--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flowcl/getOntology.xml	Mon Feb 27 12:56:34 2017 -0500
@@ -0,0 +1,102 @@
+<tool id="get_cell_ontology" name="Explore cell ontology" version="1.0">
+  <description>given a phenotype using flowCL.</description>
+  <requirements>
+    <requirement type="package" version="2.8">jinja2</requirement>
+    <requirement type="package" version="3.2.3">r</requirement>
+    <requirement type="package" version="1.11.1">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 $__tool_directory__/getOntology.py -o "${html_file}" -d "${html_file.files_path}" -t $__tool_directory__ -m "${marker1}" -y "${type1}"
+      #for $mrkrs in $Markers
+        -m "${mrkrs.markername}"
+        -y "${mrkrs.markertype}"
+      #end for
+  ]]>
+  </command>
+  <inputs>
+    <param name="marker1" type="text" label="First marker"/>
+    <param name="type1" type="select" label="First marker type">
+      <option value="+">+</option>
+      <option value="-">-</option>
+      <option value="lo">lo</option>
+      <option value="lo">low</option>
+      <option value="lo">dim</option>
+      <option value="lo">--</option>
+      <option value="hi">hi</option>
+      <option value="hi">high</option>
+      <option value="hi">bri</option>
+      <option value="hi">bright</option>
+      <option value="hi">++</option>
+    </param>
+    <repeat name="Markers" title="Marker">
+      <param name="markername" type="text" label="Add marker"/>
+      <param name="markertype" type="select" label="Marker type">
+        <option value="+">+</option>
+        <option value="-">-</option>
+        <option value="lo">lo</option>
+        <option value="lo">low</option>
+        <option value="lo">dim</option>
+        <option value="lo">--</option>
+        <option value="hi">hi</option>
+        <option value="hi">high</option>
+        <option value="hi">bri</option>
+        <option value="hi">bright</option>
+        <option value="hi">++</option>
+      </param>
+    </repeat>
+  </inputs>
+  <outputs>
+    <data format="html" name="html_file" label="flowCL run"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="marker1" value="CD4"/>
+      <param name="type1" value="+"/>
+      <output name="html_file" file="out.html">
+        <extra_files type="file" name="flowCL_res.pdf" value="flowCL_res.pdf" compare="contains"/>
+        <extra_files type="file" name="flowCL_run_summary.txt" value="flowCL_run_summary.txt"/>
+        <extra_files type="file" name="flowCL_table.txt" value="flowCL_table.txt"/>
+      </output>
+    </test>
+  </tests>
+ <help><![CDATA[
+   This tool uses flowCL to find the most likely match to a given set a markers.
+
+-----
+
+**Input**
+
+Type in the marker names and select the expression level in the drop-down menu.
+
+**Output**
+
+A summary of the ouptut of flowCL is captured in a txt file. For more details, please refer to the flowCL documentation.
+
+**Graphical output**
+
+FlowCL generates a plot for the most likely matches to ontology.
+
+-----
+
+**Example**
+
+*Output summary*
+
+The CL terms hyperlink to their representation in the Immport Cell Ontology browser.
+
+.. image:: static/images/flowcl_summary.png
+
+*Graphical output*
+
+.. image:: static/flowtools/flowcl_graph.png
+
+  ]]>
+  </help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btu807</citation>
+  </citations>
+</tool>