comparison overlay_images.xml @ 3:22ff7c705a83 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 8cd85b185acbfaa9ee6f4e9a389abc1f7b7c44bb

2:b74693340624

<tool id="ip_overlay_images" name="Overlay Images" version="0.0.3" profile="20.05"> 
    <description>for visualization</description>
    <requirements>
        <requirement type="package" version="0.18.1">scikit-image</requirement> 
        <requirement type="package" version="3.3.4">matplotlib</requirement>
        <requirement type="package" version="2020.10.1">tifffile</requirement>
        <requirement type="package" version="1.20.2">numpy</requirement>
    </requirements>
    <command detect_errors="aggressive">
    <![CDATA[
        python '$__tool_directory__/overlay_images.py'
        '$method_option.im1' '$method_option.im2' ./output.tif
        --method $method_option.method
        #if $method_option.method == "blending"
            --alpha $method_option.alpha
        #elif $method_option.method == "seg_contour"
            --thickness $method_option.thickness

                <param name="label_color" type="color" value="#ffff00" label="Label color"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="tiff" name="out" from_work_dir="output.tif" />
    </outputs>
    <tests>
        <test>
            <param name="im1" value="mask1.tif"/>
            <param name="im2" value="mask1r.tif"/>
            <param name="method" value="coloc_vis"/>
            <output name="out" value="test1.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
        </test>
        <test>
            <param name="im1" value="mask1.tif"/>
            <param name="im2" value="mask1r.tif"/>
            <param name="method" value="blending"/>
            <param name="alpha" value="0.3"/>
            <output name="out" value="test2.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
        </test>
        <test>
            <param name="im1" value="sample1.tif"/>
            <param name="im2" value="mask1.tif"/>
            <param name="method" value="seg_contour"/>
            <param name="thickness" value="2"/>
            <param name="color" value="#ff0000"/>
            <param name="show_label" value="--show_label"/>
            <output name="out" value="test3.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
        </test>
        <test>
            <param name="im1" value="sample1.tif"/>
            <param name="im2" value="mask2.tif"/>
            <param name="method" value="seg_contour"/>
            <param name="thickness" value="2"/>
            <param name="color" value="#ff0000"/>
            <output name="out" value="test4.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
        </test>
    </tests>
    <help>
    **What it does**

3:22ff7c705a83

<tool id="ip_overlay_images" name="Overlay images" version="0.0.3-3" profile="20.05">
    <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="0.18.1">scikit-image</requirement> 
        <requirement type="package" version="3.3.4">matplotlib</requirement>
        <requirement type="package" version="2020.10.1">tifffile</requirement>
        <requirement type="package" version="1.20.2">numpy</requirement>
    </requirements>
    <command detect_errors="aggressive">
    <![CDATA[
        python '$__tool_directory__/overlay_images.py'
        '$method_option.im1' '$method_option.im2'
        #if $method_option.method == "seg_contour"
            ./output.png
        #else
            ./output.tif
        #end if
        --method $method_option.method
        #if $method_option.method == "blending"
            --alpha $method_option.alpha
        #elif $method_option.method == "seg_contour"
            --thickness $method_option.thickness

                <param name="label_color" type="color" value="#ffff00" label="Label color"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="tiff" name="out_tiff" from_work_dir="output.tif" label="${tool.name} on ${on_string} output:tiff">
            <filter>method_option['method'] != 'seg_contour'</filter>
        </data>
        <data format="png" name="out_png" from_work_dir="output.png" label="${tool.name} on ${on_string} output:png">
            <filter>method_option['method'] == 'seg_contour'</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="im1" value="mask1.tif"/>
            <param name="im2" value="mask1r.tif"/>
            <param name="method" value="coloc_vis"/>
            <output name="out_tiff" value="test1.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
        </test>
        <test expect_num_outputs="1">
            <param name="im1" value="mask1.tif"/>
            <param name="im2" value="mask1r.tif"/>
            <param name="method" value="blending"/>
            <param name="alpha" value="0.3"/>
            <output name="out_tiff" value="test2.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
        </test>
        <test expect_num_outputs="1">
            <param name="im1" value="sample1.tif"/>
            <param name="im2" value="mask1.tif"/>
            <param name="method" value="seg_contour"/>
            <param name="thickness" value="2"/>
            <param name="color" value="#ff0000"/>
            <param name="show_label" value="--show_label"/>
            <output name="out_png" value="test3.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
        </test>
        <test expect_num_outputs="1">
            <param name="im1" value="sample1.tif"/>
            <param name="im2" value="mask2.tif"/>
            <param name="method" value="seg_contour"/>
            <param name="thickness" value="2"/>
            <param name="color" value="#ff0000"/>
            <output name="out_png" value="test4.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
        </test>
    </tests>
    <help>
    **What it does**