--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/profileCLs.xml	Thu Jul 23 08:58:29 2020 -0400
@@ -0,0 +1,65 @@
+<tool id="get_profiles_cell_ontology" name="Associate FLOCK populations" version="1.1+galaxy0" profile="18.01">
+  <description>with cell ontology</description>
+  <requirements>
+    <requirement type="package" version="2.11.2">jinja2</requirement>
+    <requirement type="package" version="1.26.0">bioconductor-flowcl</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="2" level="fatal" description="There was a problem running flowCL. You might want to check your marker names - See stderr for more details." />
+    <exit_code range="3:" level="fatal" description="See stderr for more details." />
+  </stdio>
+  <command><![CDATA[
+    python '$__tool_directory__/profileCLs.py' -i '${input}' -o '${html_file}' -d '${html_file.files_path}' -t '$__tool_directory__'
+  ]]>
+  </command>
+  <inputs>
+    <param format="flowscore" name="input" type="data" label="Population score profiles from FLOCK"/>
+  </inputs>
+  <outputs>
+    <data format="html" name="html_file" label="Cell ontology of ${input.name}">
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="input.flowscore"/>
+      <output name="html_file" file="out.html">
+        <extra_files type="file" name="CLprofiles.txt" value="CLprofiles.txt"/>
+        <extra_files type="file" name="flowcl_pop01.pdf" value="flowcl_pop01.pdf" compare="sim_size"/>
+        <extra_files type="file" name="flowcl_pop01.txt" value="flowcl_pop01.txt"/>
+        <extra_files type="file" name="flowcl_pop03.pdf" value="flowcl_pop03.pdf" compare="sim_size"/>
+        <extra_files type="file" name="flowcl_pop03.txt" value="flowcl_pop03.txt"/>
+        <extra_files type="file" name="scores.txt" value="scores.txt"/>
+      </output>
+    </test>
+  </tests>
+  <help><![CDATA[
+   This tool uses flowCL to find a match for each of the populations defined by FLOCK.
+.. class:: warningmark
+Please note that the scores computed for each markers and population correspond to quartiles binning, and not necessarily to what would be considered +, -, low or high.
+-----
+**Input**
+This tool reads in the population score profiles from FLOCK.
+.. class:: warningmark
+**The marker names need to be in the cell ontology for this to work**
+**Output**
+The output is a page that allows visualization of the data.
+-----
+**Example**
+*Input*
+*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
+   ...           ...     ...     ...     ... ...   ...
+*Output*
+The CL terms hyperlink to their representation in the Immport Cell Ontology browser. The full flowCL run summary is accessible by clicking on the phenotype.
+.. image:: ../../static/images/flowtools/profileCL.png
+.. image:: ../../static/images/flowtools/popprofiles.png
+  ]]>
+  </help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btu807</citation>
+  </citations>
+</tool>