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comparison overlay_segmentation_mask.xml @ 0:9e67f52b3eaf draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:20:46 -0500
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children 8077f714ad94
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-1:000000000000 0:9e67f52b3eaf
1 <tool id="ip_overlay_segmentation" name="Overlay Segmentation Mask" version="0.0.6">
2 <description>Overlay Segmentation Mask</description>
3 <requirements>
4 <requirement type="package" version="0.14.2">scikit-image</requirement>
5 <requirement type="package" version="3.0.2">matplotlib</requirement>
6 <requirement type="package" version="5.3.0">pillow</requirement>
7 <requirement type="package" version="0.10.0">tifffile</requirement>
8 </requirements>
9 <command detect_errors="aggressive"><![CDATA[
10 python '$__tool_directory__/overlay_segmentation_mask.py'
11 $greyscale
12 #if str($label_option.label) == '--label'
13 --label --label_color '$label_option.label_color'
14 #end if
15 --thickness $thickness
16 --stroke_color '$stroke_color'
17 '$input_image' '$input_mask' ./tmp.png
18 ]]>
19 </command>
20 <inputs>
21 <param name="input_image" type="data" label="Image Source File" format="tif,bmp,jpg,png"/>
22 <param name="input_mask" type="data" label="Mask Source File" format="tif,bmp,jpg,png"/>
23 <param name="greyscale" type="boolean" checked='true' truevalue='--grey' falsevalue='' label="Image Is Greyscale" />
24 <param name="thickness" size="4" type="float" value="0.3" label="Thickness" />
25 <param name="stroke_color" type="color" value="#ff0000" label="Stroke Color"/>
26 <conditional name="label_option">
27 <param name="label" type="boolean" checked='false' truevalue='--label' falsevalue='' label="Plot Labels" />
28 <when value=""> </when>
29 <when value="--label">
30 <param name="label_color" type="color" value="#ffff00" label="Label Color"/>
31 </when>
32 </conditional>
33 </inputs>
34 <outputs>
35 <data format="png" name="output" from_work_dir="tmp.png" />
36 </outputs>
37 <tests>
38 <test>
39 <conditional name="label_option">
40 <param name="label" value="--label"/>
41 <param name="label_color" value="#ffff00"/>
42 </conditional>
43 <param name="stroke_color" value="#ffaa00"/>
44 <param name="label_option['label']" value="--label"/>
45 <param name="input_image" value="sample.tif"/>
46 <param name="input_mask" value="sample_seg.tif"/>
47 <param name="greyscale" value="--grey"/>
48 <output name="output" value="outt.png" ftype="png" compare="sim_size"/>
49 </test>
50 </tests>
51 <help>
52 **What it does**
53
54 This tool overlays a segmentation mask over an image.
55 </help>
56 <citations>
57 <citation type="doi">10.7717/peerj.453</citation>
58 </citations>
59 </tool>