Mercurial > repos > iuc > imagej2_watershed_binary

annotate imagej2_watershed_binary.xml @ 1:7507cbee7554 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
author iuc
date Fri, 22 Jul 2016 23:20:46 -0400
parents e6c00b485c38
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
1 <?xml version='1.0' encoding='UTF-8'?>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
2 <tool id="imagej2_watershed_binary" name="Watershed segmentation" version="@WRAPPER_VERSION@.0">
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
3 <description>of binary image</description>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
4 <macros>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
5 <import>imagej2_macros.xml</import>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
6 </macros>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
7 <expand macro="fiji_requirements" />
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
8 <command>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
9 <![CDATA[
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
10 python $__tool_directory__/imagej2_watershed_binary.py
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
11 --input "$input"
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
12 --input_datatype $input.ext
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
13 --black_background $black_background
1
7507cbee7554 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents: 0
diff changeset
14 --jython_script $__tool_directory__/imagej2_watershed_binary_jython_script.py
0
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
15 --output_datatype $output.ext
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
16 --output "$output"
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
17 ]]>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
18 </command>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
19 <inputs>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
20 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
21 <expand macro="black_background_param" />
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
22 </inputs>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
23 <outputs>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
24 <data name="output" format_source="input" label="${tool.name} on ${on_string}" />
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
25 </outputs>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
26 <tests>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
27 <test>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
28 <param name="input" value="blobs.gif" />
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
29 <output name="output" file="blobs_watershed_binary.gif" compare="sim_size" />
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
30 </test>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
31 </tests>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
32 <help>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
33 .. class:: warningmark
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
34
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
35 @requires_binary_input@
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
36
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
37 **What it does**
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
38
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
39 <![CDATA[
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
40 Watershed segmentation is a way of automatically separating or cutting apart particles that touch.
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
41 It first calculates the Euclidian distance map (EDM) and finds the ultimate eroded points (UEPs).
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
42 It then dilates each of the UEPs (the peaks or local maxima of the EDM) as far as possible — either
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
43 until the edge of the particle is reached, or the edge touches a region of another (growing) UEP.
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
44 Watershed segmentation works best for smooth convex objects that don’t overlap too much.
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
45 ]]>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
46
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
47 </help>
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
48 <expand macro="fiji_headless_citations" />
e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
iuc
parents:
diff changeset
49 </tool>