Mercurial > repos > imgteam > imagej2_bunwarpj_adapt_transform

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author imgteam
date Sun, 05 Nov 2023 14:24:23 +0000
parents 5d633d30316e
children c4774c1a35ea
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fa64e8aed5a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
imgteam
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1 <tool id="imagej2_bunwarpj_adapt_transform" name="Adapt an elastic transformation" version="@WRAPPER_VERSION@.1">
fa64e8aed5a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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2 <description>with ImageJ2</description>
0
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3 <macros>
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4 <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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5 </macros>
2
fa64e8aed5a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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6 <edam_operations>
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7 <edam_operation>operation_3443</edam_operation>
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8 </edam_operations>
fa64e8aed5a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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9 <xrefs>
fa64e8aed5a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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10 <xref type="bio.tools">imagej</xref>
fa64e8aed5a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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11 <xref type="biii">imagej2</xref>
fa64e8aed5a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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12 </xrefs>
1
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13 <expand macro="fiji_requirements"/>
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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14 <command detect_errors="exit_code"><![CDATA[
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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15 #import os
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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16 #set output_log = 'output_log.txt'
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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17 #set source_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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18 #set source_with_ext = '.'.join([source_sans_ext, $source_image.ext])
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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19 ln -s '$source_image.file_name' '$source_with_ext' &&
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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20 #set target_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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21 #set target_with_ext = '.'.join([target_sans_ext, $target_image.ext])
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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22 ln -s '$target_image.file_name' '$target_with_ext' &&
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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23 bunwarpj -adapt_transform
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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24 '$target_with_ext'
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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25 '$source_with_ext'
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26 '$input_elastic_transformation'
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27 '$output'
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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28 $image_size_factor
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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29 &>'$output_log';
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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30 if [[ $? -ne 0 ]]; then
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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31 cat '$output_log' >&2;
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32 fi
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33 ]]></command>
0
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34 <inputs>
1
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35 <expand macro="param_target_image"/>
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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36 <expand macro="param_source_image"/>
0
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37 <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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38 <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)"/>
706af1d7028a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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39 </inputs>
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40 <outputs>
1
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41 <data name="output" format="txt"/>
0
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42 </outputs>
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43 <tests>
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44 <test>
1
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45 <expand macro="test_target_source_images"/>
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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46 <param name="input_elastic_transformation" value="source_elastic_transformation.txt"/>
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47 <output name="output" file="adapted_transformation.txt" ftype="txt"/>
0
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48 </test>
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49 </tests>
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50 <help>
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51 **What it does**
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52
706af1d7028a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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53 <![CDATA[
706af1d7028a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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54 Transforms the coefficients of an elastic transformation according to a real image
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55 factor. This is useful, for example, for very large images, where sub-sampled versions
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56 of the image (e.g., 4 times smaller) can be registered with the resulting transformations
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57 adapted to the smaller image size (image factor = 4) so they can be applied to the high
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58 resolution images.
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59
706af1d7028a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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60 ]]>
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61
706af1d7028a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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62 </help>
1
5d633d30316e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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63 <expand macro="bunwarpj_citations"/>
0
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64 </tool>