--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runFlockMFI.xml	Fri Jul 17 09:06:54 2020 -0400
@@ -0,0 +1,166 @@
+<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>