<tool id="get_profiles_cell_ontology" name="Associate FLOCK populations" version="1.1+galaxy0" profile="18.01">
  <description>with cell ontology</description>
  <requirements>
    <requirement type="package" version="2.11.2">jinja2</requirement>
    <requirement type="package" version="1.26.0">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 '$__tool_directory__/profileCLs.py' -i '${input}' -o '${html_file}' -d '${html_file.files_path}' -t '$__tool_directory__'
  ]]>
  </command>
  <inputs>
    <param format="flowscore" name="input" type="data" label="Population score profiles from FLOCK"/>
  </inputs>
  <outputs>
    <data format="html" name="html_file" label="Cell ontology of ${input.name}">
    </data>
  </outputs>
  <tests>
    <test>
      <param name="input" value="input.flowscore"/>
      <output name="html_file" file="out.html">
        <extra_files type="file" name="CLprofiles.txt" value="CLprofiles.txt"/>
        <extra_files type="file" name="flowcl_pop01.pdf" value="flowcl_pop01.pdf" compare="sim_size"/>
        <extra_files type="file" name="flowcl_pop01.txt" value="flowcl_pop01.txt"/>
        <extra_files type="file" name="flowcl_pop03.pdf" value="flowcl_pop03.pdf" compare="sim_size"/>
        <extra_files type="file" name="flowcl_pop03.txt" value="flowcl_pop03.txt"/>
        <extra_files type="file" name="scores.txt" value="scores.txt"/>
      </output>
    </test>
  </tests>
  <help><![CDATA[
   This tool uses flowCL to find a match for each of the populations defined by FLOCK.
.. class:: warningmark
Please note that the scores computed for each markers and population correspond to quartiles binning, and not necessarily to what would be considered +, -, low or high.
-----
**Input**
This tool reads in the population score profiles from FLOCK.
.. class:: warningmark
**The marker names need to be in the cell ontology for this to work**
**Output**
The output is a page that allows visualization of the data.
-----
**Example**
*Input*
*Population profile file*::
   Population_ID Marker1 Marker2 Marker3 ... Count Percentage
   1             1       3       2       ... 3885  6.44
   2             1       3       4       ... 2774  4.62
   3             2       2       3       ... 2151  3.59
   4             1       3       2       ... 1207  2.01
   ...           ...     ...     ...     ... ...   ...
*Output*
The CL terms hyperlink to their representation in the Immport Cell Ontology browser. The full flowCL run summary is accessible by clicking on the phenotype.
.. image:: ../../static/images/flowtools/profileCL.png
.. image:: ../../static/images/flowtools/popprofiles.png
  ]]>
  </help>
  <citations>
    <citation type="doi">10.1093/bioinformatics/btu807</citation>
  </citations>
</tool>