annotate generateMFI.xml @ 1:91e856e5ec7a draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"

<tool id="generate_mfi" name="Generate the centroids" version="1.0+galaxy0" profile="18.01">
  <description>from a flow result file</description>
  <requirements>
    <requirement type="package" version="1.0.5">pandas</requirement>
    <requirement type="package" version="1.5.1">scipy</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command><![CDATA[
      python '$__tool_directory__/generateMFI.py' -i '${input}' -o '${output}' -M '${mfi}'
  ]]>
  </command>
  <inputs>
    <param format="flowclr" name="input" type="data" label="Flow Text file"/>
    <param name="mfi" type="select" label="Calculate centroids using:">
      <option value="mfi" selected="true">Mean Fluorescence Intensity</option>
      <option value="mdfi">Median Fluorescence Intensity</option>
      <option value="gmfi">Geometric Mean Fluorescence Intensity</option>
    </param>
  </inputs>
  <outputs>
    <data format="flowmfi" name="output" label="${mfi} centroids from ${input.name}"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="input.flowclr"/>
      <param name="mfi" value="mfi"/>
      <output name="output" file="mfi.flowmfi"/>
    </test>
    <test>
      <param name="input" value="input.flowclr"/>
      <param name="mfi" value="mdfi"/>
      <output name="output" file="mdfi.flowmfi"/>
    </test>
    <test>
      <param name="input" value="input.flowclr"/>
      <param name="mfi" value="gmfi"/>
      <output name="output" file="gmfi.flowmfi"/>
    </test>
  </tests>
  <help><![CDATA[
   This tool generates the Mean, Median or Geometric Mean Fluorescence Intensity of clustered flow files.
.. class:: infomark
Tip: This tool can be used to generate the centroids table required by the visualization tool multiple samples mapping result.
-----
**Input file**
This tool reads in a tab-separated file containing markers fluorescence intensities for each event as well as population or cluster attribution, for instance text output from a FLOCK or FlowSOM run.
**Output file**
The output is a table containing the mean, median or geometric mean fluorescent intensity values of each marker within each population or cluster defined in the input file.
-----
**Example**
*Input*::
   Marker1 Marker2 Marker3 ... Population
   34      45      12      ... 1
   13      65      10      ... 5
   19      62      98      ... 2
   32      46      10      ... 1
   ...     ...     ...     ... ...
*Output*::
   Population Marker1 Marker2 Marker3 ...
   1          38      49      10      ...
   2          21      63      100     ...
   3          31      52      45      ...
   4          11      78      25      ...
   ...        ...     ...     ...     ...
  ]]>
  </help>
</tool>