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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 574caf027453f080a7f86f80eae9775ed1c8afa0
author imgteam
date Mon, 23 Sep 2024 10:26:14 +0000
parents f42d21fe65d8
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2:f42d21fe65d8 3:eb173a1fabc4
1 <tool id="ip_overlay_images" name="Overlay Images" version="0.0.3" profile="20.05"> 1 <tool id="ip_overlay_images" name="Overlay images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>for visualization</description> 2 <description></description>
3 <macros>
4 <import>creators.xml</import>
5 <import>tests.xml</import>
6 <token name="@TOOL_VERSION@">0.0.4</token>
7 <token name="@VERSION_SUFFIX@">4</token>
8 </macros>
9 <creator>
10 <expand macro="creators/bmcv"/>
11 <expand macro="creators/thawn"/>
12 </creator>
13 <edam_operations>
14 <edam_operation>operation_3443</edam_operation>
15 </edam_operations>
16 <xrefs>
17 <xref type="bio.tools">galaxy_image_analysis</xref>
18 </xrefs>
3 <requirements> 19 <requirements>
4 <requirement type="package" version="0.18.1">scikit-image</requirement> 20 <requirement type="package" version="0.18.1">scikit-image</requirement>
5 <requirement type="package" version="3.3.4">matplotlib</requirement> 21 <requirement type="package" version="3.3.4">matplotlib</requirement>
6 <requirement type="package" version="2020.10.1">tifffile</requirement> 22 <requirement type="package" version="2020.10.1">tifffile</requirement>
7 <requirement type="package" version="1.20.2">numpy</requirement> 23 <requirement type="package" version="1.21">numpy</requirement>
24 <requirement type="package" version="10.4.0">pillow</requirement>
25 <requirement type="package" version="0.1">giatools</requirement>
8 </requirements> 26 </requirements>
9 <command detect_errors="aggressive"> 27 <command detect_errors="aggressive">
10 <![CDATA[ 28 <![CDATA[
11 python '$__tool_directory__/overlay_images.py' 29 python '$__tool_directory__/overlay_images.py'
12 '$method_option.im1' '$method_option.im2' ./output.tif 30 '$method_option.im1' '$method_option.im2'
31 #if $method_option.method == "seg_contour"
32 ./output.png
33 #else
34 ./output.tif
35 #end if
13 --method $method_option.method 36 --method $method_option.method
14 #if $method_option.method == "blending" 37 #if $method_option.method == "blending"
15 --alpha $method_option.alpha 38 --alpha $method_option.alpha
16 #elif $method_option.method == "seg_contour" 39 #elif $method_option.method == "seg_contour"
17 --thickness $method_option.thickness 40 --thickness $method_option.thickness
21 #end if 44 #end if
22 ]]> 45 ]]>
23 </command> 46 </command>
24 <inputs> 47 <inputs>
25 <conditional name="method_option"> 48 <conditional name="method_option">
26 <param name="method" type="select" label="How to visualize the overlay?"> 49 <param name="method" type="select" label="Type of the overlay">
27 <option value="coloc_vis" selected="True">Colocalization</option> 50 <option value="coloc_vis" selected="True">Colocalization</option>
28 <option value="blending">Blending</option> 51 <option value="blending">Linear blending</option>
29 <option value="seg_contour">Segmentation mask over image</option> 52 <option value="seg_contour">Segmentation contours over image</option>
30 </param> 53 </param>
31 <when value="coloc_vis"> 54 <when value="coloc_vis">
32 <param name="im1" type="data" format="tiff,png" label="Image #1 (red channel)" /> 55 <param name="im1" type="data" format="tiff,png" label="Image 1 (red channel)" />
33 <param name="im2" type="data" format="tiff,png" label="Image #2 (green channel)" /> 56 <param name="im2" type="data" format="tiff,png" label="Image 2 (green channel)" />
34 </when> 57 </when>
35 <when value="blending"> 58 <when value="blending">
36 <param name="im1" type="data" format="tiff,png" label="Image #1" /> 59 <param name="im1" type="data" format="tiff,png" label="Image 1" />
37 <param name="im2" type="data" format="tiff,png" label="Image #2" /> 60 <param name="im2" type="data" format="tiff,png" label="Image 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."/> 61 <param name="alpha" type="float" value="0.5" min="0.0" max="1.0" label="The weight for blending: result = (1 - weight) * image1 + weight * image2." />
39 </when> 62 </when>
40 <when value="seg_contour"> 63 <when value="seg_contour">
41 <param name="im1" type="data" format="tiff,png" label="Image" /> 64 <param name="im1" type="data" format="tiff,png" label="Intensity image" />
42 <param name="im2" type="data" format="tiff,png" label="Label image" /> 65 <param name="im2" type="data" format="tiff,png" label="Label map" />
43 <param name="thickness" type="integer" value="2" min="1" label="Contour thickness (in pixels)" /> 66 <param name="thickness" type="integer" value="2" min="1" label="Contour thickness (in pixels)" />
44 <param name="color" type="color" value="#ff0000" label="Contour color"/> 67 <param name="color" type="color" value="#ff0000" label="Contour color"/>
