--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_analyze_skeleton.xml	Tue Sep 17 17:04:59 2019 -0400
@@ -0,0 +1,127 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>imagej2_macros.xml</import>
+    </macros>
+    <expand macro="fiji_requirements" />
+    <command>
+<![CDATA[
+    python $__tool_directory__/imagej2_analyze_skeleton.py
+    --input "$input"
+    --input_datatype $input.ext
+    --black_background $black_background
+    --prune_cycle_method $prune_cycle_method
+    --prune_ends $prune_ends
+    --calculate_largest_shortest_path $calculate_largest_shortest_path
+    ##TODO: seel below--show_detailed_info $show_detailed_info
+    --jython_script $__tool_directory__/imagej2_analyze_skeleton_jython_script.py
+    --output "$output"
+]]>
+    </command>
+    <inputs>
+        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select grayscale image"/>
+        <expand macro="black_background_param" />
+        <param name="prune_cycle_method" type="select" label="Prune cycle method">
+            <option value="none" selected="True">None</option>
+            <option value="shortest_branch">Shortest branch</option>
+            <option value="lowest_intensity_voxel">Lowest intensity voxel</option>
+            <option value="lowest_intensity_branch">Lowest intensity branch</option>
+        </param>
+        <param name="prune_ends" type="select" label="Prune ends">
+            <option value="no" selected="True">No</option>
+            <option value="yes">Yes</option>
+        </param>
+        <param name="calculate_largest_shortest_path" type="select" label="Calculate largest shortest path">
+            <option value="no" selected="True">No</option>
+            <option value="yes">Yes</option>
+        </param>
+        <!-- TODO: Uncomment this option when the tool has been enhanced to use the
+        future "Display labeled skeletons" option.  See http://fiji.sc/AnalyzeSkeleton.
+        <param name="show_detailed_info" type="select" label="Show detailed info">
+            <option value="no" selected="True">No</option>
+            <option value="yes">Yes</option>
+        </param>
+        -->
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="skeletonized_blobs.gif" />
+            <param name="input_datatype" value="gif" />
+            <output name="output" file="basic.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="input" value="skeletonized_clown.jpg" />
+            <param name="input_datatype" value="jpg" />
+            <param name="prune_cycle_method" value="shortest_branch" />
+            <output name="output" file="shortest_branch_basic.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="input" value="skeletonized_blobs.gif" />
+            <param name="input_datatype" value="gif" />
+            <param name="calculate_largest_shortest_path" value="yes" />
+            <output name="output" file="largest_shortest_path_basic.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <!-- TODO: Change this test and the following test to set "show_detailed_info"
+            to "yes" when the tool has been enhanced to use the future "Display labeled skeletons"
+            option.  See http://fiji.sc/AnalyzeSkeleton.  -->
+            <param name="input" value="skeletonized_blobs.gif" />
+            <param name="input_datatype" value="gif" />
+            <!-- <param name="show_detailed_info" value="yes" /> -->
+            <output name="output" file="detailed.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="input" value="skeletonized_clown.jpg" />
+            <param name="input_datatype" value="jpg" />
+            <param name="prune_cycle_method" value="shortest_branch" />
+            <param name="calculate_largest_shortest_path" value="yes" />
+            <!-- <param name="show_detailed_info" value="yes" /> -->
+            <output name="output" file="shortest_branch_all_yes.tabular" ftype="tabular" />
+        </test>
+    </tests>
+    <help>
+
+.. class:: warningmark
+
+The underlying AnalyzeSkeleton Fiji plugin works on binary images, so other image types will
+automatically be converted to binary before they are analyzed.  This step is performed using the
+ImageJ2 **Make Binary** command with the following settings: **Iterations:** 1, **Count:** 1,
+**Black background:** No, **Pad edges when eroding:** No.  If these settings are not appropriate,
+first manually convert the image to binary using the **Convert to binary (black and white) with
+ImageJ2** tool, which allows you to change them.
+
+.. class:: warningmark
+
+The **Skeletonize images** tool produces skeleton images that can be used as input to this tool.
+Images that have not been skeletonized will not result in errors, but the results may or may not
+be useful.
+
+**What it does**
+
+<![CDATA[
+Tags all pixel/voxels in a skeleton image and then counts all its junctions, triple and quadruple
+points and branches, and measures their average and maximum length.  The voxels are classified into
+three different categories depending on their 26 neighbors:
+
+- **End-point** voxels: if they have less than 2 neighbors.
+- **Junction** voxels: if they have more than 2 neighbors.
+- **Slab** voxels: if they have exactly 2 neighbors.
+
+-----
+
+**Options**
+
+- **Prune cycle method**: prune the possible loops in the skeleton.
+- **Prune ends**: prunes any branch that ends in an end-point.
+- **Calculate largest shortest path**: calculate the largest shortest path of each skeleton using the APSP (all pairs shortest path).
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1002/jemt.20829</citation>
+        <citation type="doi">10.1038/nmeth.2102</citation>
+    </citations>
+</tool>