Mercurial > repos > imgteam > imagej2_shadows

comparison imagej2_shadows.xml @ 1:c8bb47840c8d draft

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 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 16:51:33 +0000
parents 7baf811ed973
children f3c9192bd0b9
comparison
equal deleted inserted replaced
0:7baf811ed973 1:c8bb47840c8d
1 <?xml version='1.0' encoding='UTF-8'?> 1 <tool id="imagej2_shadows" name="Add shadow effect" version="@WRAPPER_VERSION@.1">
2 <tool id="imagej2_shadows" name="Add shadow effect" 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 $__tool_directory__/imagej2_shadows.py 9 #set error_log = 'output_log.txt'
11 --input "$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 --direction $direction 12 #set input_with_ext = '.'.join([input_sans_ext, $input.ext])
14 --jython_script $__tool_directory__/imagej2_shadows_jython_script.py 13 ln -s '$input.file_name' '$input_with_ext' &&
15 --output_datatype $output.ext 14 #set output_filename = '.'.join(['output', $input.ext])
16 --output "$output" 15 touch '$output_filename' &&
17 ]]> 16 ImageJ --ij2 --headless --debug
18 </command> 17 --jython '$__tool_directory__/imagej2_shadows_jython_script.py'
18 '$error_log'
19 '$input_with_ext'
20 '$direction'
21 '$output_filename'
22 '$input.ext'
23 &>'$error_log';
24 if [[ $? -ne 0 ]]; then
25 cat '$error_log' >&2;
26 else
27 mv '$output_filename' '$output';
28 fi
29 ]]></command>
19 <inputs> 30 <inputs>
20 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/> 31 <expand macro="param_input"/>
21 <param name="direction" type="select" label="Direction" help="Light will appear to come from the selected direction"> 32 <param name="direction" type="select" label="Direction" help="Light will appear to come from the selected direction">
22 <option value="East" selected="True">East</option> 33 <option value="East" selected="True">East</option>
23 <option value="North">North</option> 34 <option value="North">North</option>
24 <option value="Northeast">Northeast</option> 35 <option value="Northeast">Northeast</option>
25 <option value="Northwest">Northwest</option> 36 <option value="Northwest">Northwest</option>
28 <option value="Southwest">Southwest</option> 39 <option value="Southwest">Southwest</option>
29 <option value="West">West</option> 40 <option value="West">West</option>
30 </param> 41 </param>
31 </inputs> 42 </inputs>
32 <outputs> 43 <outputs>
33 <data name="output" format_source="input" label="${tool.name} on ${on_string}: Light from ${direction}"/> 44 <data name="output" format_source="input"/>
34 </outputs> 45 </outputs>
35 <tests> 46 <tests>
36 <test> 47 <test>
37 <param name="input" value="blobs.gif" /> 48 <param name="input" value="blobs.gif"/>
38 <param name="direction" value="Northwest" /> 49 <param name="direction" value="Northwest"/>
39 <output name="output" file="blobs_northwest.gif" compare="sim_size" /> 50 <output name="output" file="blobs_northwest.gif" compare="sim_size"/>
40 </test> 51 </test>
41 </tests> 52 </tests>
42 <help> 53 <help>
43 54
44 **What it does** 55 **What it does**
50 convolution function. 61 convolution function.
51 62
52 ]]> 63 ]]>
53 64
54 </help> 65 </help>
55 <expand macro="fiji_headless_citations" /> 66 <expand macro="fiji_headless_citations"/>
56 </tool> 67 </tool>