45 <param argument="--show_label" type="boolean" checked='false' truevalue="--show_label" falsevalue="" label="Show labels" /> 68 <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"/> 69 <param name="label_color" type="color" value="#ffff00" label="Label color"/>
47 </when> 70 </when>
48 </conditional> 71 </conditional>
49 </inputs> 72 </inputs>
50 <outputs> 73 <outputs>
51 <data format="tiff" name="out" from_work_dir="output.tif" /> 74 <data format="tiff" name="out_tiff" from_work_dir="output.tif" label="${tool.name} on ${on_string} output:tiff">
75 <filter>method_option['method'] != 'seg_contour'</filter>
76 </data>
77 <data format="png" name="out_png" from_work_dir="output.png" label="${tool.name} on ${on_string} output:png">
78 <filter>method_option['method'] == 'seg_contour'</filter>
79 </data>
52 </outputs> 80 </outputs>
53 <tests> 81 <tests>
54 <test> 82 <test expect_num_outputs="1">
55 <param name="im1" value="mask1.tif"/> 83 <param name="im1" value="mask1.tif"/>
56 <param name="im2" value="mask1r.tif"/> 84 <param name="im2" value="mask1r.tif"/>
57 <param name="method" value="coloc_vis"/> 85 <param name="method" value="coloc_vis"/>
58 <output name="out" value="test1.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> 86 <expand macro="tests/intensity_image_diff" name="out_tiff" value="test1.tif" ftype="tiff"/>
59 </test> 87 </test>
60 <test> 88 <test expect_num_outputs="1">
61 <param name="im1" value="mask1.tif"/> 89 <param name="im1" value="mask1.tif"/>
62 <param name="im2" value="mask1r.tif"/> 90 <param name="im2" value="mask1r.tif"/>
63 <param name="method" value="blending"/> 91 <param name="method" value="blending"/>
64 <param name="alpha" value="0.3"/> 92 <param name="alpha" value="0.3"/>
65 <output name="out" value="test2.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> 93 <expand macro="tests/intensity_image_diff" name="out_tiff" value="test2.tif" ftype="tiff"/>
66 </test> 94 </test>
67 <test> 95 <test expect_num_outputs="1">
68 <param name="im1" value="sample1.tif"/> 96 <param name="im1" value="sample1_uint8.tif"/>
69 <param name="im2" value="mask1.tif"/> 97 <param name="im2" value="mask1.tif"/>
70 <param name="method" value="seg_contour"/> 98 <param name="method" value="seg_contour"/>
71 <param name="thickness" value="2"/> 99 <param name="thickness" value="2"/>
72 <param name="color" value="#ff0000"/> 100 <param name="color" value="#ff0000"/>
73 <param name="show_label" value="--show_label"/> 101 <param name="show_label" value="--show_label"/>
74 <output name="out" value="test3.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> 102 <expand macro="tests/intensity_image_diff" name="out_png" value="test3.png" ftype="png"/>
75 </test> 103 </test>
76 <test> 104 <test expect_num_outputs="1"><!-- segmentation overlay, 8bit test -->
77 <param name="im1" value="sample1.tif"/> 105 <param name="im1" value="sample1_uint8.tif"/>
78 <param name="im2" value="mask2.tif"/> 106 <param name="im2" value="mask2.tif"/>
79 <param name="method" value="seg_contour"/> 107 <param name="method" value="seg_contour"/>
80 <param name="thickness" value="2"/> 108 <param name="thickness" value="2"/>
81 <param name="color" value="#ff0000"/> 109 <param name="color" value="#ff0000"/>
82 <output name="out" value="test4.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> 110 <expand macro="tests/intensity_image_diff" name="out_png" value="test4.png" ftype="png"/>
111 </test>
112 <test expect_num_outputs="1"><!-- segmentation overlay, 16bit test -->
113 <param name="im1" value="sample1_uint16.tif"/>
114 <param name="im2" value="mask2.tif"/>
115 <param name="method" value="seg_contour"/>
116 <param name="thickness" value="2"/>
117 <param name="color" value="#ff0000"/>
118 <expand macro="tests/intensity_image_diff" name="out_png" value="test4.png" ftype="png" eps="1"/>
119 </test>
120 <test expect_num_outputs="1"><!-- segmentation overlay, 8bit RGB test -->
121 <param name="im1" value="sample1_uint8_rgb.png"/>
122 <param name="im2" value="mask2.tif"/>
123 <param name="method" value="seg_contour"/>
124 <param name="thickness" value="2"/>
125 <param name="color" value="#ff0000"/>
126 <expand macro="tests/intensity_image_diff" name="out_png" value="test5.png" ftype="png"/>
83 </test> 127 </test>
84 </tests> 128 </tests>
85 <help> 129 <help><![CDATA[
86 **What it does**
87 130
88 This tool overlays two image to visualize 1) image blending, 2) colocalization, or 3) a segmentation mask over an image. 131 **Overlays two images for visualization.**
89 </help> 132
133 This tool overlays two image to visualize *linear image blending*, *colocalization*, or *segmentation contours*
134 over an intensity image. For *image blending* and *colocalization*, the input images must be single-channel 2-D
135 images. For *segmentation contours*, the intensity must be a 2-D single-channel or 2-D RGB image.
136
137 ]]></help>
90 <citations> 138 <citations>
91 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 139 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
92 </citations> 140 </citations>
93 </tool> 141 </tool>