Mercurial > repos > imgteam > imagej2_sharpen

comparison imagej2_sharpen.xml @ 3:418b1fa32b83 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 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author imgteam
date Wed, 25 Sep 2024 16:08:08 +0000
parents 49e29abe0fce
children
comparison
equal deleted inserted replaced
2:49e29abe0fce 3:418b1fa32b83
1 <tool id="imagej2_sharpen" name="Sharpen" version="@WRAPPER_VERSION@.1"> 1 <tool id="imagej2_sharpen" name="Sharpen" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
2 <description>with ImageJ2</description> 2 <description>with ImageJ2</description>
3 <macros> 3 <macros>
4 <import>imagej2_macros.xml</import> 4 <import>imagej2_macros.xml</import>
5 </macros> 5 </macros>
6 <edam_operations> 6 <edam_operations>
11 <xref type="biii">imagej2</xref> 11 <xref type="biii">imagej2</xref>
12 </xrefs> 12 </xrefs>
13 <expand macro="fiji_requirements"/> 13 <expand macro="fiji_requirements"/>
14 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
15 #import os 15 #import os
16 #set error_log = 'output_log.txt'
17 touch '$error_log' &&
18 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0] 16 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
19 #set input_with_ext = '.'.join([input_sans_ext, $input.ext]) 17 #set input_with_ext = './' + '.'.join([input_sans_ext, $input.ext])
20 ln -s '$input.file_name' '$input_with_ext' && 18 ln -s '$input.file_name' '$input_with_ext' &&
21 #set output_filename = '.'.join(['output', $input.ext]) 19 #set output_filename = '.'.join(['output', $input.ext])
22 touch '$output_filename' && 20 touch '$output_filename' &&
23 ImageJ --ij2 --headless --debug 21 ImageJ --ij2 --headless --debug
24 --jython '$__tool_directory__/imagej2_sharpen_jython_script.py' 22 --jython '$__tool_directory__/imagej2_sharpen_jython_script.py'
25 '$error_log'
26 '$input_with_ext' 23 '$input_with_ext'
27 '$output_filename' 24 '$output_filename'
28 '$input.ext' 25 '$input.ext'
29 &>'$error_log'; 26 && mv '$output_filename' '$output';
30 if [[ $? -ne 0 ]]; then
31 cat '$error_log' >&2;
32 else
33 mv '$output_filename' '$output';
34 fi
35 ]]></command> 27 ]]></command>
36 <inputs> 28 <inputs>
37 <expand macro="param_input"/> 29 <expand macro="param_input"/>
38 </inputs> 30 </inputs>
39 <outputs> 31 <outputs>
40 <data name="output" format_source="input"/> 32 <data name="output" format_source="input"/>
41 </outputs> 33 </outputs>
42 <tests> 34 <tests>
43 <test> 35 <test>
44 <param name="input" value="blobs.gif"/> 36 <param name="input" value="blobs.gif"/>
45 <output name="output" file="blobs_sharpen.gif" compare="sim_size"/> 37 <output name="output" file="blobs_sharpen.gif" compare="image_diff"/>
46 </test> 38 </test>
47 </tests> 39 </tests>
48 <help> 40 <help>
49 41
50 **What it does** 42 **What it does**