annotate runFlockMFI.xml @ 2:b6b4d08b6858 draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"

<tool id="run_flock" name="Run FLOCK" version="1.2+galaxy0" profile="18.01">
  <description>using a FCS file that was converted/transformed to a text file</description>
  <requirements>
    <requirement type="package" version="1.5.1">scipy</requirement>
    <requirement type="package" version="1.0.5">pandas</requirement>
    <requirement type="package" version="1.0">flock</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command><![CDATA[
    python3 '$__tool_directory__/runFlockMFI.py' -i '${input}' -m '${method}' -o '${output}' -c '${centroid}' -M '${mfi}' -p '${profile}'
    #if $bins
      -b $bins
    #end if
    #if $density
      -d $density
    #end if
  ]]>
  </command>
  <inputs>
    <param format="flowtext" name="input" type="data" label="Source file"/>
    <param name="method" type="select" label="Method">
      <option value="flock1" selected="true">Flock Version 1</option>
      <option value="flock2">Flock Version 2</option>
    </param>
    <param name="bins" type="integer" min="6" max="30" optional="true" value="" label="bins (6-30)"/>
    <param name="density" type="integer" min="2" max="100" optional="true" value="" label="density (2-100)"/>
    <param name="mfi" type="select" label="Calculate centroids using:">
      <option value="mfi" selected="true">Mean Fluorescence Intensity</option>
      <option value="mdfi">Median Fluorescence Intensity</option>
      <option value="gmfi">Geometric Mean Fluorescence Intensity</option>
    </param>
  </inputs>
  <outputs>
    <data format="flowclr" name="output" label="${method} with ${mfi} on ${input.name}"/>
    <data format="flowmfi" name="centroid" label="${mfi} centroids from ${method} on ${input.name}"/>
    <data format="flowscore" name="profile" label="Population score profiles from ${method} on ${input.name}"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="input.flowtext"/>
      <param name="method" value="flock1"/>
      <param name="bins" value=""/>
      <param name="density" value=""/>
      <param name="mfi" value="mfi"/>
      <output name="output" file="out1.flowclr"/>
      <output name="centroid" file="mfi.flowmfi"/>
      <output name="profile" file="out1.flowscore"/>
    </test>
    <test>
      <param name="input" value="input.flowtext"/>
      <param name="method" value="flock2"/>
      <param name="bins" value=""/>
      <param name="density" value=""/>
      <param name="mfi" value="mfi"/>
      <output name="output" file="out2.flowclr"/>
      <output name="centroid" file="mfi2.flowmfi"/>
      <output name="profile" file="out2.flowscore"/>
    </test>
    <test>
      <param name="input" value="input.flowtext"/>
      <param name="method" value="flock1"/>
      <param name="bins" value="7"/>
      <param name="density" value="3"/>
      <param name="mfi" value="mfi"/>
      <output name="output" file="out3.flowclr"/>
      <output name="centroid" file="mfi3.flowmfi"/>
      <output name="profile" file="out3.flowscore"/>
    </test>
  </tests>
  <help><![CDATA[
   This tool runs FLOCK using a FCS file that was converted to a text file.

-----

.. image::  ./static/images/flowtools/flock_logo.png

FLOCK (FLOw Clustering without K) is a computational approach to flow cytometry analysis which:

  1. Computationally determines the number of unique populations in high dimensional flow data using a rapid binning approach
  2. Can handle non-spherical hyper-shapes
  3. Maps populations across independent samples
  4. Calculates many useful summary statistics
  5. Finds the most informative parameters
  6. Reduces subjective factors in manual gating

.. class:: warningmark

This tool is not intended to analyze CyTOF data as is.

-----

**Input**

FLOCK requires a text file, generated from a FCS file, as input.
In order to define the populations in a given dataset collection for a given set of markers, run FLOCK on a super-set of FCS file. Use the Downsample and merge tool to concatenate and/or downsample datasets, and remove, edit or rearrange markers before running FLOCK on your favorite set of markers.

.. class:: infomark

Tip: Make sure to keep only columns containing data from markers.

**Output**

*FLOCK*

FLOCK attributes each event to a population and generates a text file.

*Centroids*

The centroid file is a table containing the mean, median or geometric mean fluorescent intensity values of each marker within each population defined by FLOCK, as determined by the user.

*Population scores*

This output is a table containing marker scores for each population. The score value is a number indicating the degree to which this population expresses each marker, as follows:

- 1 implies negative expression
- 2 implies low expression
- 3 implies positive expression
- 4 implies highly positive expression

-----

**Example**

*Input* - fluorescence intensities per marker per event::

   Marker1 Marker2 Marker3 ...
   34      45      12      ...
   33      65      10      ...
   19      62      98      ...
   12      36      58      ...
   ...     ...     ...     ...

*FLOCK Output* - fluorescence intensities per marker and population ID per event::

   Marker1 Marker2 Marker3 ... Population
   34      45      12      ... 1
   33      65      10      ... 5
   19      62      98      ... 2
   12      36      58      ... 1
   ...     ...     ...     ... ...

*Centroid file* - mean, geometric mean or median fluorescence intensity per marker per population::

   Population Marker1 Marker2 Marker3 ...
   1          38      49      10      ...
   2          21      63      100     ...
   3          31      52      45      ...
   4          11      78      25      ...
   ...        ...     ...     ...     ...

*Population profile file*::

   Population_ID Marker1 Marker2 Marker3 ... Count Percentage
   1             1       3       2       ... 3885  6.44
   2             1       3       4       ... 2774  4.62
   3             2       2       3       ... 2151  3.59
   4             1       3       2       ... 1207  2.01
   ...           ...     ...     ...     ... ...   ...
  ]]>
  </help>
  <citations>
    <citation type="doi">10.1002/cyto.b.20554</citation>
  </citations>
</tool>