Mercurial > repos > imgteam > imagej2_bunwarpj_adapt_transform

annotate imagej2_bunwarpj_adapt_transform.xml @ 0:706af1d7028a draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author imgteam
date Tue, 17 Sep 2019 17:11:26 -0400
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children 5d633d30316e
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706af1d7028a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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1 <?xml version='1.0' encoding='UTF-8'?>
706af1d7028a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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2 <tool id="imagej2_bunwarpj_adapt_transform" name="Adapt an elastic transformation" version="@WRAPPER_VERSION@.0">
706af1d7028a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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3 <description>to a new image size with bUnwarpJ</description>
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4 <macros>
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5 <import>imagej2_macros.xml</import>
706af1d7028a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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6 </macros>
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7 <expand macro="fiji_requirements" />
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8 <command>
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9 <![CDATA[
706af1d7028a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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10 python $__tool_directory__/imagej2_bunwarpj_adapt_transform.py
706af1d7028a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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11 --target_image "$target_image"
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12 --target_image_format $target_image.ext
706af1d7028a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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13 --source_image "$source_image"
706af1d7028a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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14 --source_image_format $source_image.ext
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15 --input_elastic_transformation "$input_elastic_transformation"
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16 --image_size_factor $image_size_factor
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17 --output "$output"
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/>
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22 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/>
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23 <param format="txt" name="input_elastic_transformation" type="data" label="Target inverse transformation"/>
706af1d7028a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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24 <param name="image_size_factor" type="float" value="2.0" label="Image size factor" help="Must be a positive or negative power of 2 (0.25, 0.5, 2, 4, 8, etc)"/>
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25 </inputs>
706af1d7028a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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26 <outputs>
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27 <data name="output" format="txt" label="${tool.name} on ${on_string}: Image size factor ${image_size_factor}" />
706af1d7028a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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28 </outputs>
706af1d7028a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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29 <tests>
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30 <test>
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31 <param name="target_image" value="dotblot.jpg" />
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32 <param name="source_image" value="blobs.gif" />
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33 <param name="input_elastic_transformation" value="source_elastic_transformation.txt" />
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34 <param name="image_size_factor" value="2.0" />
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35 <output name="output" file="adapted_transformation.txt" ftype="txt" />
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36 </test>
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37 </tests>
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38 <help>
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39 **What it does**
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40
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41 <![CDATA[
706af1d7028a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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42 Transforms the coefficients of an elastic transformation according to a real image
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43 factor. This is useful, for example, for very large images, where sub-sampled versions
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44 of the image (e.g., 4 times smaller) can be registered with the resulting transformations
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45 adapted to the smaller image size (image factor = 4) so they can be applied to the high
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46 resolution images.
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47
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48 ]]>
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49
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50 </help>
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51 <expand macro="bunwarpj_citations" />
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52 </tool>