Mercurial > repos > imgteam > imagej2_bunwarpj_raw_transform

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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 16:59:38 -0400
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e313a9d0b613 "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'?>
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2 <tool id="imagej2_bunwarpj_raw_transform" name="Apply raw transformation" version="@WRAPPER_VERSION@.0">
e313a9d0b613 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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3 <description>with bUnwarpJ</description>
e313a9d0b613 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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4 <macros>
e313a9d0b613 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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5 <import>imagej2_macros.xml</import>
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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[
e313a9d0b613 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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10 python $__tool_directory__/imagej2_bunwarpj_raw_transform.py
e313a9d0b613 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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11 --target_image "$target_image"
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12 --target_image_format $target_image.ext
e313a9d0b613 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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13 --source_image "$source_image"
e313a9d0b613 "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
e313a9d0b613 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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15 --raw_transformation $raw_transformation
e313a9d0b613 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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16 --source_out "$source_out"
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17 --source_out_datatype $source_out_datatype
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18 --jython_script $__tool_directory__/imagej2_bunwarpj_raw_transform_jython_script.py
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/>
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23 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/>
e313a9d0b613 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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24 <!-- Support for a bUnwarpJ raw transformation datatype should be added to Galaxy -->
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25 <param format="txt" name="raw_transformation" type="data" label="Elastic transformation" help="As saved by bUnwarpJ in raw format"/>
e313a9d0b613 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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26 <param name="source_out_datatype" type="select" label="Save registered source image as format">
e313a9d0b613 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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27 <expand macro="image_datatypes" />
e313a9d0b613 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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28 </param>
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29 </inputs>
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30 <outputs>
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31 <data name="source_out" format="png" label="${tool.name} on ${on_string}: Registered source image">
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32 <actions>
e313a9d0b613 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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33 <action type="format">
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34 <option type="from_param" name="source_out_datatype" />
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35 </action>
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36 </actions>
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37 </data>
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="target_image" value="dotblot.jpg" />
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42 <param name="source_image" value="blobs.gif" />
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43 <param name="raw_transformation" value="source_raw_transformation.txt" />
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44 <param name="source_out_datatype" value="png" />
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45 <output name="source_out" file="raw_trans_registered_source1.png" compare="sim_size" />
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46 </test>
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47 </tests>
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48 <help>
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49 **What it does**
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50
e313a9d0b613 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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51 <![CDATA[
e313a9d0b613 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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52 Applies a raw transformation to an image, producing another image which is deformed according
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53 to the transformation. The transformation file must be in the same format as the files created
e313a9d0b613 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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54 with the **Convert elastic transformation to raw with bUnwarpJ** tool.
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55
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56 ]]>
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57
e313a9d0b613 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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58 </help>
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59 <expand macro="bunwarpj_citations" />
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60 </tool>