diff overlay_images.xml @ 0:589af0005df5 draft

"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/overlay_images.xml	Sat Feb 26 15:16:10 2022 +0000
@@ -0,0 +1,88 @@
+<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>