view convert_fcs_to_text/convertFCSToText.xml @ 0:8e10184368a0 draft

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<tool id="convert_fcs_to_text" name="Convert FCS to Text" version="1.0">
  <description>with no transformation.</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="1:" />
  </stdio>
  <command><![CDATA[
      Rscript --slave --vanilla $__tool_directory__/FCSConvert.R --args "${input}" "${output_file}" $compensate
  ]]>
  </command>
  <inputs>
    <param format="fcs" name="input" type="data" label="FCS file"/>
    <param name="compensate" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Compensate?">
    </param>
  </inputs>
  <outputs>
    <data format="flowtext" name="output_file" label="No Transformation ${input.name}"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="testfcs1.fcs"/>
      <param name="compensate" value="FALSE"/>
      <output name="output_file" file="nocomp.flowtext"/>
    </test>
    <test>
      <param name="input" value="testfcs1.fcs"/>
      <param name="compensate" value="TRUE"/>
      <output name="output_file" file="withcomp.flowtext"/>
    </test>
  </tests>
  <help><![CDATA[
   This tool converts FCS files to text format with no tranformation.

-----

**Input files**

This tool requires valid FCS files as input. Files are processed serially. Applying compensation is an option for FCS files including a compensation matrix.

**Output file**

The output is tab-separated text, containing the fluorescence intensity values for each marker.

-----

**Example**::

   Forward Scatter Side Scatter Marker1 Marker2 Marker3 Marker4
   449             157          551     129     169     292
   894             1023	        199     277     320     227
   262             73           437     69      0       146
   340             115          509     268     0       74
  ]]>
  </help>
</tool>