Mercurial > repos > imgteam > imagej2_bunwarpj_compare_elastic_raw

annotate test-data/regenerate_outputs.sh @ 3:da91b5eaf92d draft default tip

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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 16:16:58 +0000
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da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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1 source $(dirname $(dirname $(which conda)))/etc/profile.d/conda.sh
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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2 conda_env=mulled-v1-9e9e3735532d83dd44ff0f622055395263f964e81ca8113d4dfa7e133e3156bf
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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3 conda activate $conda_env
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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4 # Adjust threshold
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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5 # Test 1
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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6 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_adjust_threshold_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 0.0 255.0 'Default' 'red' 'no' 'tools/image_processing/imagej2/test-data/blobs_threshold_default.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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7 # Test 2
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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8 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_adjust_threshold_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 0.0 255.0 'Percentile' 'over_under' 'no' 'tools/image_processing/imagej2/test-data/blobs_threshold_percentile.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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9 # Test 3
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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10 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_adjust_threshold_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 0.0 255.0 'Huang' 'bw' 'yes' 'tools/image_processing/imagej2/test-data/blobs_threshold_huang_dark.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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11 # Test 4
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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12 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_adjust_threshold_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 8.0 255.0 'Manual' 'bw' 'no' 'tools/image_processing/imagej2/test-data/blobs_threshold_8-255.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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13 # Test 5
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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14 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_adjust_threshold_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 0.0 8.0 'Manual' 'bw' 'no' 'tools/image_processing/imagej2/test-data/blobs_threshold_0-8.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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15 # Test 6
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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16 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_adjust_threshold_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel.tif' 0.0 255.0 'Default' 'bw' 'yes' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_threshold_default.tiff' 'tiff'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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17
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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19 # Analyze particles
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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20 # Test 1
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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21 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_particles_binary_jython_script.py' '' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' '0-Infinity' 0.0 1.0 'Nothing' 'yes' 'no' 'no' '' '' 'tools/image_processing/imagej2/test-data/analyze_particles_nothing.tabular'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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22 # Test 2
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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23 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_particles_binary_jython_script.py' '' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' '0-Infinity' 0.0 1.0 'Outlines' 'no' 'no' 'no' 'tools/image_processing/imagej2/test-data/analyze_particles_outlines.gif' 'gif' ''
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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24 # Test 3
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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25 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_particles_binary_jython_script.py' '' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' '0-Infinity' 0.0 1.0 'Bare_Outlines' 'no' 'yes' 'yes' 'tools/image_processing/imagej2/test-data/analyze_particles_bareoutlines.gif' 'gif' ''
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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26 # Test 4
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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27 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_particles_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/analyze_particles_rois.tabular' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' '0-Infinity' 0.0 1.0 'Overlay_Masks' 'yes' 'no' 'no' 'tools/image_processing/imagej2/test-data/analyze_particles_overlaymasks.gif' 'gif' 'tools/image_processing/imagej2/test-data/analyze_particles_nothing.tabular'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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28 # Test 5
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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29 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_particles_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/confocal_analyze_particles_rois.tabular' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_threshold_default.tiff' 'yes' '0-Infinity' 0.0 1.0 'Overlay_Masks' 'yes' 'no' 'no' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_threshold_default_overlay_mask.tiff' 'tiff' 'tools/image_processing/imagej2/test-data/confocal_analyze_particles.tabular'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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31 # Skeleton
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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32 # Test 1
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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33 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_skeleton_jython_script.py' 'tools/image_processing/imagej2/test-data/skeletonized_blobs.gif' 'no' 'none' 'no' 'no' 'no' 'tools/image_processing/imagej2/test-data/basic.tabular'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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34 # Test 2
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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35 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_skeleton_jython_script.py' 'tools/image_processing/imagej2/test-data/skeletonized_clown.jpg' 'no' 'shortest_branch' 'no' 'no' 'no' 'tools/image_processing/imagej2/test-data/shortest_branch_basic.tabular'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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36 # Test 3
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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37 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_skeleton_jython_script.py' 'tools/image_processing/imagej2/test-data/skeletonized_blobs.gif' 'no' 'none' 'no' 'yes' 'no' 'tools/image_processing/imagej2/test-data/largest_shortest_path_basic.tabular'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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38 # Test 4
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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39 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_skeleton_jython_script.py' 'tools/image_processing/imagej2/test-data/skeletonized_clown.jpg' 'no' 'shortest_branch' 'no' 'yes' 'no' 'tools/image_processing/imagej2/test-data/shortest_branch_all_yes.tabular'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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41 # binary_to_edm
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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42 # Test 1
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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43 ImageJ --ij2 --headless --debug --jython '/home/ldelisle/Documents/mygit/galaxytools/tools/image_processing/imagej2/imagej2_binary_to_edm_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 1 1 'no' 'no' 'tools/image_processing/imagej2/test-data/blobs_edm.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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44 # Test 2
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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45 ImageJ --ij2 --headless --debug --jython '/home/ldelisle/Documents/mygit/galaxytools/tools/image_processing/imagej2/imagej2_binary_to_edm_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 10 3 'yes' 'yes' 'tools/image_processing/imagej2/test-data/blobs_black_edm.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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47 # bunwarpj_adapt_transform
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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48 # Test 1
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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49 bunwarpj -adapt_transform 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/source_elastic_transformation.txt' 'tools/image_processing/imagej2/test-data/adapted_transformation.txt' 2.0
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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51 # bunwarpj_align gets different outputs when the number of CPUS is contrainted.
