Mercurial > repos > imgteam > imagej2_create_image
comparison imagej2_create_image.xml @ 1:1a7c29d5fc11 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author | imgteam |
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date | Mon, 28 Sep 2020 16:43:06 +0000 |
parents | dc3935a0165a |
children | 666af1279007 |
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0:dc3935a0165a | 1:1a7c29d5fc11 |
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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> |