<tool id="cp_cellprofiler" name="cellProfiler" version="@CP_VERSION@">
    <description>runs a cellProfiler pipeline assembled by all the cellProfiler tools upstream in the workflow</description>
    <macros>
        <import>macros.xml</import>
        <xml name="test_assert_content" token_n="291">
            <assert_contents>
                <has_n_lines n="@N@" />
            </assert_contents>
        </xml>
    </macros>
    <expand macro="cp_requirements" />
    <command detect_errors="aggressive"><![CDATA[
        bash '$script_file' &&
        cellprofiler -c -r --file-list list.txt -o ./output -p '$pipeline' 
        #if '$detailed_output'
            -L 10 > ./cp.log 2>&1
        #end if 
    ]]></command>
    <configfiles>
        <configfile name="script_file">
mkdir ./input
mkdir ./output
#for $i, $filename in enumerate($input_images):
    ln -s '$filename' './input/${filename.element_identifier}.${filename.ext}'
#end for

find `pwd`/input -name "*.*" > list.txt
        </configfile>
    </configfiles>
  
    <inputs>
        <param name="pipeline" type="data" format="txt" label="Pipeline file" help="A ready-to-run .cppipe file. It can be created with various CellProfiler modules." />
        <param name="input_images" type="data" multiple="true" format="@FORMATS@" label="Images" />
        <param name="detailed_output" type="boolean" label="Detailed logging file?" help="If set, a detailed cellprofiler log file will be generated." />
    </inputs>

    <outputs>
        <collection name="pipeline_output" type="list" label="Cellprofiler pipeline output files">
            <discover_datasets pattern="__designation_and_ext__" visible="false" directory="output"/>
        </collection>
        <data format="txt" name="logs" from_work_dir="cp.log" label="CellProfiler log">
            <filter>detailed_output</filter>
        </data>
    </outputs>

    <tests>
        <test expect_num_outputs="1">
            <param name="pipeline" value="ExampleHuman.cppipe" />
            <param name="input_images" value="images/AS_09125_050116030001_D03f00d0.tif,images/AS_09125_050116030001_D03f00d1.tif,images/AS_09125_050116030001_D03f00d2.tif" />
            <param name="detailed_output" value="False" />
            <output_collection name="pipeline_output" type="list" count="7">
                <element name="AS_09125_050116030001_D03f00d0.tif_Overlay">
                    <assert_contents>
                      <has_size value="183808"/>
                    </assert_contents>
                </element>
                <element name="Cells">
                    <expand macro="test_assert_content" n="290" />
                </element>
                <element name="Cytoplasm">
                  <expand macro="test_assert_content" n="290" />
                </element>
                <element name="Experiment">
                  <expand macro="test_assert_content" n="259" />
                </element>
                <element name="Image">
                  <expand macro="test_assert_content" n="2" />
                </element>
                <element name="Nuclei">
                  <expand macro="test_assert_content" n="290" />
                </element>
                <element name="PH3">
                  <expand macro="test_assert_content" n="21" />
                </element>
            </output_collection>
        </test>
        <test expect_num_outputs="2">
            <param name="pipeline" value="ExampleHuman.cppipe" />
            <param name="input_images" value="images/AS_09125_050116030001_D03f00d0.tif,images/AS_09125_050116030001_D03f00d1.tif,images/AS_09125_050116030001_D03f00d2.tif" />
            <param name="detailed_output" value="True" />
            <output_collection name="pipeline_output" type="list" count="7">
                <element name="AS_09125_050116030001_D03f00d0.tif_Overlay">
                    <assert_contents>
                      <has_size value="183808"/>
                    </assert_contents>
                </element>
                <element name="Cells">
                    <expand macro="test_assert_content" n="290" />
                </element>
                <element name="Cytoplasm">
                  <expand macro="test_assert_content" n="290" />
                </element>
                <element name="Experiment">
                  <expand macro="test_assert_content" n="259" />
                </element>
                <element name="Image">
                  <expand macro="test_assert_content" n="2" />
                </element>
                <element name="Nuclei">
                  <expand macro="test_assert_content" n="290" />
                </element>
                <element name="PH3">
                  <expand macro="test_assert_content" n="21" />
                </element>
            </output_collection>
            <output name="logs" ftype='txt'>
                <assert_contents>
                    <has_text_matching expression="JVM will be started with AWT in headless mode" />
                </assert_contents>
            </output>
        </test>
    </tests>
    
    <help>
    This tool runs a cellProfiler @CP_VERSION@ pipeline file. 

    *** Parameters ***

    images: multi-select image files
    
    pipeline: cellProfiler pipeline file(.cppipe) file.

    *** Note ***

    Only version @CP_VERSION@ pipeline can be run, other versions may cause problems.

    </help>
    <expand macro="citations" />
</tool>