Mercurial > repos > imgteam > imagej2_watershed_binary

comparison imagej2_watershed_binary.xml @ 1:5b154339fd90 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 16:36:30 +0000
parents b143159845b4
children aeae7e29d525
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0:b143159845b4 1:5b154339fd90
1 <?xml version='1.0' encoding='UTF-8'?> 1 <tool id="imagej2_watershed_binary" name="Watershed segmentation" version="@WRAPPER_VERSION@.1">
2 <tool id="imagej2_watershed_binary" name="Watershed segmentation" version="@WRAPPER_VERSION@.0">
3 <description>of binary image</description> 2 <description>of binary image</description>
4 <macros> 3 <macros>
5 <import>imagej2_macros.xml</import> 4 <import>imagej2_macros.xml</import>
6 </macros> 5 </macros>
7 <expand macro="fiji_requirements" /> 6 <expand macro="fiji_requirements"/>
8 <command> 7 <command detect_errors="exit_code"><![CDATA[
9 <![CDATA[ 8 #import os
10 python $__tool_directory__/imagej2_watershed_binary.py 9 #set error_log = 'output_log.txt'
11 --input "$input" 10 touch '$error_log' &&
12 --input_datatype $input.ext 11 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
13 --black_background $black_background 12 #set input_with_ext = '.'.join([input_sans_ext, $input.ext])
14 --jython_script $__tool_directory__/imagej2_watershed_binary_jython_script.py 13 ln -s '$input.file_name' '$input_with_ext' &&
15 --output_datatype $output.ext 14 #set output_filename = '.'.join(['output', $input.ext])
16 --output "$output" 15 touch '$output_filename' &&
17 ]]> 16 ImageJ --ij2 --headless --debug
18 </command> 17 --jython '$__tool_directory__/imagej2_watershed_binary_jython_script.py'
18 '$error_log'
19 '$input_with_ext'
20 '$black_background'
21 '$output_filename'
22 '$input.ext'
23 &>'$error_log';
24 if [[ $? -ne 0 ]]; then
25 cat '$error_log' >&2;
26 else
27 mv '$output_filename' '$output';
28 fi
29 ]]></command>
19 <inputs> 30 <inputs>
20 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/> 31 <expand macro="param_input"/>
21 <expand macro="black_background_param" /> 32 <expand macro="black_background_param"/>
22 </inputs> 33 </inputs>
23 <outputs> 34 <outputs>
24 <data name="output" format_source="input" label="${tool.name} on ${on_string}" /> 35 <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
25 </outputs> 36 </outputs>
26 <tests> 37 <tests>
27 <test> 38 <test>
28 <param name="input" value="blobs.gif" /> 39 <param name="input" value="blobs.gif"/>
29 <output name="output" file="blobs_watershed_binary.gif" compare="sim_size" /> 40 <output name="output" file="blobs_watershed_binary.gif" compare="sim_size"/>
30 </test> 41 </test>
31 </tests> 42 </tests>
32 <help> 43 <help>
33 .. class:: warningmark 44 .. class:: warningmark
34 45
43 until the edge of the particle is reached, or the edge touches a region of another (growing) UEP. 54 until the edge of the particle is reached, or the edge touches a region of another (growing) UEP.
44 Watershed segmentation works best for smooth convex objects that don’t overlap too much. 55 Watershed segmentation works best for smooth convex objects that don’t overlap too much.
45 ]]> 56 ]]>
46 57
47 </help> 58 </help>
48 <expand macro="fiji_headless_citations" /> 59 <expand macro="fiji_headless_citations"/>
49 </tool> 60 </tool>