Mercurial > repos > imgteam > overlay_images
view overlay_images.xml @ 0:589af0005df5 draft
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
author | imgteam |
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date | Sat, 26 Feb 2022 15:16:10 +0000 |
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children | bf590a9733ed |
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<tool id="ip_overlay_images" name="Overlay Images" version="0.0.1" 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 '$__tool_directory__/overlay_images.py' '$im1' '$im2' ./output.tif --method '$method_option.method' #if '$method_option.method' == 'blending': --alpha '$alpha' #elif '$method_option.method' == 'seg_contour': --thickness '$thickness' --color '$color' $show_label #end if ]]> </command> <inputs> <conditional name="method_option"> <param name="method" type="select" label="How to visualize the overlay?"> <option value="coloc_vis" selected="True">Colocalization</option> <option value="blending">Blending</option> <option value="seg_contour">Segmentation mask over image</option> </param> <when value="coloc_vis"> <param name="im1" type="data" format="tiff,png" label="Image #1 (red channel)" /> <param name="im2" type="data" format="tiff,png" label="Image #2 (green channel)" /> </when> <when value="blending"> <param name="im1" type="data" format="tiff,png" label="Image #1" /> <param name="im2" type="data" format="tiff,png" label="Image #2" /> <param name="alpha" type="float" value="0.5" min="0.0" max="1.0" label="The weight for blending: I_out = (1 - w) * I_1 + w * I_2."/> </when> <when value="seg_contour"> <param name="im1" type="data" format="tiff,png" label="Image" /> <param name="im2" type="data" format="tiff,png" label="Label image" /> <param name="thickness" type="float" value="0.3" label="Contour thickness" /> <param name="color" type="color" value="#ff0000" label="Contour color"/> <param argument="--show_label" type="boolean" checked='false' truevalue="--show_label" falsevalue="" label="Show labels" /> </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"/> <conditional name="method_option"> <param name="method" value="coloc_vis"/> </conditional> <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"/> <conditional name="method_option"> <param name="method" value="blending"/> </conditional> <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"/> <conditional name="method_option"> <param name="method" value="seg_contour"/> </conditional> <param name="thickness" value="0.4"/> <param name="color" value="#ffaa00"/> <param name="show_label" value="true"/> <output name="out" value="test3.tif" ftype="tiff" compare="sim_size" delta="20000" delta_frac="0.2"/> </test> </tests> <help> **What it does** This tool overlays two image to visualize 1) image blending, 2) colocalization, or 3) a segmentation mask over an image. </help> <citations> </citations> </tool>