Mercurial > repos > imgteam > overlay_images
comparison overlay_images.xml @ 2:b74693340624 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
author | imgteam |
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date | Thu, 10 Aug 2023 07:29:34 +0000 |
parents | bf590a9733ed |
children | 22ff7c705a83 |
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1:bf590a9733ed | 2:b74693340624 |
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1 <tool id="ip_overlay_images" name="Overlay Images" version="0.0.2" profile="20.05"> | 1 <tool id="ip_overlay_images" name="Overlay Images" version="0.0.3" profile="20.05"> |
2 <description>for visualization</description> | 2 <description>for visualization</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.18.1">scikit-image</requirement> | 4 <requirement type="package" version="0.18.1">scikit-image</requirement> |
5 <requirement type="package" version="3.3.4">matplotlib</requirement> | 5 <requirement type="package" version="3.3.4">matplotlib</requirement> |
6 <requirement type="package" version="2020.10.1">tifffile</requirement> | 6 <requirement type="package" version="2020.10.1">tifffile</requirement> |
13 --method $method_option.method | 13 --method $method_option.method |
14 #if $method_option.method == "blending" | 14 #if $method_option.method == "blending" |
15 --alpha $method_option.alpha | 15 --alpha $method_option.alpha |
16 #elif $method_option.method == "seg_contour" | 16 #elif $method_option.method == "seg_contour" |
17 --thickness $method_option.thickness | 17 --thickness $method_option.thickness |
18 --color '$method_option.colour' | 18 --color '$method_option.color' |
19 $method_option.show_label | 19 $method_option.show_label |
20 --label_color '$method_option.label_color' | |
20 #end if | 21 #end if |
21 ]]> | 22 ]]> |
22 </command> | 23 </command> |
23 <inputs> | 24 <inputs> |
24 <conditional name="method_option"> | 25 <conditional name="method_option"> |
37 <param name="alpha" type="float" value="0.5" min="0.0" max="1.0" label="The weight for blending: I_out = (1 - w) * I_1 + w * I_2."/> | 38 <param name="alpha" type="float" value="0.5" min="0.0" max="1.0" label="The weight for blending: I_out = (1 - w) * I_1 + w * I_2."/> |
38 </when> | 39 </when> |
39 <when value="seg_contour"> | 40 <when value="seg_contour"> |
40 <param name="im1" type="data" format="tiff,png" label="Image" /> | 41 <param name="im1" type="data" format="tiff,png" label="Image" /> |
41 <param name="im2" type="data" format="tiff,png" label="Label image" /> | 42 <param name="im2" type="data" format="tiff,png" label="Label image" /> |
42 <param name="thickness" type="float" value="0.3" label="Contour thickness" /> | 43 <param name="thickness" type="integer" value="2" min="1" label="Contour thickness (in pixels)" /> |
43 <param name="colour" type="color" value="#ff0000" label="Contour color"/> | 44 <param name="color" type="color" value="#ff0000" label="Contour color"/> |
44 <param argument="--show_label" type="boolean" checked='false' truevalue="--show_label" falsevalue="" label="Show labels" /> | 45 <param argument="--show_label" type="boolean" checked='false' truevalue="--show_label" falsevalue="" label="Show labels" /> |
46 <param name="label_color" type="color" value="#ffff00" label="Label color"/> | |
45 </when> | 47 </when> |
46 </conditional> | 48 </conditional> |
47 </inputs> | 49 </inputs> |
48 <outputs> | 50 <outputs> |
49 <data format="tiff" name="out" from_work_dir="output.tif" /> | 51 <data format="tiff" name="out" from_work_dir="output.tif" /> |
64 </test> | 66 </test> |
65 <test> | 67 <test> |
66 <param name="im1" value="sample1.tif"/> | 68 <param name="im1" value="sample1.tif"/> |
67 <param name="im2" value="mask1.tif"/> | 69 <param name="im2" value="mask1.tif"/> |
68 <param name="method" value="seg_contour"/> | 70 <param name="method" value="seg_contour"/> |
69 <param name="thickness" value="0.4"/> | 71 <param name="thickness" value="2"/> |
70 <param name="colour" value="#ffaa00"/> | 72 <param name="color" value="#ff0000"/> |
71 <param name="show_label" value="--show_label"/> | 73 <param name="show_label" value="--show_label"/> |
72 <output name="out" value="test3.tif" ftype="tiff" compare="sim_size" delta="20000" delta_frac="0.2"/> | 74 <output name="out" value="test3.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> |
75 </test> | |
76 <test> | |
77 <param name="im1" value="sample1.tif"/> | |
78 <param name="im2" value="mask2.tif"/> | |
79 <param name="method" value="seg_contour"/> | |
80 <param name="thickness" value="2"/> | |
81 <param name="color" value="#ff0000"/> | |
82 <output name="out" value="test4.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> | |
73 </test> | 83 </test> |
74 </tests> | 84 </tests> |
75 <help> | 85 <help> |
76 **What it does** | 86 **What it does** |
77 | 87 |
78 This tool overlays two image to visualize 1) image blending, 2) colocalization, or 3) a segmentation mask over an image. | 88 This tool overlays two image to visualize 1) image blending, 2) colocalization, or 3) a segmentation mask over an image. |
79 </help> | 89 </help> |
80 <citations> | 90 <citations> |
91 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> | |
81 </citations> | 92 </citations> |
82 </tool> | 93 </tool> |