Mercurial > repos > imgteam > imagej2_find_edges
comparison imagej2_find_edges.xml @ 1:c8dfbf4b899c draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author | imgteam |
---|---|
date | Mon, 28 Sep 2020 16:55:03 +0000 |
parents | 8e608a6e44ac |
children | 5023cbf98ca3 |
comparison
equal
deleted
inserted
replaced
0:8e608a6e44ac | 1:c8dfbf4b899c |
---|---|
1 <?xml version='1.0' encoding='UTF-8'?> | 1 <tool id="imagej2_find_edges" name="Find edges" version="@WRAPPER_VERSION@.1"> |
2 <tool id="imagej2_find_edges" name="Find edges" 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 $__tool_directory__/imagej2_find_edges.py | 9 #set error_log = '$output_log.txt' |
11 --input "$input" | 10 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0] |
12 --input_datatype $input.ext | 11 #set input_with_ext = '.'.join([input_sans_ext, $input.ext]) |
13 --jython_script $__tool_directory__/imagej2_find_edges_jython_script.py | 12 ln -s '$input.file_name' '$input_with_ext' && |
14 --output_datatype $output.ext | 13 #set output_filename = '.'.join(['output', $input.ext]) |
15 --output "$output" | 14 touch '$output_filename' && |
16 ]]> | 15 ImageJ --ij2 --headless --debug |
17 </command> | 16 --jython '$__tool_directory__/imagej2_find_edges_jython_script.py' |
17 '$error_log' | |
18 '$input_with_ext' | |
19 '$output_filename' | |
20 '$input.ext' | |
21 &>'$error_log'; | |
22 if [[ $? -ne 0 ]]; then | |
23 cat '$error_log' >&2; | |
24 else | |
25 mv '$output_filename' '$output'; | |
26 fi | |
27 ]]></command> | |
18 <inputs> | 28 <inputs> |
19 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/> | 29 <expand macro="param_input"/> |
20 </inputs> | 30 </inputs> |
21 <outputs> | 31 <outputs> |
22 <data name="output" format_source="input" label="${tool.name} on ${on_string}"/> | 32 <data name="output" format_source="input"/> |
23 </outputs> | 33 </outputs> |
24 <tests> | 34 <tests> |
25 <test> | 35 <test> |
26 <param name="input" value="blobs.gif" /> | 36 <param name="input" value="blobs.gif"/> |
27 <output name="output" file="blobs_find_edges.gif" compare="sim_size" /> | 37 <output name="output" file="blobs_find_edges.gif" compare="sim_size"/> |
28 </test> | 38 </test> |
29 </tests> | 39 </tests> |
30 <help> | 40 <help> |
31 | 41 |
32 **What it does** | 42 **What it does** |
41 ``0 0 0 2 0 -2`` | 51 ``0 0 0 2 0 -2`` |
42 | 52 |
43 ``-1 -2 -1 1 0 -1`` | 53 ``-1 -2 -1 1 0 -1`` |
44 | 54 |
45 </help> | 55 </help> |
46 <expand macro="fiji_headless_citations" /> | 56 <expand macro="fiji_headless_citations"/> |
47 </tool> | 57 </tool> |