diff background_removal.xml @ 0:e2c6bedc6b73 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/background_removal.xml	Mon Jul 15 20:55:08 2024 +0000
@@ -0,0 +1,72 @@
+<tool id="background_removal" name="Remove image background" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
+        <description>with scikit-image</description>  
+    <macros>  
+        <import>creators.xml</import>
+        <import>tests.xml</import>
+        <token name="@TOOL_VERSION@">0.24.0</token>  
+        <token name="@VERSION_SUFFIX@">0</token>  
+    </macros>  
+    <creator>
+        <expand macro="creators/rmassei"/>
+    </creator>
+    <requirements>
+        <requirement type="package" version="0.24.0">scikit-image</requirement>
+    </requirements>
+    <command detect_errors="aggressive">
+        <![CDATA[
+        python "$__tool_directory__/background_removal.py" $input_image $filter $radius $output
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_image" type="data" format="tiff, jpg, jpeg, png, tif" label="Input Image"/>
+        <param name="filter" type="select" label="Select Filter">
+            <option value="rolling_ball">Rolling-ball algorithm</option>
+            <option value="dog">Difference of Gaussians</option>
+            <option value="top_hat">Top-hat filter</option>
+        </param>
+        <param name="radius" type="float" label="Radius" value="20"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tiff" label="Background substraction output"/>
+    </outputs>
+    <tests>
+        <!-- uint8 tests -->  
+        <test>  
+            <param name="input_image" value="input1_uint8.tif"/>  
+            <param name="filter" value="dog"/>  
+            <param name="radius" value="20"/>  
+            <expand macro="tests/intensity_image_diff" name="output" value="input1_output_dog.tif" ftype="tiff"/>  
+        </test> 
+        <test>
+            <param name="input_image" value="input3_uint8.tif"/>
+            <param name="filter" value="top_hat"/>
+            <param name="radius" value="15"/>
+            <expand macro="tests/intensity_image_diff" name="output" value="input3_output_tophat.tif" ftype="tiff"/>
+        </test>
+        <!-- uint16 tests -->  
+        <test>  
+            <param name="input_image" value="input2_uint16.tif"/>
+            <param name="filter" value="rolling_ball"/>
+            <param name="radius" value="20"/>
+            <expand macro="tests/intensity_image_diff" name="output" value="input2_output_rb.tif" ftype="tiff"/>
+        </test>
+        <test>
+            <param name="input_image" value="input2_uint16.tif"/>
+            <param name="filter" value="dog"/>
+            <param name="radius" value="20"/>
+            <expand macro="tests/intensity_image_diff" name="output" value="input2_output_dog.tif" ftype="tiff"/>
+        </test>
+    </tests>
+    <help>
+        This tool applies different background removal algorithms to an image:
+
+        - Rolling-ball algorithm
+
+        - Difference of Gaussians
+
+        - Top-hat filter
+    </help>
+    <citations>
+        <citation type="doi">10.1109/MC.1983.1654163</citation>
+    </citations>
+</tool>