diff imagej2_watershed_binary.xml @ 0:b143159845b4 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_watershed_binary.xml	Tue Sep 17 17:02:55 2019 -0400
@@ -0,0 +1,49 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="imagej2_watershed_binary" name="Watershed segmentation" version="@WRAPPER_VERSION@.0">
+    <description>of binary image</description>
+    <macros>
+        <import>imagej2_macros.xml</import>
+    </macros>
+    <expand macro="fiji_requirements" />
+    <command>
+<![CDATA[
+    python $__tool_directory__/imagej2_watershed_binary.py
+    --input "$input"
+    --input_datatype $input.ext
+    --black_background $black_background
+    --jython_script $__tool_directory__/imagej2_watershed_binary_jython_script.py
+    --output_datatype $output.ext
+    --output "$output"
+]]>
+    </command>
+    <inputs>
+        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
+        <expand macro="black_background_param" />
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="blobs.gif" />
+            <output name="output" file="blobs_watershed_binary.gif" compare="sim_size" />
+        </test>
+    </tests>
+    <help>
+.. class:: warningmark
+
+@requires_binary_input@
+
+**What it does**
+
+<![CDATA[
+Watershed segmentation is a way of automatically separating or cutting apart particles that touch.
+It first calculates the Euclidian distance map (EDM) and finds the ultimate eroded points (UEPs).
+It then dilates each of the UEPs (the peaks or local maxima of the EDM) as far as possible — either
+until the edge of the particle is reached, or the edge touches a region of another (growing) UEP.
+Watershed segmentation works best for smooth convex objects that don’t overlap too much.
+]]>
+
+    </help>
+    <expand macro="fiji_headless_citations" />
+</tool>