Mercurial > repos > imgteam > imagej2_bunwarpj_align
annotate imagej2_bunwarpj_align.xml @ 3:711adedc5bb8 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author | imgteam |
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date | Wed, 25 Sep 2024 15:56:56 +0000 |
parents | 0a0d2dfd17e0 |
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rev | line source |
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3
711adedc5bb8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
2
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changeset
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1 <tool id="imagej2_bunwarpj_align" name="Align two images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> |
2
0a0d2dfd17e0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
imgteam
parents:
1
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2 <description>with ImageJ2</description> |
0
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
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3 <macros> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
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4 <import>imagej2_macros.xml</import> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
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5 </macros> |
2
0a0d2dfd17e0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
imgteam
parents:
1
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changeset
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6 <edam_operations> |
0a0d2dfd17e0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
imgteam
parents:
1
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changeset
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7 <edam_operation>operation_3443</edam_operation> |
0a0d2dfd17e0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
imgteam
parents:
1
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changeset
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8 </edam_operations> |
0a0d2dfd17e0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
imgteam
parents:
1
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9 <xrefs> |
0a0d2dfd17e0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
imgteam
parents:
1
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10 <xref type="bio.tools">imagej</xref> |
0a0d2dfd17e0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
imgteam
parents:
1
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11 <xref type="biii">imagej2</xref> |
0a0d2dfd17e0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
imgteam
parents:
1
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12 </xrefs> |
1
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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13 <expand macro="fiji_requirements"/> |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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14 <command detect_errors="exit_code"><![CDATA[ |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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15 #import os |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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16 #set error_log = 'output_log.txt' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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17 touch '$error_log'; |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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18 |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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19 ## ImageJ2 requires file extensions to be valid image data types. |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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20 #set source_out_suffix = '.' + str($source_out_datatype) |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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21 #set target_out_suffix = '.' + str($target_out_datatype) |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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22 #set source_image_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0] |
3
711adedc5bb8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
2
diff
changeset
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23 #set source_image_with_ext = './' + '.'.join([$source_image_sans_ext, $source_image.ext]) |
1
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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24 ln -s '$source_image.file_name' '$source_image_with_ext'; |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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changeset
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25 #set target_image_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0] |
3
711adedc5bb8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
2
diff
changeset
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26 #set target_image_with_ext = './' + '.'.join([$target_image_sans_ext, $target_image.ext]) |
1
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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27 ln -s '$target_image.file_name' '$target_image_with_ext'; |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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28 |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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29 #set save_transformation = str($advanced_options_cond.advanced_options) == 'save_transformation' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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30 #set mono = str($advanced_options_cond.advanced_options) == 'mono' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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31 #set landmarks = str($advanced_options_cond.advanced_options) == 'landmarks' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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32 #set affine = str($advanced_options_cond.advanced_options) == 'affine' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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33 |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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34 #if str($align_with_mask_cond.align_with_mask) == 'yes': |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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35 #set source_mask_sans_ext = $os.path.splitext($os.path.basename($align_with_mask_cond.source_mask.file_name))[0] |
3
711adedc5bb8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
2
diff
changeset
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36 #set source_mask_with_ext = './' + '.'.join([$source_mask_sans_ext, $source_mask.ext]) |
1
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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37 #set source_mask = $source_mask_with_ext |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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38 ln -s '$align_with_mask_cond.source_mask.file_name' '$source_mask_with_ext'; |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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39 #set target_mask_sans_ext = $os.path.splitext($os.path.basename($align_with_mask_cond.target_mask.file_name))[0] |
3
711adedc5bb8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
2
diff
changeset
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40 #set target_mask_with_ext = './' + '.'.join([$target_mask_sans_ext, $target_mask.ext]) |
1
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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41 #set target_mask = $target_mask_with_ext |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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changeset
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42 ln -s '$align_with_mask_cond.target_mask.file_name' '$target_mask_with_ext'; |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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43 #else: |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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44 #set source_mask = 'NULL' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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45 #set target_mask = 'NULL' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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46 #end if |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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47 |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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48 #if not $mono: |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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49 #set tmp_target_out = 'tmp_target_out' + $target_out_suffix |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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50 touch '$tmp_target_out'; |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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51 |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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52 ## bUnwarpJ automatically names the transformation files based |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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53 ## on the names of the source and target image file names. |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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54 #set tmp_target_out_transf_name_sans_ext = $os.path.splitext($target_out.file_name)[0] |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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55 #set tmp_target_out_transf_name = $tmp_target_out_transf_name_sans_ext + '_transf.txt' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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56 touch '$tmp_target_out_transf_name'; |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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57 #end if |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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58 #set tmp_source_out = 'tmp_source_out' + $source_out_suffix |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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59 touch '$tmp_source_out'; |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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60 |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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61 ## bUnwarpJ automatically names the transformation files based |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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62 ## on the names of the source and target image file names. |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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63 #set tmp_source_out_transf_name_sans_ext = $os.path.splitext($source_out.file_name)[0] |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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64 #set tmp_source_out_transf_name = $tmp_source_out_transf_name_sans_ext + '_transf.txt' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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65 touch '$tmp_source_out_transf_name'; |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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66 |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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67 ## Align the two images using bUnwarpJ. |
3
711adedc5bb8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
2
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68 ## The option -XX:ActiveProcessorCount="1" was set in version 20231211 to ensure reproducibility |
711adedc5bb8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
2
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69 bunwarpj -XX:ActiveProcessorCount="1" -align |
1
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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70 '$target_image_with_ext' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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71 '$target_mask' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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72 '$source_image_with_ext' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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73 '$source_mask' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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74 $min_scale_def |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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75 $max_scale_def |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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76 $max_subsamp_fact |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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77 $divergence_weight |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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78 $curl_weight |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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79 $image_weight |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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80 $consistency_weight |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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81 '$source_out' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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82 #if not $mono: |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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83 '$target_out' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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84 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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85 #if $landmarks: |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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86 '-landmarks' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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87 $advanced_options_cond.landmarks_weight |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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88 '$landmarks_file' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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89 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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90 #if $affine: |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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91 '-affine' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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92 '$advanced_options_cond.target_affine_file' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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93 '$advanced_options_cond.source_affine_file' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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94 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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95 #if $mono: |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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96 '-mono' |
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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97 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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98 #if $save_transformation: |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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99 '-save_transformation' |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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100 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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101 #if $save_transformation: |
3
711adedc5bb8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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102 && mv '$tmp_source_out_transf_name' '$source_trans_out' |
711adedc5bb8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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103 && mv '$tmp_target_out_transf_name' '$target_trans_out'; |
1
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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104 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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105 ]]></command> |
0
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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106 <inputs> |
1
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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107 <expand macro="param_target_image"/> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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108 <expand macro="param_source_image"/> |
0
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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109 <conditional name="align_with_mask_cond"> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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110 <param name="align_with_mask" type="select" label="Align with masks?" help="Source and target mask can be any image format."> |
1
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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111 <option value="no" selected="true">No</option> |
0
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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112 <option value="yes">Yes</option> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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113 </param> |
1
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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114 <when value="no"/> |
0
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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115 <when value="yes"> |
1
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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116 <expand macro="param_target_mask"/> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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117 <expand macro="param_source_mask"/> |
0
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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118 </when> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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119 </conditional> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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120 <param name="min_scale_def" type="select" label="Initial deformation"> |
1
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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121 <option value="0" selected="true">Very Coarse</option> |
0
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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122 <option value="1">Coarse</option> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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123 <option value="2">Fine</option> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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124 <option value="3">Very Fine</option> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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125 </param> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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126 <param name="max_scale_def" type="select" label="Final deformation"> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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127 <option value="0">Very Coarse</option> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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128 <option value="1">Coarse</option> |
