Mercurial > repos > imgteam > imagej2_bunwarpj_elastic_transform

annotate imagej2_bunwarpj_elastic_transform.xml @ 2:55bf135d6b0c draft

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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 14:26:15 +0000
parents 39b2bc251b2f
children f72f8e6787cd
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55bf135d6b0c 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_elastic_transform" name="Apply elastic transformation" version="@WRAPPER_VERSION@.2">
55bf135d6b0c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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2 <description>with ImageJ</description>
0
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3 <macros>
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4 <import>imagej2_macros.xml</import>
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5 </macros>
2
55bf135d6b0c 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>
55bf135d6b0c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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8 </edam_operations>
55bf135d6b0c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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9 <xrefs>
55bf135d6b0c 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>
55bf135d6b0c 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>
55bf135d6b0c 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"/>
39b2bc251b2f "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[
39b2bc251b2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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15 #import os
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16 #set error_log = 'output_log.txt'
39b2bc251b2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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17 touch '$error_log' &&
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18
39b2bc251b2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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19 ## ImageJ2 requires file extensions to be valid image data types.
39b2bc251b2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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20 #set source_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
39b2bc251b2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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21 #set source_with_ext = '.'.join([source_sans_ext, $source_image.ext])
39b2bc251b2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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22 ln -s '$source_image.file_name' '$source_with_ext' &&
39b2bc251b2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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23 #set target_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
39b2bc251b2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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24 #set target_with_ext = '.'.join([target_sans_ext, $target_image.ext])
39b2bc251b2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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25 ln -s '$target_image.file_name' '$target_with_ext' &&
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26
39b2bc251b2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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27 bunwarpj -elastic_transform
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28 '$target_with_ext'
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29 '$source_with_ext'
39b2bc251b2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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30 '$elastic_transformation'
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31 '$source_out'
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32 &>'$error_log';
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33 if [[ $? -ne 0 ]]; then
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34 cat '$error_log' >&2;
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35 fi
39b2bc251b2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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36 ]]></command>
0
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37 <inputs>
1
39b2bc251b2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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38 <expand macro="param_target_image"/>
39b2bc251b2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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39 <expand macro="param_source_image"/>
0
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40 <!-- Support for a bUnwarpJ elastic transformation datatype should be added to Galaxy -->
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41 <param format="txt" name="elastic_transformation" type="data" label="Elastic transformation" help="As saved by bUnwarpJ in elastic format"/>
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42 <param name="source_out_datatype" type="select" label="Save registered source image as format">
1
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43 <expand macro="image_datatypes"/>
0
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44 </param>
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45 </inputs>
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46 <outputs>
1
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47 <data name="source_out" format="png">
0
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48 <actions>
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49 <action type="format">
1
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50 <option type="from_param" name="source_out_datatype"/>
0
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51 </action>
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52 </actions>
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53 </data>
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54 </outputs>
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55 <tests>
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56 <test>
1
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57 <expand macro="test_target_source_images"/>
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58 <param name="elastic_transformation" value="blobs_direct_transf.txt"/>
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59 <output name="source_out" file="elastic_trans_registered_source1.png" compare="sim_size"/>
0
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60 </test>
301f24849032 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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61 </tests>
301f24849032 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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62 <help>
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63 **What it does**
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64
301f24849032 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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65 <![CDATA[
301f24849032 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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66 Applies an elastic transformation to an image, producing another image which is elastically
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67 deformed according to the transformation. The transformation file must be in the same format
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68 as the files created with the **Save Transformation** option in the **Align two images with bUnwarpJ**
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69 tool.
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70
301f24849032 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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71 ]]>
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72
301f24849032 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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73 </help>
1
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74 <expand macro="bunwarpj_citations"/>
0
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75 </tool>