view flowtext_summary/FCSstats_text.xml @ 0:d61ed37c06ee draft

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<tool id="get_txt_fcs_stats" name="Get summary" version="1.0">
  <description>of txt-converted FCS files.</description>
  <requirements>
    <requirement type="package" version="0.17.1">pandas</requirement>
  </requirements>
  <stdio>
    <exit_code range="2:" level="fatal" description="See stderr for more details." />
  </stdio>
  <command><![CDATA[
    python $__tool_directory__/FCSstats_txt.py -i "${input}" -o "${output}"
  ]]>
  </command>
  <inputs>
    <param format="flowtext" name="input" type="data" label="txt-converted FCS file"/>
  </inputs>
  <outputs>
    <data format="tabular" name="output" label="Summary statisitics of ${input.name}"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="input.flowtext"/>
      <output name="output" file="output.tabular"/>
    </test>
  </tests>
  <help><![CDATA[
   This tool generates a summary of a txt-converted FCS file and list of markers.

-----

**Input file**

This tool uses txt-converted FCS files as input.

**Output file**

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

-----

**Example**

*Output*::

        FSC    SSC    CD4   CCR3   CD8    CCR4
   mean 475.4  413.4  288.8 157.9  218.1  179.6
   std  165.2  390.7  199.9 117.3  201.7  95.7
   min  261.0  18.0   0.0   0.0    0.0	   0.0
   25%  354.0  121.0  112.0 65.0   58.0   109.0
   50%  398.0  167.0  209.0 159.0  180.0  179.0
   75%  609.0  951.2  512.0 237.0  275.0  245.0
   max  1023.0 1023.0 775.0 1023.0 1023.0 841.0
   20000 events
  ]]>
  </help>
</tool>