--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/basic_illumination.xml	Fri Mar 12 00:13:46 2021 +0000
@@ -0,0 +1,50 @@
+<tool id="basic_illumination" name="BaSiC Illumination" version="@VERSION@.3" profile="17.09">
+    <description>ImageJ BaSiC shading correction for use with Ashlar</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+ 
+    <expand macro="requirements"/>
+    @VERSION_CMD@
+
+    <command detect_errors="exit_code"><![CDATA[
+    ln -s $in_files "${in_files.name}" &&
+
+    #set $outname = str($in_files.name).replace('.ome.tiff','')
+
+    @CMD_BEGIN@
+
+    "filename='${in_files.name}',output_dir='.',experiment_name='output'";
+
+    ]]></command>
+
+    <inputs>
+        <param type="data" name="in_files" format="tiff" label="Raw Cycle Images"/>
+   </inputs>
+
+   <outputs>
+       <data format="tiff" name="output_dfp" label="${tool.name} on ${on_string}: DFP" from_work_dir="output-dfp.tif"/>
+       <data format="tiff" name="output_ffp" label="${tool.name} on ${on_string}: FFP" from_work_dir="output-ffp.tif"/>
+    </outputs>
+
+    <help><![CDATA[
+basic-illumination
+ImageJ BaSiC shading correction for use with Ashlar
+
+Running as a Docker container
+Create a container:
+
+docker run -it -v /path/to/data:/data labsyspharm/basic-illumination bash
+(where /path/to/data is the data directory on your local machine. Your data will be mapped to /data inside the container)
+
+Once inside the container, do ls /data to ensure your data is there, followed by
+
+ImageJ-linux64 --ij2 --headless --run imagej_basic_ashlar.py \
+  "filename='/data/input.ome.tiff',output_dir='/data/',experiment_name='my_experiment'"
+for each input.ome.tiff in your data directory.
+
+OHSU Wrapper Repo: https://github.com/ohsu-comp-bio/basic-illumination
+Conda Package Available From: https://anaconda.org/ohsu-comp-bio/basic-illumination
+    ]]></help>
+    <expand macro="citations" />
+</tool>