<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>