view fcs_summary/FCSstats.xml @ 0:1d926a8daa92 draft

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<tool id="get_fcs_stats" name="Get summary" version="1.0">
  <description>of 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[
      Rscript --slave --vanilla $__tool_directory__/FCSstats.R --args "${input}" "${output}"
  ]]>
  </command>
  <inputs>
    <param format="fcs" name="input" type="data" label="FCS file"/>
  </inputs>
  <outputs>
    <data format="txt" name="output" label="Summary statisitics of ${input.name}"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="testfcs1.fcs"/>
      <output name="output" file="summary.txt"/>
    </test>
  </tests>
  <help><![CDATA[
   This tool generates a summary of a FCS file and list of markers.

-----

**Input file**

This tool uses valid FCS files as input.

**Output file**

FCS file summary includes number of events, list of markers and parameters, and summary statistics for each.

-----

**Example**

*Output*::

       events parameters
        20000          6


   =========================
   ==     FCS SUMMARY     ==
   =========================
           FSC-H SSC-H FL1-H FL2-H  FL3-H  FL4-H
   Min.      261    23   0.0   0.0    0.0    0.0
   1st Qu.   371   120 129.0 153.0  257.0  252.0
   Median    432   196 206.0 237.0  432.0  331.0
   Mean      512   476 284.8 236.7  433.2  372.3
   3rd Qu.   657  1023 499.0 297.0  628.0  510.0
   Max.     1023  1023 729.0 925.0 1023.0 1023.0


   =========================
   ==    MARKERS IN FCS   ==
   =========================
     channels         markers
   1    FSC-H Forward Scatter
   2    SSC-H    Side Scatter
   3    FL1-H        FITC CD4
   4    FL2-H         PE CD25
   5    FL3-H          PP CD3
   6    FL4-H      APC CD45RA
  ]]>
  </help>
</tool>