<tool id="get_fcs_headers" name="Get list of markers" version="2.0+galaxy0">
  <description>in FCS files.</description>
  <requirements>
    <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement>
  </requirements>
  <stdio>
    <exit_code range="10" level="warning" description="Not all files are valid FCS files, see output for details." />
  </stdio>
  <command><![CDATA[
         Rscript '$__tool_directory__/getFCSheader.R' '${output_file}'
    #for $f in $input
 	'${f}' '${f.name}'
    #end for
  ]]>
  </command>
  <inputs>
    <param format="fcs" name="input" type="data_collection" collection_type="list" label="FCS files Collection"/>
  </inputs>
  <outputs>
      <data format="tabular" name="output_file" label="Headers of files in ${input.name}"/>
  </outputs>
  <tests>
    <test>
      <param name="input">
        <collection type="list">
          <element name="input1.fcs" value="input1.fcs"/>
          <element name="input2.fcs" value="input2.fcs"/>
          <element name="input3.fcs" value="input3.fcs"/>
        </collection>
      </param>
      <output name="output_file" file="output.tabular" lines_diff="8"/>
    </test>
  </tests>
  <help><![CDATA[
  This tool returns a table of the headers of a set of FCS files.

-----

**Input files**

This tool requires collections of FCS files as input.

**Output file**

The output file is a table listing the markers and channels for each file.

-----

**Example**

*File1*::

   Marker1 Marker2 Marker3
   34      45      12
   33      65      10

*File2*::

   Marker4 Marker5 Marker3
   19      62      98
   12      36      58

*Output*::

   Filename Index    1        2        3
   File1 channels Channel1 Channel2 Channel3
   File2 channels Channel4 Channel5 Channel3
   File1 markers  Marker1  Marker2  Marker3
   File2 markers  Marker4  Marker5  Marker3
 ]]>
  </help>
</tool>