Mercurial > repos > imgteam > imagej2_skeletonize3d
comparison imagej2_skeletonize3d.xml @ 1:768825d9034a draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author | imgteam |
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date | Mon, 28 Sep 2020 17:01:19 +0000 |
parents | f6df6830d5ec |
children | 49b5288dcd8c |
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0:f6df6830d5ec | 1:768825d9034a |
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1 <?xml version='1.0' encoding='UTF-8'?> | 1 <tool id="imagej2_skeletonize3d" name="Skeletonize" version="@WRAPPER_VERSION@.1"> |
2 <tool id="imagej2_skeletonize3d" name="Skeletonize" version="@WRAPPER_VERSION@.0"> | |
3 <description></description> | 2 <description></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 $__tool_directory__/imagej2_skeletonize3d.py | 9 #set error_log = 'output_log.txt' |
11 --input "$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 $__tool_directory__/imagej2_skeletonize3d_jython_script.py | 13 ln -s '$input.file_name' '$input_with_ext' && |
15 --output "$output" | 14 #set output_filename = '.'.join(['output', $input.ext]) |
16 --output_datatype $output.ext | 15 touch '$output_filename' && |
17 ]]> | 16 ImageJ --ij2 --headless --debug |
18 </command> | 17 --jython '$__tool_directory__/imagej2_skeletonize3d_jython_script.py' |
18 '$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 grayscale 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 <param name="input_datatype" value="gif" /> | 40 <output name="output" file="skeletonized_blobs.gif" compare="sim_size"/> |
30 <param name="output_datatype" value="gif" /> | |
31 <output name="output" file="skeletonized_blobs.gif" compare="sim_size" /> | |
32 </test> | 41 </test> |
33 <test> | 42 <test> |
34 <param name="input" value="clown.jpg" /> | 43 <param name="input" value="clown.jpg"/> |
35 <param name="input_datatype" value="jpg" /> | 44 <output name="output" file="skeletonized_clown.jpg" compare="sim_size"/> |
36 <param name="output_datatype" value="jpg" /> | |
37 <output name="output" file="skeletonized_clown.jpg" compare="sim_size" /> | |
38 </test> | 45 </test> |
39 </tests> | 46 </tests> |
40 <help> | 47 <help> |
41 | 48 |
42 .. class:: warningmark | 49 .. class:: warningmark |