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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52 # When galaxy uses docker, the CPUs are always constrainted.
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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53 # Currently the CPUS are fixed to 1 to ensure consistency.
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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54 # bunwarpj_align
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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55 # Outputs without CPU fixed:
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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56 # Test 1
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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57 bunwarpj -align 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'NULL' 'tools/image_processing/imagej2/test-data/blobs.gif' 'NULL' 0 2 1 0.0 0.0 1.0 10.0 'tools/image_processing/imagej2/test-data/registered_source1.png' 'tools/image_processing/imagej2/test-data/registered_target1.png'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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58 # Test 2
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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59 bunwarpj -align 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'NULL' 'tools/image_processing/imagej2/test-data/blobs.gif' 'NULL' 0 2 1 0.0 0.0 1.0 10.0 'tools/image_processing/imagej2/test-data/registered_source1.png' 'tools/image_processing/imagej2/test-data/registered_target1.png' '-save_transformation'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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60 mv 'tools/image_processing/imagej2/test-data/registered_source1_transf.txt' 'tools/image_processing/imagej2/test-data/source_elastic_transformation_out_full.txt'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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61 mv 'tools/image_processing/imagej2/test-data/registered_target1_transf.txt' 'tools/image_processing/imagej2/test-data/target_elastic_transformation_out_full.txt'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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62 # Test 3
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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63 bunwarpj -align 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/mask_white.png' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/mask_ramp.gif' 0 2 1 0.0 0.0 1.0 10.0 'tools/image_processing/imagej2/test-data/registered_source2.png' 'tools/image_processing/imagej2/test-data/registered_target2.png'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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64
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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65 # Outputs with CPU fixed to 1:
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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66 # Test 1
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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67 bunwarpj -XX:ActiveProcessorCount="1" -align 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'NULL' 'tools/image_processing/imagej2/test-data/blobs.gif' 'NULL' 0 2 1 0.0 0.0 1.0 10.0 'tools/image_processing/imagej2/test-data/registered_source1_forced1cpu.png' 'tools/image_processing/imagej2/test-data/registered_target1_forced1cpu.png'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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68 # Test 2
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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69 bunwarpj -XX:ActiveProcessorCount="1" -align 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'NULL' 'tools/image_processing/imagej2/test-data/blobs.gif' 'NULL' 0 2 1 0.0 0.0 1.0 10.0 'tools/image_processing/imagej2/test-data/registered_source1_forced1cpu.png' 'tools/image_processing/imagej2/test-data/registered_target1_forced1cpu.png' '-save_transformation'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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70 mv 'tools/image_processing/imagej2/test-data/registered_source1_forced1cpu_transf.txt' 'tools/image_processing/imagej2/test-data/source_elastic_transformation_forced1cpu_out_full.txt'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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71 mv 'tools/image_processing/imagej2/test-data/registered_target1_forced1cpu_transf.txt' 'tools/image_processing/imagej2/test-data/target_elastic_transformation_forced1cpu_out_full.txt'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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72 # Test 3
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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73 bunwarpj -XX:ActiveProcessorCount="1" -align 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/mask_white.png' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/mask_ramp.gif' 0 2 1 0.0 0.0 1.0 10.0 'tools/image_processing/imagej2/test-data/registered_source2_forced1cpu.png' 'tools/image_processing/imagej2/test-data/registered_target2_forced1cpu.png'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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74
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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75 # bunwarpj_compare_elastic_raw
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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76 # Test 1
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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77 bunwarpj -compare_elastic_raw 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/target_elastic_transformation.txt' 'tools/image_processing/imagej2/test-data/source_raw_transformation.txt' 'tools/image_processing/imagej2/test-data/warping_index_raw_full.txt' 2>&1 | tee 'output_log.txt' && grep -Po 'Warping index = \K[^ ]+' 'output_log.txt' > 'tools/image_processing/imagej2/test-data/warping_index_raw_full.txt'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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78
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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79 # bunwarpj_compare_elastic
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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80 bunwarpj -compare_elastic 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/target_elastic_transformation.txt' 'tools/image_processing/imagej2/test-data/source_elastic_transformation.txt' 2>&1 | tee 'output_log.txt' && grep -Po 'Warping index = \K[^ ]+' 'output_log.txt' > 'tools/image_processing/imagej2/test-data/warping_index.txt'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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81
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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82 # bunwarpj_compare_raw
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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83 # Test 1
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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84 bunwarpj -compare_raw 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/target_raw_transformation.txt' 'tools/image_processing/imagej2/test-data/source_raw_transformation.txt' 2>&1 | tee 'output_log.txt' && grep -Po 'Warping index = \K[^ ]+' 'output_log.txt' > 'tools/image_processing/imagej2/test-data/warping_index1_full.txt'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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85 # Test 2
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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86 bunwarpj -compare_raw 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/source_raw_transformation.txt' 'tools/image_processing/imagej2/test-data/source_raw_transformation.txt' 2>&1 | tee 'output_log.txt' && grep -Po 'Warping index = \K[^ ]+' 'output_log.txt' > 'tools/image_processing/imagej2/test-data/warping_index2.txt'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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87
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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88 # bunwarpj_compose_elastic
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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89 bunwarpj -compose_elastic 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/target_elastic_transformation.txt' 'tools/image_processing/imagej2/test-data/source_elastic_transformation.txt' 'tools/image_processing/imagej2/test-data/raw_transformation_full.txt'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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90
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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91 # bunwarpj_compose_raw_elastic
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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92 bunwarpj -compose_raw_elastic 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/target_raw_transformation.txt' 'tools/image_processing/imagej2/test-data/source_elastic_transformation.txt' 'tools/image_processing/imagej2/test-data/composed_raw_elastic_transformation_full.txt'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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93
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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94 # bunwarpj_compose_raw
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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95 bunwarpj -compose_raw 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/target_raw_transformation.txt' 'tools/image_processing/imagej2/test-data/source_raw_transformation.txt' 'tools/image_processing/imagej2/test-data/composed_raw_transformation_full.txt'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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96
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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97 # bunwarpj_convert_to_raw
