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annotate overlay_moving_and_fixed_image.xml @ 1:f9df2b32b632 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 09:58:34 +0000
parents 5cda6b23a47e
children 93533276bf1d
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f9df2b32b632 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
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1 <tool id="ip_viz_overlay_moving_and_fixed_image" name="Overlay" version="0.0.2">
0
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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2 <description>moving and fixed image</description>
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3 <requirements>
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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4 <requirement type="package" version="0.14.2">scikit-image</requirement>
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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5 <requirement type="package" version="0.23.4">pandas</requirement>
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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6 <requirement type="package" version="1.15.4">numpy</requirement>
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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7 <requirement type="package" version="1.1.0">scipy</requirement>
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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8 <requirement type="package" version="5.3.0">pillow</requirement>
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f9df2b32b632 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
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9 <requirement type="package" version="0.15.1">tifffile</requirement>
0
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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10 </requirements>
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f9df2b32b632 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
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11 <command detect_errors="aggressive"><![CDATA[
0
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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12 python '$__tool_directory__/overlay_moving_and_fixed_image.py'
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 '$fixed_image'
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f9df2b32b632 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
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14 '$moving_image'
0
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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15 '$warp_matrix'
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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16 '$overlay_out'
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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17 --factor $factor
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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18 $inverse_transform
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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19 ]]></command>
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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20 <inputs>
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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21 <param name="fixed_image" type= "data" format="png" label="Fixed image" />
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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22 <param name="moving_image" type= "data" format="png" label="Moving image" />
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23 <param name="warp_matrix" type= "data" format="tabular" label="Warp Matrix" />
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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24 <param name="factor" type="float" value="0.5"
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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25 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."/>
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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26 <param name="inverse_transform" type="boolean" checked="false" truevalue="--inverse_transform" falsevalue=""
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 label="Set to Yes if inverse transformation should be displayed" />
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28 </inputs>
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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29 <outputs>
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 <data format="png" name="overlay_out" />
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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31 </outputs>
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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32 <tests>
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33 <test>
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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34 <param name="fixed_image" value="sample1.png" />
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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35 <param name="moving_image" value="sample2.png" />
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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36 <param name="warp_matrix" value="warp_matrix.tsv" />
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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37 <param name="factor" value="0.75" />
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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38 <output name="overlay_out" value="out.png" ftype="png" compare="sim_size" />
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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39 </test>
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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40 </tests>
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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41 <help>
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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42 **What it does**
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43
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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44 This tool performs an overlay of two images of which one was transformed to match the other.
5cda6b23a47e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_moving_and_fixed_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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45 </help>
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46 <citations>
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47 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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48 </citations>
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49 </tool>