annotate detection_viz.xml @ 4:99433164b593 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf

<tool id="ip_detection_viz" name="Visualize detections" version="0.3-2">
    <description></description>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">galaxy_image_analysis</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="0.14.2">scikit-image</requirement>
        <requirement type="package" version="3.0.2">matplotlib</requirement>
        <requirement type="package" version="0.15.1">tifffile</requirement>
    </requirements>
    <command detect_errors="aggressive">
        <![CDATA[
        python '$__tool_directory__/detection_viz.py' '$input' '$output' 
        --stroke_size $thickness --circle_radius $circle_radius 
        #if $tp_option['display'] == 'true'
        --tp '$tp'
        #end if
        #if $fn_option['display'] == 'true'
        --fn '$fn'
        #end if
        #if $fp_option['display'] == 'true'
        --fp '$fp'
        #end if
        ]]> 
    </command>
    <inputs>
        <param name="input" type="data" format="tiff,png,jpg,bmp" label="Binary Image File"/>
        <conditional name="tp_option">
            <param label="Display true positives" name="display" type="select">
                <option selected="True" value="false">No</option>
                <option value="true">Yes</option>
            </param>
            <when value="false"></when>
            <when value="true">
                <param name="tp" type="data" format="tabular" label="True positives file" />
            </when>
        </conditional>
        <conditional name="fn_option">
            <param label="Display false negatives" name="display" type="select">
                <option selected="True" value="false">No</option>
                <option value="true">Yes</option>
            </param>
            <when value="false"></when>
            <when value="true">
                <param name="fn" type="data" format="tabular" label="False negatives file" />
            </when>
        </conditional>
        <conditional name="fp_option">
            <param label="Display false positives" name="display" type="select">
                <option selected="True" value="false">No</option>
                <option value="true">Yes</option>
            </param>
            <when value="false"></when>
            <when value="true">
                <param name="fp" type="data" format="tabular" label="False positives file" />
            </when>
        </conditional>
        <param name="thickness" type="float" value="3.0" label="Stroke thickness"/>
        <param name="circle_radius" type="float" value="50.0" label="Circle radius"/>
    </inputs>
    <outputs>
        <data format="png" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="sample.png"/>
            <conditional name="tp_option">
                <param name="display" value="false"/>
            </conditional>
            <conditional name="fn_option">
                <param name="display" value="false"/>
            </conditional>
            <conditional name="fp_option">
                <param name="display" value="false"/>
            </conditional>
            <output name="output" value="out.png" ftype="png"/>
        </test>
    </tests>
    <help>
    **What it does**

    Draws circles of different colors around detected true positives, false negatives and false positives.
    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>