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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98 bunwarpj -convert_to_raw 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/source_elastic_transformation.txt' 'tools/image_processing/imagej2/test-data/source_raw_transformation.txt'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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99
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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100 # bunwarpj_elastic_transform
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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101 bunwarpj -elastic_transform 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/blobs_direct_transf.txt' 'tools/image_processing/imagej2/test-data/elastic_trans_registered_source1.png'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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102
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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103 # bunwarpj_raw_transform
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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104 bunwarpj -raw_transform 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/source_raw_transformation.txt' 'tools/image_processing/imagej2/test-data/raw_trans_registered_source1.png'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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105
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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106 # Create image
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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107 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_create_image_jython_script.py' 'MyTitle' 256 256 1 '8-bit_ramp' 'tools/image_processing/imagej2/test-data/create_image1.jpg'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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108
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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109 # Crop
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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110 # Test 1
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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111 # ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_crop_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 0 0 0 0 1 0 1 0 1 0 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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112 # Test 2
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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113 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_crop_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 0 50 0 0 1 0 1 0 1 0 'tools/image_processing/imagej2/test-data/blobs_crop_width50.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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114 # Test 3
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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115 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_crop_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 0 0 50 0 1 0 1 0 1 0 'tools/image_processing/imagej2/test-data/blobs_crop_top50.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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116 # Test 4
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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117 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_crop_jython_script.py' 'tools/image_processing/imagej2/test-data/confocal-series-both-channels.tiff' 17 16 18 8 1 1 1 0 1 0 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_cropped.tiff' 'tiff'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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118 # Test 5
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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119 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_crop_jython_script.py' 'tools/image_processing/imagej2/test-data/confocal-series-both-channels.tiff' 17 16 18 8 1 0 1 1 1 0 'tools/image_processing/imagej2/test-data/confocal-series-both-channels_cropped_singleZ.tiff' 'tiff'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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120 # Test 6
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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121 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_crop_jython_script.py' 'tools/image_processing/imagej2/test-data/confocal-series-both-channels.tiff' 17 16 18 8 1 1 1 1 1 0 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_cropped_singleZ.tiff' 'tiff'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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122
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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123 # Enhance contrast
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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124 # Test 1
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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125 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_enhance_contrast_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'yes' 'None' 'no' 'tools/image_processing/imagej2/test-data/blobs_equalize.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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126 # Test 2
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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127 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_enhance_contrast_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' 6.2 'no' 'tools/image_processing/imagej2/test-data/blobs_saturate.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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128 # Test 3
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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129 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_enhance_contrast_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' 13.0 'yes' 'tools/image_processing/imagej2/test-data/blobs_normalize.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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130
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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131 # Filter
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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132 # Test 1
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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133 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_filter_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'gaussian_blur' 5.0 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/gaussian_blur.gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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134 # Test 2
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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135 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_filter_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'median' 2.5 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/median.gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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136 # Test 3
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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137 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_filter_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'unsharp_mask' 5.0 0.1 'None' 'None' 'tools/image_processing/imagej2/test-data/unsharp_mask.gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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138 # Test 4
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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139 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_filter_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'top_hat' 7.0 'None' 'light' 'dont' 'tools/image_processing/imagej2/test-data/top_hat.gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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140 # Test 5
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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141 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_filter_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'top_hat' 7.0 'None' '' '' 'tools/image_processing/imagej2/test-data/top_hat2.gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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142 # Test 6
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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143 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_filter_jython_script.py' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel.tif' 'tiff' 'gaussian_blur' 2.0 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_gaussian_blur.tiff'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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144
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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145 # Find edges
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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146 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_find_edges_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/blobs_find_edges.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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147
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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148 # Find maxima
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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149 # Test 1
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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150 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_find_maxima_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'yes' 'no' 10 'Single_Points' 'no' 'no' 'tools/image_processing/imagej2/test-data/blobs_single_points.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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151 # Test 2
