Mercurial > repos > imgteam > imagej2_create_image

comparison imagej2_create_image.xml @ 3:69e28b06e027 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 15:56:08 +0000
parents 666af1279007
children
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2:666af1279007 3:69e28b06e027
1 <tool id="imagej2_create_image" name="Create new image" version="@WRAPPER_VERSION@.1"> 1 <tool id="imagej2_create_image" name="Create new image" 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>
10 <xref type="bio.tools">imagej</xref> 10 <xref type="bio.tools">imagej</xref>
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 #set output_log = '$output_log.txt' 15 #set output_log = 'output_log.txt'
16 #set output_name = '.'.join(['new_image', str($output_datatype)]) 16 #set output_name = '.'.join(['new_image', str($output_datatype)])
17 ImageJ --ij2 --headless --debug 17 ImageJ --ij2 --headless --debug
18 --jython '$__tool_directory__/imagej2_create_image_jython_script.py' 18 --jython '$__tool_directory__/imagej2_create_image_jython_script.py'
19 '$image_title' 19 '$image_title'
20 $width 20 $width
21 $height 21 $height
22 $depth 22 $depth
23 '$image_type' 23 '$image_type'
24 '$output_name' 24 '$output_name'
25 &>'$output_log'; 25 && mv '$output_name' '$output';
26 if [[ $? -ne 0 ]]; then
27 cat '$output_log' >&2;
28 else
29 mv '$output_name' '$output';
30 fi
31 ]]></command> 26 ]]></command>
32 <inputs> 27 <inputs>
33 <expand macro="image_type"/> 28 <expand macro="image_type"/>
34 <param name="image_title" type="text" label="Image title" help="Leave blank for no title"/> 29 <param name="image_title" type="text" label="Image title" help="Leave blank for no title"/>
35 <param name="width" type="integer" value="512" min="1" label="Image width in pixels"/> 30 <param name="width" type="integer" value="512" min="1" label="Image width in pixels"/>
54 <param name="image_title" value="MyTitle"/> 49 <param name="image_title" value="MyTitle"/>
55 <param name="width" value="256"/> 50 <param name="width" value="256"/>
56 <param name="height" value="256"/> 51 <param name="height" value="256"/>
57 <param name="depth" value="1"/> 52 <param name="depth" value="1"/>
58 <param name="output_datatype" value="jpg"/> 53 <param name="output_datatype" value="jpg"/>
59 <output name="output" file="create_image1.jpg" ftype="jpg"/> 54 <output name="output" file="create_image1.jpg" ftype="jpg" compare="image_diff"/>
60 </test> 55 </test>
61 </tests> 56 </tests>
62 <help> 57 <help>
63 **What it does** 58 **What it does**
64 59