1
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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129 <option value="2" selected="true">Fine</option> |
0
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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130 <option value="3">Very Fine</option> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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131 </param> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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132 <param name="max_subsamp_fact" type="integer" value="0" min="0" label="Image sub-sample factor" help="Power of 2: [0, 1, 2 .. 7]"/> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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133 <param name="divergence_weight" type="float" value="0.0" label="Weight of the divergence term" help="Value is a floating point number"/> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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134 <param name="curl_weight" type="float" label="Weight of the curl term" value="0.0" help="Value is a floating point number"/> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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135 <param name="image_weight" type="float" label="Weight of the image term" value="1.0" help="Value is a floating point number"/> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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136 <param name="consistency_weight" type="float" label="Weight of the deformation consistency" value="10.0" help="Value is a floating point number"/> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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137 <param name="target_out_datatype" type="select" label="Save registered target image as format"> |
1
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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138 <expand macro="image_datatypes"/> |
0
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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139 </param> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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140 <param name="source_out_datatype" type="select" label="Save registered source image as format"> |
1
e9243cad1d67
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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141 <expand macro="image_datatypes"/> |
0
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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142 </param> |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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143 <!-- |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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144 The following additional options can be added to the advanced_options select |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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145 list as soon as appropriate. Their use is supported in the imagej2_bunwarp_align.py |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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146 wrapper. |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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147 |
ab54024c0a88
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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148 I invested heavily in working with landmarks, but could never get them to |
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149 produce the same results from both the ImageJ GUI and the command line. I'm |
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150 convinced this is not a result of using Galaxy as I tested using ImageJ in headless |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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151 mode outside of Galaxy and the results differed from using the ImageJ GUI. Until |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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152 we know the reasons for these differences, we will eliminate this option. |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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153 <option value="landmarks">Apply landmarks</option> |
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154 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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155 A separate tool will be needed to create an affine matrix transformation file, |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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156 so we'll eliminate this option until we have that tool. |
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157 <option value="affine">Apply affine matrix transformation</option> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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158 |
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159 Similar to landmarks, I could not get the ImageJ mono option to produce the same |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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160 results from the ImageJ GUI and in headless mode from the command line. |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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161 <option value="mono">Unidirectional registration (source to target)</option> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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162 --> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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163 <conditional name="advanced_options_cond"> |
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164 <param name="advanced_options" type="select" label="Advanced options" help="These are mutually exclusive for each execution"> |
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165 <option value="none" selected="true">None</option> |
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166 <option value="save_transformation">Save calculated transformations</option> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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167 </param> |
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168 <when value="none"/> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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169 <!-- |
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170 <when value="landmarks"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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171 <param name="landmarks_weight" type="float" label="Landmark weight" value="0.0" help="Value is a floating point number"/> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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172 <param format="txt" name="landmarks_file" type="data" label="Landmark file"/> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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173 </when> |
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174 <when value="affine"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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175 <param format="txt" name="target_affine_file" type="data" label="Initial target affine matrix transformation"/> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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176 <param format="txt" name="source_affine_file" type="data" label="Initial source affine matrix transformation"/> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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177 </when> |
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178 <when value="mono"/> |
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179 --> |
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180 <when value="save_transformation"/> |
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181 </conditional> |
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182 </inputs> |
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183 <outputs> |
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184 <data name="source_out" format="png" label="${tool.name} (registered source) ${on_string}"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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185 <actions> |
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186 <action type="format"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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187 <option type="from_param" name="source_out_datatype"/> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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188 </action> |
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189 </actions> |
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190 </data> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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191 <data name="target_out" format="png" label="${tool.name} (registered target) ${on_string}"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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192 <filter>advanced_options_cond['advanced_options'] != "mono"</filter> |
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193 <actions> |
