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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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bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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1 <?xml version="1.0"?>
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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2 <tool name="Overlay" id="viz_overlay_moving_and_fixed_image" version="0.0.1">
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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3 <description>Overlay moving and fixed image</description>
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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4 <requirements>
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5 <requirement type="package" version="0.14.0">scikit-image</requirement>
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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6 <requirement type="package" version="0.23.4">pandas</requirement>
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7 <requirement type="package" version="1.15.4">numpy</requirement>
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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8 <requirement type="package" version="1.1.0">scipy</requirement>
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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9 <requirement type="package" version="5.3.0">pillow</requirement>
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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10 </requirements>
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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11 <command><![CDATA[
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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12 python '$__tool_directory__/overlay_moving_and_fixed_image.py'
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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13 '$fixed_image'
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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14 '$moving_image'
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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15 '$warp_matrix'
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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16 '$overlay_out'
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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17 --factor $factor
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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18 $inverse_transform
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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19 ]]></command>
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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20 <inputs>
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21 <param name="fixed_image" type= "data" format="png" label="Fixed image" />
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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22 <param name="moving_image" type= "data" format="png" label="Moving image" />
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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23 <param name="warp_matrix" type= "data" format="csv" label="Warp Matrix" />
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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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."/>
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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25 <param name="inverse_transform" type="boolean" checked="false" truevalue="--inverse_transform" falsevalue=""
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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26 label="Set to Yes if inverse transformation should be displayed" />
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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27 </inputs>
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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28 <outputs>
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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29 <data format="png" name="overlay_out" />
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="fixed_image" value="sample1.png" />
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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34 <param name="moving_image" value="sample2.png" />
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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35 <param name="warp_matrix" value="warp_matrix.csv" />
bd06c3ba70b0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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36 <param name="factor" value="0.75" />
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37 <output name="overlay_out" value="out.png" ftype="png" compare="sim_size" />
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38 </test>
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39 </tests>
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40 <help>
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41 This tool performs an overlay of two images of which one was transformed to match the other.
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42 </help>
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43 <citations>
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44 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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45 </citations>
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46 </tool>