Mercurial > repos > imgteam > imagej2_filter
annotate imagej2_macros.xml @ 0:e04905c22f5a 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 16:27:49 +0000 |
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e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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1 <macros> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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2 <token name="@TOOL_VERSION@">20240614</token> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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3 <token name="@VERSION_SUFFIX@">0</token> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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4 <xml name="fiji_requirements"> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
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5 <requirements> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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6 <requirement type="package" version="@TOOL_VERSION@">fiji</requirement> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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7 <requirement type="package" version="3.11">grep</requirement> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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8 </requirements> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
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9 </xml> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
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10 <xml name="image_type"> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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11 <param name="image_type" type="select" label="Image type"> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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12 <option value="8-bit_white" selected="true">8-bit white</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
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13 <option value="8-bit_black">8-bit black</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff
changeset
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14 <option value="8-bit_random">8-bit random</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff
changeset
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15 <option value="8-bit_ramp">8-bit ramp</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff
changeset
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16 <option value="16-bit_white">16-bit white</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff
changeset
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17 <option value="16-bit_black">16-bit black</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff
changeset
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18 <option value="16-bit_random">16-bit random</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff
changeset
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19 <option value="16-bit_ramp">16-bit ramp</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff
changeset
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20 <option value="32-bit_white">32-bit white</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff
changeset
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21 <option value="32-bit_black">32-bit black</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff
changeset
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22 <option value="32-bit_random">32-bit random</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff
changeset
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23 <option value="32-bit_ramp">32-bit ramp</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff
changeset
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24 <option value="RGB_white">RGB white</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff
changeset
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25 <option value="RGB_black">RGB black</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff
changeset
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26 <option value="RGB_random">RGB random</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff
changeset
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27 <option value="RGB_ramp">RGB ramp</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
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changeset
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28 </param> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff
changeset
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29 </xml> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
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30 <xml name="make_binary_params"> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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31 <param name="iterations" type="integer" value="1" min="1" max="100" label="Iterations" help="The number of times (1-100) erosion, dilation, opening, and closing are performed."/> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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32 <param name="count" type="integer" value="1" min="1" max="8" label="Count" help="The number of adjacent background pixels necessary (1-8) for erosion or dilation."/> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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33 <param name="black_background" type="select" label="Black background" help="If Yes, the background is black and the foreground is white (no implies the opposite)."> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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34 <option value="no" selected="true">No</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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35 <option value="yes">Yes</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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36 </param> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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37 <param name="pad_edges_when_eroding" type="select" label="Pad edges when eroding" help="If Yes, eroding does not erode from the edges of the image."> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
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38 <option value="no" selected="true">No</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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39 <option value="yes">Yes</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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40 </param> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
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41 </xml> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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42 <xml name="black_background_param"> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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43 <param name="black_background" type="select" label="Black background" help="If Yes, the background is black and the foreground is white (no implies the opposite)."> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
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44 <option value="no" selected="true">No</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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45 <option value="yes">Yes</option> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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46 </param> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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47 </xml> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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48 <xml name="param_input"> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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49 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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50 </xml> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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51 <xml name="param_source_image"> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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52 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
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53 </xml> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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54 <xml name="param_source_mask"> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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55 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_mask" type="data" label="Source mask"/> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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56 </xml> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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57 <xml name="param_target_image"> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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58 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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59 </xml> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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60 <xml name="param_target_mask"> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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61 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_mask" type="data" label="Target mask"/> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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62 </xml> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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63 <xml name="test_bunwarpj_raw_transform"> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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64 <param name="target_image" value="dotblot.jpg"/> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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65 <param name="source_image" value="blobs.gif"/> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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66 <param name="target_raw_transformation" value="target_raw_transformation.txt"/> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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67 <param name="source_raw_transformation" value="source_raw_transformation.txt"/> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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68 </xml> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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69 <xml name="test_target_source_images"> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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70 <param name="target_image" value="dotblot.jpg"/> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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71 <param name="source_image" value="blobs.gif"/> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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72 </xml> |
e04905c22f5a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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73 <token name="@make_binary_args@"> |
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74 --iterations $iterations |
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75 --count $count |
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76 --black_background $black_background |
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77 --pad_edges_when_eroding $pad_edges_when_eroding |
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78 </token> |
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79 <token name="@requires_binary_input@"> |
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80 .. class:: warningmark |
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81 |
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82 This tool works on binary images, so other image types will automatically be converted to binary |
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83 before they are analyzed. This step is performed using the ImageJ2 **Make Binary** command with |
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84 the following settings: **Iterations:** 1, **Count:** 1, **Pad edges when eroding:** No. The tool |
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85 allows you to choose the **Black background** setting. If these settings are not appropriate, |
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86 first manually convert the image to binary using the **Convert to binary (black and white)** |
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87 tool, which allows you to change them. |
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88 </token> |
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89 <xml name="image_datatypes"> |
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90 <option value="bmp">bmp</option> |
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91 <option value="gif">gif</option> |
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92 <option value="jpg">jpg</option> |
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93 <option value="png" selected="true">png</option> |
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94 <option value="tiff">tiff</option> |
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95 </xml> |
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96 <xml name="bunwarpj_citations"> |
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97 <citations> |
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98 <citation type="bibtex"> |
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99 @InProceedings(Arganda-Carreras2006, |
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100 author = "Ignacio Arganda-Carreras and |
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101 Carlos Oscar S{\'a}nchez Sorzano and |
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102 Roberto Marabini and |
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103 Jos{\'e} Mar\'{\i}a Carazo and |
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104 Carlos Ortiz-de-Solorzano and |
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105 Jan Kybic", |
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106 title = "Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization", |
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107 publisher = "Springer Berlin / Heidelberg", |
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108 booktitle = "Computer Vision Approaches to Medical Image Analysis", |
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109 series = "Lecture Notes in Computer Science", |
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110 year = "2006", |
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111 volume = "4241", |
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112 pages = "85-95", |
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113 month = "May", |
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114 city = "Graz, Austria") |
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115 </citation> |
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116 <citation type="doi">10.1038/nmeth.2019</citation> |
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117 </citations> |
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118 </xml> |
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119 <xml name="fiji_headless_citations"> |
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120 <citations> |
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121 <citation type="doi">10.1038/nmeth.2102</citation> |
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122 </citations> |
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123 </xml> |
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124 </macros> |