Mercurial > repos > imgteam > morphological_operations
annotate morphological_operations.xml @ 0:f10112b317a1 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
| author | imgteam |
|---|---|
| date | Fri, 08 Mar 2024 11:00:41 +0000 |
| parents | |
| children | ad795d260ba8 |
| rev | line source |
|---|---|
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0
f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
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1 <tool id="morphological_operations" name="Apply a morphological operation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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2 <description>with SciPy</description> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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3 <macros> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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4 <token name="@TOOL_VERSION@">1.12.0</token> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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5 <token name="@VERSION_SUFFIX@">0</token> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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6 </macros> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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7 <edam_operations> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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8 <edam_operation>operation_3443</edam_operation> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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9 </edam_operations> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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10 <xrefs> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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11 <xref type="biii">scipy</xref> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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changeset
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12 </xrefs> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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13 <requirements> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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14 <requirement type="package" version="1.12.0">scipy</requirement> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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15 <requirement type="package" version="0.22.0">scikit-image</requirement> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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16 </requirements> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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17 <command><![CDATA[ |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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18 |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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19 ## Inputs |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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20 |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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21 python '$__tool_directory__/morphological_operations.py' '$image' |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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22 --operation $operation |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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23 --selem-shape $selem_shape |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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24 --selem-size $selem_size |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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25 |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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26 ## Outputs |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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27 |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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28 ./result.tiff |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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29 |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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30 ]]> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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31 </command> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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32 <inputs> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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33 <param name="image" type="data" format="png,tiff" label="Input image" /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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34 <param label="Morphological operation" argument="--operation" type="select"> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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35 <option value="erosion" selected="True">Erosion</option> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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36 <option value="dilation">Dilation</option> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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37 <option value="opening">Opening</option> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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38 <option value="closing">Closing</option> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
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39 <option value="fill_holes">Fill holes</option> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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40 </param> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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41 <param label="Structuring element" argument="--selem-shape" type="select"> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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42 <option value="disk" selected="True">Disk</option> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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43 <option value="square">Square</option> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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44 </param> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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45 <param label="Structuring element size" argument="--selem-size" type="integer" min="1" max="256" value="1" help="The radius of the disk, or the width of the square, in pixels." /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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46 </inputs> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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parents:
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47 <outputs> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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48 <data format="tiff" name="result" from_work_dir="result.tiff" /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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49 </outputs> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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parents:
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50 <tests> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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51 <!-- Test binary operations (input images with two distinct values) --> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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52 <test> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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53 <param name="image" value="input1.tiff" /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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54 <param name="operation" value="erosion" /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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parents:
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55 <param name="selem_shape" value="disk" /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
imgteam
parents:
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56 <param name="selem_size" value="1" /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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57 <output name="result" value="output1_erosion.tiff" ftype="tiff" compare="sim_size" delta="10" /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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58 </test> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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parents:
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59 <test> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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60 <param name="image" value="input1.tiff" /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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61 <param name="operation" value="dilation" /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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62 <param name="selem_shape" value="disk" /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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63 <param name="selem_size" value="2" /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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64 <output name="result" value="output1_dilation.tiff" ftype="tiff" compare="sim_size" delta="10" /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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65 </test> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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66 <test> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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67 <param name="image" value="input1.tiff" /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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68 <param name="operation" value="opening" /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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69 <param name="selem_shape" value="square" /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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70 <param name="selem_size" value="1" /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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71 <output name="result" value="output1_opening.tiff" ftype="tiff" compare="sim_size" delta="10" /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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72 </test> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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73 <test> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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74 <param name="image" value="input1.tiff" /> |
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f10112b317a1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
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75 <param name="operation" value="closing" /> |
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76 <param name="selem_shape" value="square" /> |
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77 <param name="selem_size" value="2" /> |
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78 <output name="result" value="output1_closing.tiff" ftype="tiff" compare="sim_size" delta="10" /> |
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79 </test> |
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80 <!-- Test intensity-based operations (more than two distinct values) --> |
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81 <test> |
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82 <param name="image" value="input3.png" /> |
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83 <param name="operation" value="erosion" /> |
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84 <param name="selem_shape" value="disk" /> |
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85 <param name="selem_size" value="1" /> |
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86 <output name="result" value="output3_erosion.tiff" ftype="tiff" compare="sim_size" delta="10" /> |
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87 </test> |
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88 <test> |
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89 <param name="image" value="input3.png" /> |
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90 <param name="operation" value="dilation" /> |
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91 <param name="selem_shape" value="disk" /> |
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92 <param name="selem_size" value="2" /> |
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93 <output name="result" value="output3_dilation.tiff" ftype="tiff" compare="sim_size" delta="10" /> |
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94 </test> |
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95 <test> |
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96 <param name="image" value="input3.png" /> |
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97 <param name="operation" value="opening" /> |
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98 <param name="selem_shape" value="square" /> |
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99 <param name="selem_size" value="1" /> |
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100 <output name="result" value="output3_opening.tiff" ftype="tiff" compare="sim_size" delta="10" /> |
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101 </test> |
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102 <test> |
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103 <param name="image" value="input3.png" /> |
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104 <param name="operation" value="closing" /> |
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105 <param name="selem_shape" value="square" /> |
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106 <param name="selem_size" value="2" /> |
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107 <output name="result" value="output3_closing.tiff" ftype="tiff" compare="sim_size" delta="10" /> |
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108 </test> |
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109 <!-- Test multi-channel image (with two distinct values per channel) --> |
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110 <test> |
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111 <param name="image" value="input2.png" /> |
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112 <param name="operation" value="fill_holes" /> |
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113 <param name="selem_shape" value="disk" /> |
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114 <param name="selem_size" value="1" /> |
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115 <output name="result" value="output2_fill_holes.tiff" ftype="tiff" compare="sim_size" delta="10" /> |
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116 </test> |
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117 </tests> |
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118 <help> |
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119 Applies a morphological operation to a 2-D image. |
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120 For multi-channel images, the operation is applied to each channel separately. |
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121 |
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122 The following operations are supported: |
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123 |
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124 - **Erosion:** Shrink bright areas. |
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125 - **Dilation:** Grow bright areas. |
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126 - **Opening:** Erosion followed by Dilation. Erases tiny bright spots. |
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127 - **Closing:** Dilation followed by Erosion. Erases tiny dark holes. |
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128 - **Fill holes:** Fills the holes (dark areas) in binary images. |
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129 </help> |
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130 <citations> |
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131 <citation type="doi">10.1038/s41592-019-0686-2</citation> |
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132 </citations> |
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133 </tool> |