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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
author thomaswollmann
date Mon, 07 Jan 2019 05:37:21 -0500
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1 <?xml version="1.0"?>
2 <tool name="Overlay" id="viz_overlay_moving_and_fixed_image" version="0.0.1">
3 <description>Overlay moving and fixed image</description>
4 <requirements>
5 <requirement type="package" version="0.14.0">scikit-image</requirement>
6 <requirement type="package" version="0.23.4">pandas</requirement>
7 <requirement type="package" version="1.15.4">numpy</requirement>
8 <requirement type="package" version="1.1.0">scipy</requirement>
9 <requirement type="package" version="5.3.0">pillow</requirement>
10 </requirements>
11 <command><![CDATA[
12 python '$__tool_directory__/overlay_moving_and_fixed_image.py'
13 '$fixed_image'
14 '$moving_image'
15 '$warp_matrix'
16 '$overlay_out'
17 --factor $factor
18 $inverse_transform
19 ]]></command>
20 <inputs>
21 <param name="fixed_image" type= "data" format="png" label="Fixed image" />
22 <param name="moving_image" type= "data" format="png" label="Moving image" />
23 <param name="warp_matrix" type= "data" format="csv" label="Warp Matrix" />
24 <param name="factor" type="float" value="0.5" label="Factor by which images are blended. 1.0 returns a copy of the fixed image, 0.0 returns a copy of the moving image."/>
25 <param name="inverse_transform" type="boolean" checked="false" truevalue="--inverse_transform" falsevalue=""
26 label="Set to Yes if inverse transformation should be displayed" />
27 </inputs>
28 <outputs>
29 <data format="png" name="overlay_out" />
30 </outputs>
31 <tests>
32 <test>
33 <param name="fixed_image" value="sample1.png" />
34 <param name="moving_image" value="sample2.png" />
35 <param name="warp_matrix" value="warp_matrix.csv" />
36 <param name="factor" value="0.75" />
37 <output name="overlay_out" value="out.png" ftype="png" compare="sim_size" />
38 </test>
39 </tests>
40 <help>
41 This tool performs an overlay of two images of which one was transformed to match the other.
42 </help>
43 <citations>
44 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
45 </citations>
46 </tool>