Mercurial > repos > imgteam > imagej2_binary_to_edm

comparison imagej2_binary_to_edm.xml @ 1:33f6b1f921e7 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 16:55:57 +0000
parents f62303e87275
children 182994b12622
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0:f62303e87275 1:33f6b1f921e7
1 <?xml version='1.0' encoding='UTF-8'?> 1 <tool id="imagej2_binary_to_edm" name="Convert binary image to EDM" version="@WRAPPER_VERSION@.1">
2 <tool id="imagej2_binary_to_edm" name="Convert binary image to EDM" version="@WRAPPER_VERSION@.0">
3 <description>(Euclidean Distance Map)</description> 2 <description>(Euclidean Distance Map)</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 $__tool_directory__/imagej2_binary_to_edm.py 9 #set error_log = 'output_log.txt'
11 --input "$input" 10 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
12 --input_datatype $input.ext 11 #set input_with_ext = '.'.join([input_sans_ext, $input.ext])
13 @make_binary_args@ 12 ln -s '$input.file_name' '$input_with_ext' &&
14 --jython_script $__tool_directory__/imagej2_binary_to_edm_jython_script.py 13 #set output_filename = '.'.join(['output', $input.ext])
15 --output_datatype $output.ext 14 touch '$output_filename' &&
16 --output "$output" 15 touch '$error_log' &&
17 ]]> 16 ImageJ --ij2 --headless --debug
18 </command> 17 --jython '$__tool_directory__/imagej2_binary_to_edm_jython_script.py'
18 '$error_log'
19 '$input_with_ext'
20 $iterations
21 $count
22 '$black_background'
23 '$pad_edges_when_eroding'
24 '$output_filename'
25 '$input.ext'
26 &>'$error_log';
27 if [[ $? -ne 0 ]]; then
28 cat '$error_log' >&2;
29 else
30 mv '$output_filename' '$output';
31 fi
32 ]]></command>
19 <inputs> 33 <inputs>
20 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/> 34 <expand macro="param_input"/>
21 <expand macro="make_binary_params" /> 35 <expand macro="make_binary_params"/>
22 </inputs> 36 </inputs>
23 <outputs> 37 <outputs>
24 <data name="output" format_source="input" label="${tool.name} on ${on_string}"/> 38 <data name="output" format_source="input"/>
25 </outputs> 39 </outputs>
26 <tests> 40 <tests>
27 <test> 41 <test>
28 <param name="input" value="blobs.gif" /> 42 <param name="input" value="blobs.gif"/>
29 <param name="iterations" value="1" /> 43 <param name="iterations" value="1"/>
30 <param name="count" value="1" /> 44 <param name="count" value="1"/>
31 <output name="output" file="blobs_edm.gif" compare="sim_size" /> 45 <output name="output" file="blobs_edm.gif" compare="sim_size"/>
32 </test> 46 </test>
33 <test> 47 <test>
34 <param name="input" value="blobs.gif" /> 48 <param name="input" value="blobs.gif"/>
35 <param name="iterations" value="10" /> 49 <param name="iterations" value="10"/>
36 <param name="count" value="3" /> 50 <param name="count" value="3"/>
37 <param name="black_background" value="yes" /> 51 <param name="black_background" value="yes"/>
38 <param name="pad_edges_when_eroding" value="yes" /> 52 <param name="pad_edges_when_eroding" value="yes"/>
39 <output name="output" file="blobs_black_edm.gif" compare="sim_size" /> 53 <output name="output" file="blobs_black_edm.gif" compare="sim_size"/>
40 </test> 54 </test>
41 </tests> 55 </tests>
42 <help> 56 <help>
43 57
44 .. class:: warningmark 58 .. class:: warningmark
58 - **Pad edges when eroding** - If **Yes**, eroding does not erode from the edges of the image. 72 - **Pad edges when eroding** - If **Yes**, eroding does not erode from the edges of the image.
59 73
60 ]]> 74 ]]>
61 75
62 </help> 76 </help>
63 <expand macro="fiji_headless_citations" /> 77 <expand macro="fiji_headless_citations"/>
64 </tool> 78 </tool>