Mercurial > repos > imgteam > imagej2_sharpen
comparison imagej2_sharpen.xml @ 1:4c43ba752312 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 16:38:24 +0000 |
parents | a84f2cbf091b |
children | 49e29abe0fce |
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0:a84f2cbf091b | 1:4c43ba752312 |
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1 <?xml version='1.0' encoding='UTF-8'?> | |
2 <tool id="imagej2_sharpen" name="Sharpen" version="@WRAPPER_VERSION@.0"> | 1 <tool id="imagej2_sharpen" name="Sharpen" 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 $__tool_directory__/imagej2_sharpen.py | 9 #set error_log = 'output_log.txt' |
11 --input "$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 --jython_script $__tool_directory__/imagej2_sharpen_jython_script.py | 12 #set input_with_ext = '.'.join([input_sans_ext, $input.ext]) |
14 --output_datatype $output.ext | 13 ln -s '$input.file_name' '$input_with_ext' && |
15 --output "$output" | 14 #set output_filename = '.'.join(['output', $input.ext]) |
16 ]]> | 15 touch '$output_filename' && |
17 </command> | 16 ImageJ --ij2 --headless --debug |
17 --jython '$__tool_directory__/imagej2_sharpen_jython_script.py' | |
18 '$error_log' | |
19 '$input_with_ext' | |
20 '$output_filename' | |
21 '$input.ext' | |
22 &>'$error_log'; | |
23 if [[ $? -ne 0 ]]; then | |
24 cat '$error_log' >&2; | |
25 else | |
26 mv '$output_filename' '$output'; | |
27 fi | |
28 ]]></command> | |
18 <inputs> | 29 <inputs> |
19 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/> | 30 <expand macro="param_input"/> |
20 </inputs> | 31 </inputs> |
21 <outputs> | 32 <outputs> |
22 <data name="output" format_source="input" label="${tool.name} on ${on_string}"/> | 33 <data name="output" format_source="input"/> |
23 </outputs> | 34 </outputs> |
24 <tests> | 35 <tests> |
25 <test> | 36 <test> |
26 <param name="input" value="blobs.gif" /> | 37 <param name="input" value="blobs.gif"/> |
27 <output name="output" file="blobs_sharpen.gif" compare="sim_size" /> | 38 <output name="output" file="blobs_sharpen.gif" compare="sim_size"/> |
28 </test> | 39 </test> |
29 </tests> | 40 </tests> |
30 <help> | 41 <help> |
31 | 42 |
32 **What it does** | 43 **What it does** |
43 ``-1 -1 -1`` | 54 ``-1 -1 -1`` |
44 | 55 |
45 ]]> | 56 ]]> |
46 | 57 |
47 </help> | 58 </help> |
48 <expand macro="fiji_headless_citations" /> | 59 <expand macro="fiji_headless_citations"/> |
49 </tool> | 60 </tool> |