<tool id="ip_slice_image" name="Slice Image" version="0.3">
    <description>into smaller patches</description>
    <requirements> 
        <requirement type="package" version="0.14.2">scikit-image</requirement>
        <requirement type="package" version="1.15.4">numpy</requirement>
        <requirement type="package" version="1.1.0">scipy</requirement>
        <requirement type="package" version="0.15.1">tifffile</requirement>
    </requirements>
    <command detect_errors="aggressive"> 
        <![CDATA[
        mkdir ./out &&
        python '$__tool_directory__/slice_image.py'
        '$input_file' ./out
        --stride $stride --window_size $patch_size --bg_thresh $bg_thresh
        --limit_slices $limit_slices 
        #if $limit_slices:
          --n_thresh $n_thresh
        #end if
        #if $control_rng:
          --seed $seed
        #end if
        && ls -l ./out
        ]]> 
    </command>
    <inputs>
        <param name="input_file" type="data" format="tiff,png,jpg,bmp" label="Input image"/> 
        <!--<param name="out_folder" type="text" label="Output folder for image slices"/> 
        <param name="label_file" type="data" format="tiff,png,jpg,bmp" label="Auxiliary label file to split in the same way"/>--> 
        <param name="stride" type="integer" optional="true" value="16"/>
        <param name="patch_size" type="integer" optional="true" value="64" label="Size of resulting (quadratic-shaped) slices"/>
        <param name="bg_thresh" type="float" optional="true" value="0" label="Threshold to not be considered background"/>
        <param name="limit_slices" type="boolean" checked="true" label="Should the number of slices be limited?"/>
        <param name="n_thresh" type="integer" optional="true" label="Maximum amount of slices; only needed if limit_slices is selected"/>  
        <param name="control_rng" type="boolean" checked="false" label="Boolean that controls if a certain seed should be selected for the random number generator"/>
        <param name="seed" type="integer" value="1"
            label="Seed chosen for the random number generator of the random choice of limited slices. Only required if cotrol_rng is selected"/>
    </inputs>
    <outputs>
        <collection name="slices" type="list" label="Slices obtained from input">
            <discover_datasets directory="out" format="tiff" pattern="__name__"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="input.tiff"/>
            <param name="limit_slices" value="true"/>
            <param name="n_thresh" value="5"/>
            <param name="control_rng" value="true"/>
            <param name="seed" value="17"/>
            <output_collection name="slices" type="list">
                <element name="148.tiff" file="input_148.tiff" ftype="tiff" compare="sim_size"/>
                <element name="155.tiff" file="input_155.tiff" ftype="tiff" compare="sim_size"/>
                <element name="187.tiff" file="input_187.tiff" ftype="tiff" compare="sim_size"/>
                <element name="212.tiff" file="input_212.tiff" ftype="tiff" compare="sim_size"/>
                <element name="267.tiff" file="input_267.tiff" ftype="tiff" compare="sim_size"/>
            </output_collection>
        </test>
    </tests>
    <help>
    **What it does**

    Slices image into multiple smaller patches.
    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>