diff imagej2_make_binary.xml @ 0:baa308e2533a 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_make_binary.xml	Tue Sep 17 17:07:31 2019 -0400
@@ -0,0 +1,54 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="imagej2_make_binary" name="Convert to binary" version="@WRAPPER_VERSION@.0">
+    <description>(black and white)</description>
+    <macros>
+        <import>imagej2_macros.xml</import>
+    </macros>
+    <expand macro="fiji_requirements" />
+    <command>
+<![CDATA[
+    python $__tool_directory__/imagej2_make_binary.py
+    --input "$input"
+    --input_datatype $input.ext
+    @make_binary_args@
+    --jython_script $__tool_directory__/imagej2_make_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="make_binary_params" />
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="clown.jpg" />
+            <param name="input_datatype" value="jpg" />
+            <param name="iterations" value="1" />
+            <param name="count" value="1" />
+            <param name="black_background" value="no" />
+            <param name="pad_edges_when_eroding" value="no" />
+            <param name="output_datatype" value="jpg" />
+            <output name="output" file="clown_binary.jpg" compare="sim_size" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+<![CDATA[
+Converts an image into a binary (black and white) image by analyzing the histogram of
+the  entire image and setting an automatic threshold level to create the binary image.
+
+- **Iterations** - Specifies the number of times erosion, dilation, opening, and closing are performed.
+- **Count** - Specifies the number of adjacent background pixels necessary before a pixel is removed from the edge of an object during erosion and the number of adjacent foreground pixels necessary before a pixel is added to the edge of an object during dilation.
+- **Black background** - If **Yes**, binary images will be created without using an inverted LUT and an assumption that the input image contains white objects on a black background will be made.
+- **Pad edges when eroding** - If **Yes**, eroding does not erode from the edges of the image.
+
+]]>
+
+    </help>
+    <expand macro="fiji_headless_citations" />
+</tool>