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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152 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_find_maxima_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'yes' 'no' 13 'Maxima_Within_Tolerance' 'no' 'no' 'tools/image_processing/imagej2/test-data/blobs_tolerance.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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153 # Test 3
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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154 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_find_maxima_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'yes' 'no' 16 'Segmented_Particles' 'yes' 'no' 'tools/image_processing/imagej2/test-data/blobs_segmented.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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155 # Test 4
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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156 # ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_find_maxima_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'yes' 'no' 10 'List' 'no' 'no' 'tools/image_processing/imagej2/test-data/blobs_list.tabular' 'tabular'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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157 # Test 5
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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158 # ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_find_maxima_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'yes' 'no' 10 'Count' 'no' 'no' 'tools/image_processing/imagej2/test-data/blobs_count.tabular' 'tabular'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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159
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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160 # make binary
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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161 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_make_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/clown.jpg' 1 1 'no' 'no' 'tools/image_processing/imagej2/test-data/clown_binary.jpg' 'jpg'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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162
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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163 # Math
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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164 # Test 1
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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165 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_math_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'Multiply' 'None' 'None' 1.25 'tools/image_processing/imagej2/test-data/blobs_multiply.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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166 # Test 2
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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167 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_math_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'Min' 'None' 'None' 255.0 'tools/image_processing/imagej2/test-data/blobs_min.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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168 # Test 3
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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169 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_math_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'Log' 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/blobs_log.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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170 # Test 4
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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171 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_math_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'Square' 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/blobs_square.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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172 # Test 5
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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173 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_math_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'Macro' 'v=v+50*sin(d/17)' 'None' 'None' 'tools/image_processing/imagej2/test-data/blobs_macro.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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174
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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175 # Noise
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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176 # Test 1
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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177 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_noise_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'add_specified_noise' 5.0 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/add_specified_noise.gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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178 # Test 2
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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179 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_noise_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'despeckle' 'None' 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/despeckle.gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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180 # Test 3
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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181 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_noise_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'remove_outliers' 'None' '10.0' '1' 'Bright' 'tools/image_processing/imagej2/test-data/remove_outliers.gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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182 # Test 4 fails
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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183 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_noise_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'remove_nans' 'None' 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/remove_nans.gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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184
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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185 # Shadows
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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186 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_shadows_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'Northwest' 'tools/image_processing/imagej2/test-data/blobs_northwest.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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187
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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188 # Sharpen
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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189 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_sharpen_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/blobs_sharpen.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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190
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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191 # Skeletonized 3D
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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192 # Test 1
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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193 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_skeletonize3d_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' 'tools/image_processing/imagej2/test-data/skeletonized_blobs.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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194 # Test 2
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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195 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_skeletonize3d_jython_script.py' 'tools/image_processing/imagej2/test-data/clown.jpg' 'no' 'tools/image_processing/imagej2/test-data/skeletonized_clown.jpg' 'jpg'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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196
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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197 # Smooth
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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198 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_smooth_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/blobs_smooth.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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199
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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200 # Watershed
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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201 # Test 1
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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202 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_watershed_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' 'tools/image_processing/imagej2/test-data/blobs_watershed_binary.gif' 'gif'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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203 # Test 2
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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204 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_watershed_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_threshold_default.tiff' 'yes' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_default_threshold_watershed.tiff' 'tiff'