<tool id="metacyto_checkpanel" name="Check markers in analysis panels" version="1.0+galaxy0" profile="18.01">
  <description>for MetaCyto</description>
  <requirements>
    <requirement type="package" version="1.4.0">bioconductor-metacyto</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:9" />
    <exit_code range="10" level="fatal" description="The input file cannot be used. Please check input format." />
    <exit_code range="11:" />
  </stdio>
  <command><![CDATA[
    Rscript --slave --vanilla '$__tool_directory__/metacyto_checkpanel.R' '${input_file}' '${output_file}';
    #if $graph=="TRUE"
      mv panel_summary.pdf '${pdf_out}'
    #end if
  ]]>
  </command>
  <inputs>
    <param format="metacyto_summary.txt" name="input_file" type="data" label="MetaCyto preprocessing summary"/>
    <param name="graph" type="boolean" label="Output visual summary?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
  </inputs>
  <outputs>
    <data format="tabular" name="output_file" label="Panel Summary of ${input_file.name}"/>
    <data format="pdf" name="pdf_out" label="Visual Panel Summary of ${input_file.name}">
      <filter>(graph)</filter>
    </data>
  </outputs>
  <tests>
      <test>
        <param name="input_file" value="mc_preprocesss_summary.metacyto_summary.txt"/>
        <param name="graph" value="True"/>
        <output name="output_file" ftype="tabular">
          <assert_contents>
            <has_n_columns n="3" />
            <has_text text="CD95" />
            <has_n_lines n="14" />
          </assert_contents>
        </output>
        <output name="pdf_out" ftype="pdf">
          <assert_contents>
            <has_size value="4569" delta="500" />
          </assert_contents>
        </output>
      </test>
  </tests>
  <help><![CDATA[
    Metacyto Check Markers in analysis panels
    -----------------------------------------

    This tool uses MetaCyto's panel summary function to compare marker names between groups of FCS files.

    **Input**
    This tool requires the MetaCyto pre-processing Summary as input.

    **Output**
    This tool generates a table and an optional visual representation in PDF of how markers are distributed in the FCS file sets.


    **Example**

    *Input* - Summary Table::

       study_id antibodies                  filenames
       group1   Marker1|Marker2|Marker3|... file1.fcs
       group2   Marker1|Marker2|Marker3|... file2.fcs
       ...      ...                         ...

    *Output* - Panel Summary::

       Markers group1 group2 ...
       Marker1 1      1      ...
       Marker2 1      1      ...
       Marker3 0      1      ...
       ...     ...    ...    ...

    *Graphical output*

    .. image:: ./images/checkpanel.png
  ]]>
  </help>
</tool>