--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/collapse_pops.xml	Mon Jun 22 16:34:35 2020 -0400
@@ -0,0 +1,91 @@
+<tool id="collapse_populations" name="Collapse populations" version="1.0+galaxy1">
+  <description>from FLOCK or Cross Sample analysis</description>
+  <requirements>
+    <requirement type="package" version="0.17.1">pandas</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="2" level="warning" description="The color code only allows populations between 1 and 40." />
+    <exit_code range="3" level="warning" description="The same population to collapse into is being used several times." />
+    <exit_code range="4" level="fatal" description="Please provide a comma separated list of populations to collapse." />
+    <exit_code range="5" level="warning" description="The color code only allows populations between 1 and 40, and the same population to collapse into is being used several times." />
+    <exit_code range="6" level="fatal" description="The populations must be integers (i.e,: 1,2,4.)" />
+    <exit_code range="7" level="fatal" description="The same population is being collapsed into 2 different populations." />
+  </stdio>
+  <command><![CDATA[
+      python '$__tool_directory__/collapse_pops.py' -o '${output}' -i '${input}' -p '${population}' -c '${collapse}'
+    #for $repeats in $repeat_option
+        -p '${repeats.population}'
+        -c '${repeats.collapse}'
+    #end for
+  ]]>
+  </command>
+  <inputs>
+    <param format="flowclr" name="input" type="data" label="Source file"/>
+    <param name="population" type="text" label="Collapse the following populations:" value="i.e.:2,3,11,25"/>
+    <param name="collapse" type="text" label="Into population:" value="i.e.:4"/>
+    <repeat name="repeat_option" title="more populations to manipulate:">
+      <param name="population" type="text" label="Collapse the following populations:" value="i.e.:2,3,11,25"/>
+      <param name="collapse" type="text" label="Into population:" value="i.e.:4"/>
+    </repeat>
+  </inputs>
+  <outputs>
+    <data format="flowclr" name="output" label="${input.name} with renamed populations"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="input.flowclr"/>
+      <param name="population" value="2,3,4"/>
+      <param name="collapse" value="1"/>
+      <output name="output" file="output.flowclr"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+   This tool collapses several populations into one.
+
+-----
+
+.. class:: warningmark
+
+Tip: You can use this tool to assign specific colors to your populations in the FLOCK and Cross Sample overview tools. The color scheme we use is the following:
+
+.. image:: ./static/images/flowtools/liz_colorcode.png
+
+-----
+
+**Input**
+
+FLOCK or Cross Sample output - a table of the fluorescence intensities for each event and the population associated with each.
+
+**Output**
+
+The input file with selected populations replaced by the indicated population.
+
+-----
+
+**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      ... 1
+   ...     ...     ...     ... ...
+
+*Populations selected:* 2, 5
+
+*Collapse into population:* 3
+
+*Output* - fluorescence intensities per marker and population ID per event::
+
+   Marker1 Marker2 Marker3 ... Population
+   34      45      12      ... 1
+   33      65      10      ... 3
+   19      62      98      ... 3
+   12      36      58      ... 1
+   ...     ...     ...     ... ...
+
+  ]]>
+  </help>
+</tool>