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comparison imagej2_smooth.xml @ 1:53fb6f4afcc8 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 16:42:12 +0000
parents dd20ee3092e3
children 6d7dd2194b4c
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0:dd20ee3092e3 1:53fb6f4afcc8
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="imagej2_smooth" name="Smooth" version="@WRAPPER_VERSION@.0"> 1 <tool id="imagej2_smooth" name="Smooth" 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 $__tool_directory__/imagej2_smooth.py 9 #set error_log = 'output_log.txt'
11 --input "$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_smooth_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 '$__tool_directory__/imagej2_smooth_jython_script.py'
18 '$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_smooth.gif" compare="sim_size" /> 38 <output name="output" file="blobs_smooth.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**
36 Blurs the image by replacing each pixel with the average of its 3x3 neighborhood. 47 Blurs the image by replacing each pixel with the average of its 3x3 neighborhood.
37 48
38 ]]> 49 ]]>
39 50
40 </help> 51 </help>
41 <expand macro="fiji_headless_citations" /> 52 <expand macro="fiji_headless_citations"/>
42 </tool> 53 </tool>