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 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author imgteam
date Wed, 25 Sep 2024 16:04:07 +0000
parents eabdcf6ad900
children
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69e951528a0b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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1 <tool id="imagej2_bunwarpj_raw_transform" name="Apply raw transformation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
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eabdcf6ad900 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
eabdcf6ad900 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>
eabdcf6ad900 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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8 </edam_operations>
eabdcf6ad900 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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9 <xrefs>
eabdcf6ad900 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>
eabdcf6ad900 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>
eabdcf6ad900 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"/>
aa4a5a8c4cfd "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[
aa4a5a8c4cfd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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15 #import os
aa4a5a8c4cfd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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16 #set error_log = 'output_log.txt'
aa4a5a8c4cfd "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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aa4a5a8c4cfd "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.
aa4a5a8c4cfd "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]
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69e951528a0b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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21 #set source_with_ext = './' + '.'.join([source_sans_ext, $source_image.ext])
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22 ln -s '$source_image.file_name' '$source_with_ext' &&
aa4a5a8c4cfd "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]
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69e951528a0b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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24 #set target_with_ext = './' + '.'.join([target_sans_ext, $target_image.ext])
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25 ln -s '$target_image.file_name' '$target_with_ext' &&
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26
aa4a5a8c4cfd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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27 bunwarpj -raw_transform
aa4a5a8c4cfd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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28 '$target_with_ext'
aa4a5a8c4cfd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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29 '$source_with_ext'
aa4a5a8c4cfd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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30 '$raw_transformation'
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31 '$source_out'
aa4a5a8c4cfd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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32 ]]></command>
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33 <inputs>
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34 <expand macro="param_target_image"/>
aa4a5a8c4cfd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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35 <expand macro="param_source_image"/>
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36 <!-- Support for a bUnwarpJ raw transformation datatype should be added to Galaxy -->
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aa4a5a8c4cfd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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37 <param format="txt" name="raw_transformation" type="data" label="Raw transformation" help="As saved by bUnwarpJ in raw format"/>
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38 <param name="source_out_datatype" type="select" label="Save registered source image as format">
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39 <expand macro="image_datatypes"/>
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40 </param>
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41 </inputs>
95b7592729e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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42 <outputs>
1
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43 <data name="source_out" format="png">
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44 <actions>
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45 <action type="format">
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46 <option type="from_param" name="source_out_datatype"/>
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47 </action>
95b7592729e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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48 </actions>
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49 </data>
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50 </outputs>
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51 <tests>
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52 <test>
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53 <expand macro="test_target_source_images"/>
aa4a5a8c4cfd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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54 <param name="raw_transformation" value="source_raw_transformation.txt"/>
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55 <param name="source_out_datatype" value="png"/>
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69e951528a0b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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56 <output name="source_out" file="raw_trans_registered_source1.png" compare="image_diff"/>
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57 </test>
95b7592729e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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58 </tests>
95b7592729e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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59 <help>
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60 **What it does**
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61
95b7592729e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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62 <![CDATA[
95b7592729e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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63 Applies a raw transformation to an image, producing another image which is deformed according
95b7592729e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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64 to the transformation. The transformation file must be in the same format as the files created
95b7592729e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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65 with the **Convert elastic transformation to raw with bUnwarpJ** tool.
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66
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67 ]]>
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68
95b7592729e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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69 </help>
1
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70 <expand macro="bunwarpj_citations"/>
0
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71 </tool>