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comparison overlay_images.xml @ 5:002f7bad3e82 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:25:58 +0000
parents 37662cbf44b8
children 2495f8b2aefd
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4:37662cbf44b8 5:002f7bad3e82
1 <tool id="ip_overlay_images" name="Overlay images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> 1 <tool id="ip_overlay_images" name="Overlay images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>creators.xml</import>
5 <import>tests.xml</import>
4 <token name="@TOOL_VERSION@">0.0.4</token> 6 <token name="@TOOL_VERSION@">0.0.4</token>
5 <token name="@VERSION_SUFFIX@">0</token> 7 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 8 </macros>
9 <creator>
10 <expand macro="creators/bmcv"/>
11 <expand macro="creators/thawn"/>
12 </creator>
7 <edam_operations> 13 <edam_operations>
8 <edam_operation>operation_3443</edam_operation> 14 <edam_operation>operation_3443</edam_operation>
9 </edam_operations> 15 </edam_operations>
10 <xrefs> 16 <xrefs>
11 <xref type="bio.tools">galaxy_image_analysis</xref> 17 <xref type="bio.tools">galaxy_image_analysis</xref>
36 #end if 42 #end if
37 ]]> 43 ]]>
38 </command> 44 </command>
39 <inputs> 45 <inputs>
40 <conditional name="method_option"> 46 <conditional name="method_option">
41 <param name="method" type="select" label="How to visualize the overlay?"> 47 <param name="method" type="select" label="Type of the overlay">
42 <option value="coloc_vis" selected="True">Colocalization</option> 48 <option value="coloc_vis" selected="True">Colocalization</option>
43 <option value="blending">Blending</option> 49 <option value="blending">Linear blending</option>
44 <option value="seg_contour">Segmentation mask over image</option> 50 <option value="seg_contour">Segmentation contours over image</option>
45 </param> 51 </param>
46 <when value="coloc_vis"> 52 <when value="coloc_vis">
47 <param name="im1" type="data" format="tiff,png" label="Image #1 (red channel)" /> 53 <param name="im1" type="data" format="tiff,png" label="Image #1 (red channel)" />
48 <param name="im2" type="data" format="tiff,png" label="Image #2 (green channel)" /> 54 <param name="im2" type="data" format="tiff,png" label="Image #2 (green channel)" />
49 </when> 55 </when>
51 <param name="im1" type="data" format="tiff,png" label="Image #1" /> 57 <param name="im1" type="data" format="tiff,png" label="Image #1" />
52 <param name="im2" type="data" format="tiff,png" label="Image #2" /> 58 <param name="im2" type="data" format="tiff,png" label="Image #2" />
53 <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."/> 59 <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."/>
54 </when> 60 </when>
55 <when value="seg_contour"> 61 <when value="seg_contour">
56 <param name="im1" type="data" format="tiff,png" label="Image" /> 62 <param name="im1" type="data" format="tiff,png" label="Intensity image" />
57 <param name="im2" type="data" format="tiff,png" label="Label image" /> 63 <param name="im2" type="data" format="tiff,png" label="Label image" />
58 <param name="thickness" type="integer" value="2" min="1" label="Contour thickness (in pixels)" /> 64 <param name="thickness" type="integer" value="2" min="1" label="Contour thickness (in pixels)" />
59 <param name="color" type="color" value="#ff0000" label="Contour color"/> 65 <param name="color" type="color" value="#ff0000" label="Contour color"/>
60 <param argument="--show_label" type="boolean" checked='false' truevalue="--show_label" falsevalue="" label="Show labels" /> 66 <param argument="--show_label" type="boolean" checked='false' truevalue="--show_label" falsevalue="" label="Show labels" />
61 <param name="label_color" type="color" value="#ffff00" label="Label color"/> 67 <param name="label_color" type="color" value="#ffff00" label="Label color"/>
73 <tests> 79 <tests>
74 <test expect_num_outputs="1"> 80 <test expect_num_outputs="1">
75 <param name="im1" value="mask1.tif"/> 81 <param name="im1" value="mask1.tif"/>
76 <param name="im2" value="mask1r.tif"/> 82 <param name="im2" value="mask1r.tif"/>
77 <param name="method" value="coloc_vis"/> 83 <param name="method" value="coloc_vis"/>
78 <output name="out_tiff" value="test1.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> 84 <expand macro="tests/intensity_image_diff" name="out_tiff" value="test1.tif" ftype="tiff"/>
