<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"/>
    <expand macro="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>
    <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**
**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>