--- a/basic_illumination.xml	Fri Mar 12 00:13:46 2021 +0000
+++ b/basic_illumination.xml	Thu Sep 01 22:46:21 2022 +0000
@@ -1,16 +1,16 @@
-<tool id="basic_illumination" name="BaSiC Illumination" version="@VERSION@.3" profile="17.09">
+<tool id="basic_illumination" name="BaSiC Illumination" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>ImageJ BaSiC shading correction for use with Ashlar</description>
     <macros>
         <import>macros.xml</import>
     </macros>
  
     <expand macro="requirements"/>
-    @VERSION_CMD@
+    <expand macro="version_cmd"/>
 
     <command detect_errors="exit_code"><![CDATA[
-    ln -s $in_files "${in_files.name}" &&
+    ln -s '$in_files' '${in_files.name}' &&
 
-    #set $outname = str($in_files.name).replace('.ome.tiff','')
+    #set $outname = str('$in_files.name').replace('.ome.tiff','')
 
     @CMD_BEGIN@
 
@@ -26,25 +26,30 @@
        <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>
-
+    <tests>
+        <test>
+            <param name="in_files" value="test.tiff" />
+            <output name="output_dfp" ftype="tiff">
+                <assert_contents>
+                    <has_size value="350000" delta="50000" />
+                </assert_contents>
+            </output>
+            <output name="output_ffp" ftype="tiff">
+                <assert_contents>
+                    <has_size value="350000" delta="50000" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <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
+**ImageJ BaSiC shading correction for use with Ashlar**
+**basic-illumination** can read image data directly from BioFormats-supported microscope
+vendor file formats as well as a directory of plain TIFF files. Output includes a flat field and
+dark field image per input file.
     ]]></help>
     <expand macro="citations" />
 </tool>