--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/auto_collapse_pops.xml	Mon Jun 22 17:22:03 2020 -0400
@@ -0,0 +1,89 @@
+<tool id="auto_collapse_populations" name="Collapse populations automatically" version="1.0+galaxy1">
+  <description>based on quartile binning from FLOCK results</description>
+  <requirements>
+    <requirement type="package" version="0.17.1">pandas</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  <command><![CDATA[
+      python '$__tool_directory__/auto_collapse_pops.py' -o '${output}' -i '${input}' -p '${profile}' -r '${report}'
+  ]]>
+  </command>
+  <inputs>
+    <param format="flowclr" name="input" type="data" label="FLOCK or Cross-Sample output file"/>
+    <param format="flowscore" name="profile" type="data" label="Population score profiles from FLOCK"/>
+  </inputs>
+  <outputs>
+    <data format="flowclr" name="output" label="Auto-collapsed pops in ${input.name}"/>
+    <data format="tabular" name="report" label="Auto-collapse report for ${input.name} with ${profile.name}"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="input.flowclr"/>
+      <param name="profile" value="profile.flowscore"/>
+      <param name="report" value="report.txt"/>
+      <output name="output" file="output.flowclr" compare="sim_size"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+   This tool automatically collapses populations together based on FLOCK score profiles.
+
+-----
+
+.. class:: warningmark
+
+*FLOCK score profiles are assigned based on quartile binning of the data. As always, use this tool with caution and be critical of your results*
+
+-----
+
+**Input**
+
+FLOCK or Cross Sample output - a table of the fluorescence intensities for each event and the population associated with each, as well as the file containing the score profiles for each FLOCK population.
+
+**Output**
+
+The input file with selected populations replaced by the indicated population. This tool also generates a report.
+
+-----
+
+**Example**
+
+*Input* - 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      ... 3
+   ...     ...     ...     ... ...
+
+*Population profile file*::
+
+   Population_ID Marker1 Marker2 Marker3 ... Count Percentage
+   1             2       2       3       ... 3885  6.44
+   2             1       3       4       ... 2774  4.62
+   3             2       2       3       ... 2151  3.59
+   4             1       3       2       ... 1207  2.01
+   ...           ...     ...     ...     ... ...   ...
+
+*Output* - fluorescence intensities per marker and population ID per event::
+
+   Marker1 Marker2 Marker3 ... Population
+   34      45      12      ... 1
+   33      65      10      ... 4
+   19      62      98      ... 2
+   12      36      58      ... 1
+   ...     ...     ...     ... ...
+
+*Output* - fluorescence intensities per marker and population ID per event::
+
+   New_Population Former_Populations Marker1 Marker2 Marker3 ...
+   1              1, 3               2       2       3       ...
+   2              2                  1       3       4       ...
+   3              4                  1       3       2       ...
+   4              5, 8, 12           3       1       1       ...
+   ...            ...                ...     ...     ...     ...
+  ]]>
+  </help>
+</tool>