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comparison imagej2_enhance_contrast.xml @ 3:1f92b1da556b draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author imgteam
date Wed, 25 Sep 2024 16:04:54 +0000
parents 056e74fbbf6c
children
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2:056e74fbbf6c 3:1f92b1da556b
1 <tool id="imagej2_enhance_contrast" name="Enhance contrast" version="@WRAPPER_VERSION@.2"> 1 <tool id="imagej2_enhance_contrast" name="Enhance contrast" 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 #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]
18 #set input_with_ext = '.'.join([input_sans_ext, $input.ext]) 17 #set input_with_ext = './' + '.'.join([input_sans_ext, $input.ext])
19 ln -s '$input.file_name' '$input_with_ext' && 18 ln -s '$input.file_name' '$input_with_ext' &&
20 #set output_filename = '.'.join(['output', $input.ext]) 19 #set output_filename = '.'.join(['output', $input.ext])
21 touch '$output_filename' && 20 touch '$output_filename' &&
22 ImageJ --ij2 --headless --debug 21 ImageJ --ij2 --headless --debug
23 --jython '$__tool_directory__/imagej2_enhance_contrast_jython_script.py' 22 --jython '$__tool_directory__/imagej2_enhance_contrast_jython_script.py'
24 '$error_log'
25 '$input_with_ext' 23 '$input_with_ext'
26 '$equalize_histogram_cond.equalize_histogram' 24 '$equalize_histogram_cond.equalize_histogram'
27 #if $equalize_histogram_cond.equalize_histogram == 'no': 25 #if $equalize_histogram_cond.equalize_histogram == 'no':
28 $equalize_histogram_cond.saturated_pixels 26 $equalize_histogram_cond.saturated_pixels
29 '$equalize_histogram_cond.normalize' 27 '$equalize_histogram_cond.normalize'
31 'None' 29 'None'
32 'no' 30 'no'
33 #end if 31 #end if
34 '$output_filename' 32 '$output_filename'
35 '$input.ext' 33 '$input.ext'
36 &>'$error_log'; 34 && mv '$output_filename' '$output';
37 if [[ $? -ne 0 ]]; then
38 cat '$error_log' >&2;
39 else
40 mv '$output_filename' '$output';
41 fi
42 ]]></command> 35 ]]></command>
43 <inputs> 36 <inputs>
44 <expand macro="param_input"/> 37 <expand macro="param_input"/>
45 <conditional name="equalize_histogram_cond"> 38 <conditional name="equalize_histogram_cond">
46 <param name="equalize_histogram" type="select" label="Equalize histogram?"> 39 <param name="equalize_histogram" type="select" label="Equalize histogram?">
64 </outputs> 57 </outputs>
65 <tests> 58 <tests>
66 <test> 59 <test>
67 <param name="input" value="blobs.gif"/> 60 <param name="input" value="blobs.gif"/>
68 <param name="equalize_histogram" value="yes"/> 61 <param name="equalize_histogram" value="yes"/>
69 <output name="output" file="blobs_equalize.gif" compare="sim_size"/> 62 <output name="output" file="blobs_equalize.gif" compare="image_diff"/>
70 </test> 63 </test>
71 <test> 64 <test>
72 <param name="input" value="blobs.gif"/> 65 <param name="input" value="blobs.gif"/>
73 <param name="saturated_pixels" value="6.2"/> 66 <param name="saturated_pixels" value="6.2"/>
74 <output name="output" file="blobs_saturate.gif" compare="sim_size"/> 67 <output name="output" file="blobs_saturate.gif" compare="image_diff"/>
75 </test> 68 </test>
76 <test> 69 <test>
77 <param name="input" value="blobs.gif"/> 70 <param name="input" value="blobs.gif"/>
78 <param name="saturated_pixels" value="13.0"/> 71 <param name="saturated_pixels" value="13.0"/>
79 <param name="normalize" value="yes"/> 72 <param name="normalize" value="yes"/>
80 <output name="output" file="blobs_normalize.gif" compare="sim_size"/> 73 <output name="output" file="blobs_normalize.gif" compare="image_diff"/>
81 </test> 74 </test>
82 </tests> 75 </tests>
83 <help> 76 <help>
84 77
85 **What it does** 78 **What it does**