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comparison overlay_images.xml @ 1:bf590a9733ed draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit cd63bc5e6eb7254111012209fac9154569355f20
author imgteam
date Tue, 19 Jul 2022 08:52:04 +0000
parents 589af0005df5
children b74693340624
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0:589af0005df5 1:bf590a9733ed
1 <tool id="ip_overlay_images" name="Overlay Images" version="0.0.1" profile="20.05"> 1 <tool id="ip_overlay_images" name="Overlay Images" version="0.0.2" 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>
7 <requirement type="package" version="1.20.2">numpy</requirement> 7 <requirement type="package" version="1.20.2">numpy</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="aggressive"> 9 <command detect_errors="aggressive">
10 <![CDATA[ 10 <![CDATA[
11 python '$__tool_directory__/overlay_images.py' 11 python '$__tool_directory__/overlay_images.py'
12 '$im1' '$im2' ./output.tif 12 '$method_option.im1' '$method_option.im2' ./output.tif
13 --method '$method_option.method' 13 --method $method_option.method
14 #if '$method_option.method' == 'blending': 14 #if $method_option.method == "blending"
15 --alpha '$alpha' 15 --alpha $method_option.alpha
16 #elif '$method_option.method' == 'seg_contour': 16 #elif $method_option.method == "seg_contour"
17 --thickness '$thickness' 17 --thickness $method_option.thickness
18 --color '$color' 18 --color '$method_option.colour'
19 $show_label 19 $method_option.show_label
20 #end if 20 #end if
21 ]]> 21 ]]>
22 </command> 22 </command>
23 <inputs> 23 <inputs>
24 <conditional name="method_option"> 24 <conditional name="method_option">
38 </when> 38 </when>
39 <when value="seg_contour"> 39 <when value="seg_contour">
40 <param name="im1" type="data" format="tiff,png" label="Image" /> 40 <param name="im1" type="data" format="tiff,png" label="Image" />
41 <param name="im2" type="data" format="tiff,png" label="Label image" /> 41 <param name="im2" type="data" format="tiff,png" label="Label image" />
42 <param name="thickness" type="float" value="0.3" label="Contour thickness" /> 42 <param name="thickness" type="float" value="0.3" label="Contour thickness" />
43 <param name="color" type="color" value="#ff0000" label="Contour color"/> 43 <param name="colour" type="color" value="#ff0000" label="Contour color"/>
44 <param argument="--show_label" type="boolean" checked='false' truevalue="--show_label" falsevalue="" label="Show labels" /> 44 <param argument="--show_label" type="boolean" checked='false' truevalue="--show_label" falsevalue="" label="Show labels" />
45 </when> 45 </when>
46 </conditional> 46 </conditional>
47 </inputs> 47 </inputs>
48 <outputs> 48 <outputs>
50 </outputs> 50 </outputs>
51 <tests> 51 <tests>
52 <test> 52 <test>
53 <param name="im1" value="mask1.tif"/> 53 <param name="im1" value="mask1.tif"/>
54 <param name="im2" value="mask1r.tif"/> 54 <param name="im2" value="mask1r.tif"/>
55 <conditional name="method_option"> 55 <param name="method" value="coloc_vis"/>
56 <param name="method" value="coloc_vis"/>
57 </conditional>
58 <output name="out" value="test1.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> 56 <output name="out" value="test1.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
59 </test> 57 </test>
60 <test> 58 <test>
61 <param name="im1" value="mask1.tif"/> 59 <param name="im1" value="mask1.tif"/>
62 <param name="im2" value="mask1r.tif"/> 60 <param name="im2" value="mask1r.tif"/>
63 <conditional name="method_option"> 61 <param name="method" value="blending"/>
64 <param name="method" value="blending"/>
65 </conditional>
66 <param name="alpha" value="0.3"/> 62 <param name="alpha" value="0.3"/>
67 <output name="out" value="test2.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> 63 <output name="out" value="test2.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
68 </test> 64 </test>
69 <test> 65 <test>
70 <param name="im1" value="sample1.tif"/> 66 <param name="im1" value="sample1.tif"/>
71 <param name="im2" value="mask1.tif"/> 67 <param name="im2" value="mask1.tif"/>
72 <conditional name="method_option"> 68 <param name="method" value="seg_contour"/>
73 <param name="method" value="seg_contour"/>
74 </conditional>
75 <param name="thickness" value="0.4"/> 69 <param name="thickness" value="0.4"/>
76 <param name="color" value="#ffaa00"/> 70 <param name="colour" value="#ffaa00"/>
77 <param name="show_label" value="true"/> 71 <param name="show_label" value="--show_label"/>
78 <output name="out" value="test3.tif" ftype="tiff" compare="sim_size" delta="20000" delta_frac="0.2"/> 72 <output name="out" value="test3.tif" ftype="tiff" compare="sim_size" delta="20000" delta_frac="0.2"/>
79 </test> 73 </test>
80 </tests> 74 </tests>
81 <help> 75 <help>
82 **What it does** 76 **What it does**