Mercurial > repos > imgteam > imagej2_analyze_skeleton
annotate imagej2_macros.xml @ 1:3272e0439968 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author | imgteam |
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date | Mon, 28 Sep 2020 16:52:29 +0000 |
parents | bb84f130a4e1 |
children | 50f2b961b192 |
rev | line source |
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0
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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1 <macros> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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2 <token name="@WRAPPER_VERSION@">3.0</token> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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3 <xml name="fiji_requirements"> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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4 <requirements> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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5 <requirement type="package" version="20170530">fiji</requirement> |
1
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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6 <requirement type="package" version="3.4">grep</requirement> |
0
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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7 </requirements> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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8 </xml> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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9 <xml name="stdio"> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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10 <stdio> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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11 <exit_code range="1:"/> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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12 <exit_code range=":-1"/> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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13 <regex match="Error:"/> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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14 <regex match="Exception:"/> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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changeset
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15 </stdio> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
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16 </xml> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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changeset
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17 <xml name="image_type"> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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changeset
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18 <param name="image_type" type="select" label="Image type"> |
1
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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19 <option value="8-bit_white" selected="true">8-bit white</option> |
0
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
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20 <option value="8-bit_black">8-bit black</option> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
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21 <option value="8-bit_random">8-bit random</option> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
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22 <option value="8-bit_ramp">8-bit ramp</option> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
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23 <option value="16-bit_white">16-bit white</option> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
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24 <option value="16-bit_black">16-bit black</option> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
|
25 <option value="16-bit_random">16-bit random</option> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
|
26 <option value="16-bit_ramp">16-bit ramp</option> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
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27 <option value="32-bit_white">32-bit white</option> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
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28 <option value="32-bit_black">32-bit black</option> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
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29 <option value="32-bit_random">32-bit random</option> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
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30 <option value="32-bit_ramp">32-bit ramp</option> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
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31 <option value="RGB_white">RGB white</option> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
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32 <option value="RGB_black">RGB black</option> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
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33 <option value="RGB_random">RGB random</option> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
changeset
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34 <option value="RGB_ramp">RGB ramp</option> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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changeset
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35 </param> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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36 </xml> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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37 <xml name="make_binary_params"> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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38 <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."/> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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39 <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."/> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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40 <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)."> |
1
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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41 <option value="no" selected="true">No</option> |
0
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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42 <option value="yes">Yes</option> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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43 </param> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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44 <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."> |
1
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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45 <option value="no" selected="true">No</option> |
0
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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46 <option value="yes">Yes</option> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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47 </param> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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48 </xml> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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49 <xml name="black_background_param"> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff
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50 <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)."> |
1
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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51 <option value="no" selected="true">No</option> |
0
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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52 <option value="yes">Yes</option> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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53 </param> |
bb84f130a4e1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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54 </xml> |
1
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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55 <xml name="param_input"> |
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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56 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/> |
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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57 </xml> |
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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58 <xml name="param_source_image"> |
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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59 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/> |
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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60 </xml> |
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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61 <xml name="param_source_mask"> |
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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62 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_mask" type="data" label="Source mask"/> |
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
0
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63 </xml> |
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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64 <xml name="param_target_image"> |
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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65 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/> |
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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66 </xml> |
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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67 <xml name="param_target_mask"> |
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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68 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_mask" type="data" label="Target mask"/> |
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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69 </xml> |
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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70 <xml name="test_bunwarpj_raw_transform"> |
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents:
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71 <param name="target_image" value="dotblot.jpg"/> |
3272e0439968
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
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72 <param name="source_image" value="blobs.gif"/> |
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73 <param name="target_raw_transformation" value="target_raw_transformation.txt"/> |
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74 <param name="source_raw_transformation" value="source_raw_transformation.txt"/> |
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75 </xml> |
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76 <xml name="test_target_source_images"> |
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77 <param name="target_image" value="dotblot.jpg"/> |
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78 <param name="source_image" value="blobs.gif"/> |
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79 </xml> |
0
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80 <token name="@make_binary_args@"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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81 --iterations $iterations |
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82 --count $count |
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83 --black_background $black_background |
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84 --pad_edges_when_eroding $pad_edges_when_eroding |
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85 </token> |
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86 <token name="@requires_binary_input@"> |
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87 .. class:: warningmark |
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88 |
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89 This tool works on binary images, so other image types will automatically be converted to binary |
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90 before they are analyzed. This step is performed using the ImageJ2 **Make Binary** command with |
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91 the following settings: **Iterations:** 1, **Count:** 1, **Pad edges when eroding:** No. The tool |
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92 allows you to choose the **Black background** setting. If these settings are not appropriate, |
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93 first manually convert the image to binary using the **Convert to binary (black and white)** |
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94 tool, which allows you to change them. |
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95 </token> |
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96 <xml name="image_datatypes"> |
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97 <option value="bmp">bmp</option> |
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98 <option value="gif">gif</option> |
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99 <option value="jpg">jpg</option> |
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100 <option value="png" selected="true">png</option> |
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101 <option value="tiff">tiff</option> |
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102 </xml> |
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103 <xml name="bunwarpj_citations"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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104 <citations> |
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105 <citation type="bibtex"> |
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106 @InProceedings(Arganda-Carreras2006, |
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107 author = "Ignacio Arganda-Carreras and |
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108 Carlos Oscar S{\'a}nchez Sorzano and |
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109 Roberto Marabini and |
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110 Jos{\'e} Mar\'{\i}a Carazo and |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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111 Carlos Ortiz-de-Solorzano and |
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112 Jan Kybic", |
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113 title = "Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization", |
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114 publisher = "Springer Berlin / Heidelberg", |
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115 booktitle = "Computer Vision Approaches to Medical Image Analysis", |
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116 series = "Lecture Notes in Computer Science", |
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117 year = "2006", |
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118 volume = "4241", |
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119 pages = "85-95", |
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120 month = "May", |
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121 city = "Graz, Austria") |
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122 </citation> |
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123 <citation type="doi">10.1038/nmeth.2019</citation> |
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124 </citations> |
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125 </xml> |
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126 <xml name="fiji_headless_citations"> |
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127 <citations> |
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128 <citation type="doi">10.1038/nmeth.2102</citation> |
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129 </citations> |
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130 </xml> |
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131 </macros> |