Mercurial > repos > imgteam > imagej2_binary_to_edm

comparison imagej2_binary_to_edm.xml @ 3:91b8f4730a93 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 16:07:20 +0000
parents 182994b12622
children
comparison
equal deleted inserted replaced
2:182994b12622 3:91b8f4730a93
1 <tool id="imagej2_binary_to_edm" name="Convert binary image to EDM" version="@WRAPPER_VERSION@.2"> 1 <tool id="imagej2_binary_to_edm" name="Convert binary image to EDM" 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 '$output_filename' &&
22 touch '$error_log' &&
23 ImageJ --ij2 --headless --debug 21 ImageJ --ij2 --headless --debug
24 --jython '$__tool_directory__/imagej2_binary_to_edm_jython_script.py' 22 --jython '$__tool_directory__/imagej2_binary_to_edm_jython_script.py'
25 '$error_log'
26 '$input_with_ext' 23 '$input_with_ext'
27 $iterations 24 $iterations
28 $count 25 $count
29 '$black_background' 26 '$black_background'
30 '$pad_edges_when_eroding' 27 '$pad_edges_when_eroding'
31 '$output_filename' 28 '$output_filename'
32 '$input.ext' 29 '$input.ext'
33 &>'$error_log'; 30 && mv '$output_filename' '$output';
34 if [[ $? -ne 0 ]]; then
35 cat '$error_log' >&2;
36 else
37 mv '$output_filename' '$output';
38 fi
39 ]]></command> 31 ]]></command>
40 <inputs> 32 <inputs>
41 <expand macro="param_input"/> 33 <expand macro="param_input"/>
42 <expand macro="make_binary_params"/> 34 <expand macro="make_binary_params"/>
43 </inputs> 35 </inputs>
47 <tests> 39 <tests>
48 <test> 40 <test>
49 <param name="input" value="blobs.gif"/> 41 <param name="input" value="blobs.gif"/>
50 <param name="iterations" value="1"/> 42 <param name="iterations" value="1"/>
51 <param name="count" value="1"/> 43 <param name="count" value="1"/>
52 <output name="output" file="blobs_edm.gif" compare="sim_size"/> 44 <output name="output" file="blobs_edm.gif" compare="image_diff" metric="iou" />
53 </test> 45 </test>
54 <test> 46 <test>
55 <param name="input" value="blobs.gif"/> 47 <param name="input" value="blobs.gif"/>
56 <param name="iterations" value="10"/> 48 <param name="iterations" value="10"/>
57 <param name="count" value="3"/> 49 <param name="count" value="3"/>
58 <param name="black_background" value="yes"/> 50 <param name="black_background" value="yes"/>
59 <param name="pad_edges_when_eroding" value="yes"/> 51 <param name="pad_edges_when_eroding" value="yes"/>
60 <output name="output" file="blobs_black_edm.gif" compare="sim_size"/> 52 <output name="output" file="blobs_black_edm.gif" compare="image_diff" metric="iou" />
61 </test> 53 </test>
62 </tests> 54 </tests>
63 <help> 55 <help>
64 56
65 .. class:: warningmark 57 .. class:: warningmark