Mercurial > repos > imgteam > imagej2_bunwarpj_compose_elastic

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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 10:59:40 +0000
parents 423400b3c47f
children e781a17b3c14
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7121957d0bbf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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1 <tool id="imagej2_bunwarpj_compose_elastic" name="Compose two elastic transformations" version="@WRAPPER_VERSION@.1">
7121957d0bbf 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>
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3 <macros>
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4 <import>imagej2_macros.xml</import>
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5 </macros>
2
7121957d0bbf 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>
7121957d0bbf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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8 </edam_operations>
7121957d0bbf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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9 <xrefs>
7121957d0bbf 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>
7121957d0bbf 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>
7121957d0bbf 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"/>
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14 <command detect_errors="exit_code"><![CDATA[
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15 #import os
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16 #set output_log = 'output_log.txt'
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17 #set source_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
423400b3c47f "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, $source_image.ext])
423400b3c47f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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19 ln -s '$source_image.file_name' '$source_with_ext' &&
423400b3c47f "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]
423400b3c47f "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, $target_image.ext])
423400b3c47f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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22 ln -s '$target_image.file_name' '$target_with_ext' &&
423400b3c47f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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23 bunwarpj -compose_elastic
423400b3c47f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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24 '$target_with_ext'
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25 '$source_with_ext'
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26 '$target_elastic_transformation'
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27 '$source_elastic_transformation'
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28 '$output'
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29 &>'$output_log';
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30 if [[ $? -ne 0 ]]; then
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31 cat '$output_log' >&2;
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32 fi
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33 ]]></command>
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34 <inputs>
1
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35 <expand macro="param_target_image"/>
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36 <expand macro="param_source_image"/>
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37 <param format="txt" name="target_elastic_transformation" type="data" label="Target inverse transformation"/>
6840ce593a91 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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38 <param format="txt" name="source_elastic_transformation" type="data" label="Source direct transformation"/>
6840ce593a91 "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"/>
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46 <param name="target_elastic_transformation" value="target_elastic_transformation.txt"/>
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47 <param name="source_elastic_transformation" value="source_elastic_transformation.txt"/>
0
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48 <output name="output" file="raw_transformation.txt" compare="contains"/>
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49 </test>
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50 </tests>
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51 <help>
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52 **What it does**
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53
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54 <![CDATA[
6840ce593a91 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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55 Composes two elastic transformations into a raw transformation. The input files must be in the elastic
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56 transformation format (i.e., the same format format as the files created with the **Save Transformation**
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57 option in the **Align two images with bUnwarpJ** tool), and the output file will be in **raw** format.
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58 .
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59
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60 ]]>
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61
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62 </help>
1
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63 <expand macro="bunwarpj_citations"/>
0
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64 </tool>