comparison imagej2_create_image.xml @ 1:1a7c29d5fc11 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 16:43:06 +0000
parents dc3935a0165a
children
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0:dc3935a0165a 1:1a7c29d5fc11
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="imagej2_create_image" name="Create new image" version="@WRAPPER_VERSION@.0"> 1 <tool id="imagej2_create_image" name="Create new image" 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 #set output_log = '$output_log.txt'
10 python $__tool_directory__/imagej2_create_image.py 9 #set output_name = '.'.join(['new_image', str($output_datatype)])
11 --width $width 10 ImageJ --ij2 --headless --debug
12 --height $height 11 --jython '$__tool_directory__/imagej2_create_image_jython_script.py'
13 --depth $depth 12 '$image_title'
14 --image_type $image_type 13 $width
15 --image_title "$image_title" 14 $height
16 --jython_script $__tool_directory__/imagej2_create_image_jython_script.py 15 $depth
17 --output_datatype $output_datatype 16 '$image_type'
18 --out_fname "$output" 17 '$output_name'
19 ]]> 18 &>'$output_log';
20 </command> 19 if [[ $? -ne 0 ]]; then
20 cat '$output_log' >&2;
21 else
22 mv '$output_name' '$output';
23 fi
24 ]]></command>
21 <inputs> 25 <inputs>
22 <expand macro="image_type" /> 26 <expand macro="image_type"/>
23 <param name="image_title" type="text" label="Image title" help="Leave blank for no title" /> 27 <param name="image_title" type="text" label="Image title" help="Leave blank for no title"/>
24 <param name="width" type="integer" value="512" min="1" label="Image width in pixels" /> 28 <param name="width" type="integer" value="512" min="1" label="Image width in pixels"/>
25 <param name="height" type="integer" value="512" min="1" label="Image height in pixels" /> 29 <param name="height" type="integer" value="512" min="1" label="Image height in pixels"/>
26 <param name="depth" type="integer" value="1" min="1" label="Image depth" help="Specifies the number of stack slices" /> 30 <param name="depth" type="integer" value="1" min="1" label="Image depth" help="Specifies the number of stack slices"/>
27 <param name="output_datatype" type="select" label="Save as format"> 31 <param name="output_datatype" type="select" label="Save as format">
28 <expand macro="image_datatypes" /> 32 <expand macro="image_datatypes"/>
29 </param> 33 </param>
30 </inputs> 34 </inputs>
31 <outputs> 35 <outputs>
32 <data name="output" format="jpg"> 36 <data name="output" format="jpg">
33 <actions> 37 <actions>
34 <action type="format"> 38 <action type="format">
35 <option type="from_param" name="output_datatype" /> 39 <option type="from_param" name="output_datatype"/>
36 </action> 40 </action>
37 </actions> 41 </actions>
38 </data> 42 </data>
39 </outputs> 43 </outputs>
40 <tests> 44 <tests>
41 <test> 45 <test>
42 <param name="image_type" value="8-bit_ramp" /> 46 <param name="image_type" value="8-bit_ramp"/>
43 <param name="image_title" value="MyTitle" /> 47 <param name="image_title" value="MyTitle"/>
44 <param name="width" value="256" /> 48 <param name="width" value="256"/>
45 <param name="height" value="256" /> 49 <param name="height" value="256"/>
46 <param name="depth" value="1" /> 50 <param name="depth" value="1"/>
47 <param name="output_datatype" value="jpg" /> 51 <param name="output_datatype" value="jpg"/>
48 <output name="output" file="create_image1.jpg" ftype="jpg" /> 52 <output name="output" file="create_image1.jpg" ftype="jpg"/>
49 </test> 53 </test>
50 </tests> 54 </tests>
51 <help> 55 <help>
52 **What it does** 56 **What it does**
53 57
61 - **Depth** specifies the number of stack slices 65 - **Depth** specifies the number of stack slices
62 - **Format** specifies the image format "jpg", "png", etc 66 - **Format** specifies the image format "jpg", "png", etc
63 ]]> 67 ]]>
64 68
65 </help> 69 </help>
66 <expand macro="fiji_headless_citations" /> 70 <expand macro="fiji_headless_citations"/>
67 </tool> 71 </tool>