79 </test> 85 </test>
80 <test expect_num_outputs="1"> 86 <test expect_num_outputs="1">
81 <param name="im1" value="mask1.tif"/> 87 <param name="im1" value="mask1.tif"/>
82 <param name="im2" value="mask1r.tif"/> 88 <param name="im2" value="mask1r.tif"/>
83 <param name="method" value="blending"/> 89 <param name="method" value="blending"/>
84 <param name="alpha" value="0.3"/> 90 <param name="alpha" value="0.3"/>
85 <output name="out_tiff" value="test2.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> 91 <expand macro="tests/intensity_image_diff" name="out_tiff" value="test2.tif" ftype="tiff"/>
86 </test> 92 </test>
87 <test expect_num_outputs="1"> 93 <test expect_num_outputs="1">
88 <param name="im1" value="sample1_uint8.tif"/> 94 <param name="im1" value="sample1_uint8.tif"/>
89 <param name="im2" value="mask1.tif"/> 95 <param name="im2" value="mask1.tif"/>
90 <param name="method" value="seg_contour"/> 96 <param name="method" value="seg_contour"/>
91 <param name="thickness" value="2"/> 97 <param name="thickness" value="2"/>
92 <param name="color" value="#ff0000"/> 98 <param name="color" value="#ff0000"/>
93 <param name="show_label" value="--show_label"/> 99 <param name="show_label" value="--show_label"/>
94 <output name="out_png" value="test3.png" ftype="png" compare="sim_size" delta_frac="0.1"/> 100 <expand macro="tests/intensity_image_diff" name="out_png" value="test3.png" ftype="png"/>
95 </test> 101 </test>
96 <test expect_num_outputs="1"><!-- segemtation overlay, 8bit test --> 102 <test expect_num_outputs="1"><!-- segmentation overlay, 8bit test -->
97 <param name="im1" value="sample1_uint8.tif"/> 103 <param name="im1" value="sample1_uint8.tif"/>
98 <param name="im2" value="mask2.tif"/> 104 <param name="im2" value="mask2.tif"/>
99 <param name="method" value="seg_contour"/> 105 <param name="method" value="seg_contour"/>
100 <param name="thickness" value="2"/> 106 <param name="thickness" value="2"/>
101 <param name="color" value="#ff0000"/> 107 <param name="color" value="#ff0000"/>
102 <output name="out_png" value="test4.png" ftype="png" compare="sim_size" delta_frac="0.1"/> 108 <expand macro="tests/intensity_image_diff" name="out_png" value="test4.png" ftype="png"/>
103 </test> 109 </test>
104 <test expect_num_outputs="1"><!-- segmentation overlay, 16bit test --> 110 <test expect_num_outputs="1"><!-- segmentation overlay, 16bit test -->
105 <param name="im1" value="sample1_uint16.tif"/> 111 <param name="im1" value="sample1_uint16.tif"/>
106 <param name="im2" value="mask2.tif"/> 112 <param name="im2" value="mask2.tif"/>
107 <param name="method" value="seg_contour"/> 113 <param name="method" value="seg_contour"/>
108 <param name="thickness" value="2"/> 114 <param name="thickness" value="2"/>
109 <param name="color" value="#ff0000"/> 115 <param name="color" value="#ff0000"/>
110 <output name="out_png" value="test4.png" ftype="png" compare="sim_size" delta_frac="0.1"/> 116 <expand macro="tests/intensity_image_diff" name="out_png" value="test4.png" ftype="png" eps="1"/>
117 </test>
118 <test expect_num_outputs="1"><!-- segmentation overlay, 8bit RGB test -->
119 <param name="im1" value="sample1_uint8_rgb.png"/>
120 <param name="im2" value="mask2.tif"/>
121 <param name="method" value="seg_contour"/>
122 <param name="thickness" value="2"/>
123 <param name="color" value="#ff0000"/>
124 <expand macro="tests/intensity_image_diff" name="out_png" value="test5.png" ftype="png"/>
111 </test> 125 </test>
112 </tests> 126 </tests>
113 <help> 127 <help><![CDATA[
114 <![CDATA[ 128
115 This tool overlays two image to visualize 1) image blending, 2) colocalization, or 3) a segmentation mask over an image. 129 **Overlays two images for visualization.**
116 ]]> 130
117 </help> 131 This tool overlays two image to visualize *linear image blending*, *colocalization*, or *segmentation contours*
132 over an intensity image. For *image blending* and *colocalization*, the input images must be single-channel 2-D
133 images. For *segmentation contours*, the intensity must be a 2-D single-channel or 2-D RGB image.
134
135 ]]></help>
118 <citations> 136 <citations>
119 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 137 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
120 </citations> 138 </citations>
121 </tool> 139 </tool>