<tool id="edit_fcs_markers" name="Edit markers or channels" version="1.0">
  <description>in FCS files</description>
  <requirements>
    <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement>
  </requirements>
  <stdio>
    <exit_code range="10" level="fatal" description="Please provide a valid FCS file." />
    <exit_code range="11" level="fatal" description="Please provide a comma separated list of integers for markers/channels you want to rename." />
    <exit_code range="12" level="fatal" description="Please provide a comma separated list of names for markers/channels you want to rename." />
    <exit_code range="13" level="fatal" description="List of marker indices and marker names must match. For instance, indices 1,3,4 and Marker4,Marker6,Marker8." />
    <exit_code range="14" level="fatal" description="Provided indices are out of range in the FCS file given as input." />
  </stdio>
  <command><![CDATA[
    Rscript --slave --vanilla '$__tool_directory__/editFCSmarkers.R' '${input}' '${output_file}' '${outformat}' '${report}' '${columns}' '${colnames}' '${corm}'
  ]]>
  </command>
  <inputs>
    <param format="fcs" name="input" type="data" label="Text file"/>
    <param name="columns" type="text" label="Channels or markers to modify" help="These are comma separated (ie.: 'ColX,ColY'). The column names provided need to exist in the flowFrame / FCS file provided as input. If you're not sure, check your markers with the list of markers tool in the FCS File Tools section."/>
    <param name="colnames" type="text" label="New column headings" help="New names for the column headers, a comma separated list of the same lenght as 'Channels or markers to modify' (i.e.: 'Marker1,Marker6,Marker4'). Check below for more details.">
    </param>
    <param name="corm" type="select" label="Modify Channels or Markers?" help="If you are not sure which to modify, check with the list of marker tools in the FCS File Tools section.">
      <option value="M">Markers</option>
      <option value="C">Channels</option>
    </param>
    <param name="outformat" type="select" label="Output Format">
      <option value="flowFrame">R Data, flowFrame</option>
      <option value="FCS">FCS 3.0</option>
    </param>
</inputs>
  <outputs>
    <data format="txt" name="report" label="Editing Report of FCS markers from ${input.name}"/>
    <data format="flowframe" name="output_file" label="Edited FCS from ${input.name} in ${outformat}">
      <change_format>
        <when input="outformat" value="FCS" format="fcs" />
      </change_format>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="input" value="input.fcs"/>
      <param name="columns" value="Forward Scatter,Side Scatter,APC CD45RA"/>
      <param name="colnames" value="m1,m2,m3"/>
      <param name="corm" value="M"/>
      <param name="outformat" value="flowFrame"/>
      <output name="report" value="report1.txt"/>
      <output name="output_file" file="output.flowframe" compare="sim_size" delta="500000"/>
    </test>
    <test>
      <param name="input" value="input.fcs"/>
      <param name="columns" value="FSC-H,SSC-H,FL4-H"/>
      <param name="colnames" value="m1,m2,m3"/>
      <param name="corm" value="C"/>
      <param name="outformat" value="FCS"/>
      <output name="report" value="report2.txt"/>
      <output name="output_file" file="output.fcs" compare="sim_size" delta="500000"/>
    </test>
  </tests>
  <help><![CDATA[
   This tool enables editing FCS markers or channels.

-----

**Input files**

This tool requires FCS files as input.

**Column names**

Please indicate the names of the markers / channels to edit (comma-separated list).

.. class:: infomark

Tip: One of the tools in the FCS File Tools section can help check the markers and channels indices:

- Get list of markers and channels in FCS files.

**Column names**

Please indicate the new marker or channel names in the order in which they should appear in the output file (comma-separated list). The number of names should match the number of indices.

**Output file**

The output contains the input data with new marker or channel names. Output can be provided in FCS format or in a RData object containing a flowFrame.

-----

**Examples**

**Input file**::

   Marker1 Marker2 Marker3 Marker4 Marker5
   4       45      123     1956    62534
   3       65      104     1254    36576
   7       26      767     4124    42235
   4       56      323     7623    74634
   5       83      532     6256    34763
   4       15      877     9312    21265
   ...     ...     ...     ...     ...

*Example 1*

- Indices: Marker1,Marker3,Marker5
- Column names: Marker7,Marker8,Marker9

*Output1*::

   Marker7 Marker2 Marker8 Marker4 Marker9
   4       45      123     1956    62534
   3       65      104     1254    36576
   7       26      767     4124    42235
   4       56      323     7623    74634
   5       83      532     6256    34763
   4       15      877     9312    21265
   ...     ...     ...     ...     ...

  ]]>
  </help>
</tool>