--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_mfi/generateMFI.xml	Mon Feb 27 13:00:34 2017 -0500
@@ -0,0 +1,77 @@
+<tool id="generate_mfi" name="Generate the centroids" version="1.0">
+  <description>from a flow result file</description>
+  <requirements>
+    <requirement type="package" version="0.17.1">pandas</requirement>
+    <requirement type="package" version="1.10.2">numpy</requirement>
+    <requirement type="package" version="0.16.0">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 a FLOCK output file.
+
+-----
+
+**Input file**
+
+This tool reads in a FLOCK output file.
+
+**Output file**
+
+The output is a table containing the mean, median or geometric mean fluorescent intensity values of each marker within each population defined by FLOCK.
+
+-----
+
+**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>