file" file="out.html">
        <extra_files type="file" name="flowCL_res.pdf" value="flowCL_res.pdf" compare="contains"/>
        <extra_files type="file" name="flowCL_run_summary.txt" value="flowCL_run_summary.txt"/>
        <extra_files type="file" name="flowCL_table.txt" value="flowCL_table.txt"/>
      </output>
    </test>
  </tests>
 <help><![CDATA[
   This tool uses flowCL to find the most likely match to a given set a markers.

-----

**Input**

Type in the marker names and select the expression level in the drop-down menu.

**Output**

A summary of the ouptut of flowCL is captured in a txt file. For more details, please refer to the flowCL documentation.

**Graphical output**

FlowCL generates a plot for the most likely matches to ontology.

-----

**Example**

*Output summary*

The CL terms hyperlink to their representation in the Immport Cell Ontology browser.

.. image:: static/images/flowcl_summary.png

*Graphical output*

.. image:: static/flowtools/flowcl_graph.png

  ]]>
  </help>
  <citations>
    <citation type="doi">10.1093/bioinformatics/btu807</citation>
  </citations>
</tool>