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194 <action type="format"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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195 <option type="from_param" name="target_out_datatype"/> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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196 </action> |
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197 </actions> |
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198 </data> |
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199 <data format="txt" name="source_trans_out" label="${tool.name} (source transf matrix) ${on_string}"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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200 <filter>advanced_options_cond['advanced_options'] == "save_transformation"</filter> |
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201 </data> |
1
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202 <data format="txt" name="target_trans_out" label="${tool.name} (target transf matrix) ${on_string}"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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203 <filter>advanced_options_cond['advanced_options'] == "save_transformation"</filter> |
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204 </data> |
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205 </outputs> |
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206 <tests> |
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207 <test expect_num_outputs="2"> |
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208 <!-- Align two images without landmarks or mask and not saving transformation matrices --> |
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209 <expand macro="test_target_source_images"/> |
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210 <param name="max_subsamp_fact" value="1"/> |
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211 <output name="source_out" file="registered_source1_forced1cpu.png" compare="image_diff"/> |
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212 <output name="target_out" file="registered_target1_forced1cpu.png" compare="image_diff"/> |
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213 </test> |
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214 <test expect_num_outputs="4"> |
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215 <!-- Align two images without landmarks or mask, but saving transformation matrices --> |
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216 <expand macro="test_target_source_images"/> |
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217 <param name="max_subsamp_fact" value="1"/> |
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218 <param name="advanced_options" value="save_transformation"/> |
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219 <output name="source_out" file="registered_source1_forced1cpu.png" compare="image_diff"/> |
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220 <output name="target_out" file="registered_target1_forced1cpu.png" compare="image_diff"/> |
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221 <output name="source_trans_out" file="source_elastic_transformation_out.txt" compare="contains"/> |
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222 <output name="target_trans_out" file="target_elastic_transformation_out.txt" compare="contains"/> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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223 </test> |
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224 <test expect_num_outputs="2"> |
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225 <!-- Align two images without landmarks but with mask, not saving transformation matrices --> |
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226 <expand macro="test_target_source_images"/> |
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227 <param name="align_with_mask" value="yes"/> |
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228 <param name="target_mask" value="mask_white.png"/> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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229 <param name="source_mask" value="mask_ramp.gif"/> |
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230 <param name="max_subsamp_fact" value="1"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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231 <output name="source_out" file="registered_source2_forced1cpu.png" compare="image_diff"/> |
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232 <output name="target_out" file="registered_target2_forced1cpu.png" compare="image_diff"/> |
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233 </test> |
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234 </tests> |
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235 <help> |
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236 **What it does** |
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237 |
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238 <![CDATA[ |
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239 Performs a simultaneous registration of two images, A and B. Image A is elastically deformed |
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240 in order to look as similar as possible to image B, and, at the same time, the "inverse" |
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241 transformation (from B to A) is also calculated so a pseudo-invertibility of the final deformation |
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242 could be guaranteed. RGB Color images will be converted to grayscale during the registration |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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243 process but the resulting transformations will be applied to the original color images. |
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244 |
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245 Two images are produced: the deformed versions of A and B images. |
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246 |
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247 .. image:: ./static/images/bunwarpj_scheme.png |
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248 |
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249 Both selected images will work simultaneously as source and target, their tags are there only for the sake |
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250 of clarification. The registration mode is currently restricted to "Fast" ("Mono" has been eliminated for now). |
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251 The registration mode "Mono" perfoms only unidirectional registration, i.e. from source to target. The |
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252 registration mode "Fast" involve performing bidirectional registration and affects the stopping criteria |
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253 internally used by the bUnwarpJ program. |
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254 |
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255 Using the **Align with masks** otion, masks are introduced together with the input images. In this mode, the |
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256 input images is treated as the first slice of the mask pair and the mask is treated as the second slice. In this |
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257 way, the mask can have any shape. |
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258 |
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259 The **Initial deformation** and **Final deformation** options allow you to select the coarsest and finest scale |
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260 of the spline deformation field. "Very coarse" corresponds to 4 splines (one in each corner of the image). As you |
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261 increase the deformation level, the number of splines is doubled in each direction (horizontal and vertical). |
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262 |
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263 The value of the **Image sub-sample factor** will enable the registration to be calculated using the subsampled |
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264 versions of the images but the results will be applied to the original ones. The image subsampling parameter can |
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265 be set from 0 and 7, i.e. the image dimensions can be reduced by a factor of 20 = 1 to 27 = 128. This is very |
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266 useful when registering large images. |
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267 |
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268 The different weights of the goal function control the relative weight of each one of the terms. These weights |
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269 are not restricted to be between 0 and 1, and they may take any value as long as it is non-negative=2E. |
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270 |
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271 If the **Advanced option - Save transformation** option is selected, two files are produced in addition to |
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272 the registerd source and target images: the direct transformation matrix of A and the inverse transformation |
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273 matrix of B. |
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274 ]]> |
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275 |
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276 </help> |
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277 <expand macro="bunwarpj_citations"/> |
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278 </tool> |