annotate check_fcs_headers/getFCSheaders.xml @ 0:d3957a51cc51 draft

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<tool id="get_fcs_headers" name="Get list of markers" version="1.0">
  <description>in FCS files.</description>
  <requirements>
    <requirement type="package" version="3.3.0">r</requirement>
    <requirement type="package" version="1.38.2">bioconductor-flowcore</requirement>
  </requirements>
  <stdio>
    <exit_code range="2:" level="fatal" description="See stderr for more details." />
  </stdio>
  <command><![CDATA[
    python $__tool_directory__/getFCSheaders.py -o "${output_file}" -t $__tool_directory__
 #for $f in $input#
    -i "${f}"
    -n "${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"/>
    </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*::

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