Mercurial > repos > thomaswollmann > coordinates_of_roi
annotate coordinates_of_roi.xml @ 0:3cbb8ae57f5b draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
author | thomaswollmann |
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date | Wed, 16 Jan 2019 15:34:10 -0500 |
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3cbb8ae57f5b
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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1 <?xml version="1.0"?> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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2 <tool name="Coordinates of ROI" id="ia_coordinates_of_roi" version="0.0.3"> |
3cbb8ae57f5b
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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3 <description>Coordinates of ROI</description> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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4 <requirements> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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5 <requirement type="package" version="0.14.0">scikit-image</requirement> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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6 <requirement type="package" version="0.23.4">pandas</requirement> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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7 </requirements> |
3cbb8ae57f5b
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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8 <command detect_errors="aggressive"> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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9 <![CDATA[ |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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10 python '$__tool_directory__/coordinates_of_roi.py' |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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11 '$im' |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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12 '$pixel_table' |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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13 $offset_x $offset_y |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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14 $white_obj |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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15 --threshold $threshold |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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16 ]]> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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17 </command> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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18 <inputs> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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19 <param name="im" type="data" format="png" label="Source file" /> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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20 <param name="white_obj" type="boolean" truevalue="--white_obj" falsevalue="" checked="false" label="Set to Yes if object is white and background black, otherwise set to No" /> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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21 <param name="threshold" type="float" value="0.5" label="Threshold value" /> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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22 <param name="offset_x" type="integer" value="0" label="Added offset in x direction (=width direction)" /> |
3cbb8ae57f5b
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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23 <param name="offset_y" type="integer" value="0" label="Added offset in y direction (=height direction)" /> |
3cbb8ae57f5b
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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24 </inputs> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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25 <outputs> |
3cbb8ae57f5b
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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26 <data format="tabular" name="pixel_table" /> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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27 </outputs> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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28 <tests> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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29 <test> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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30 <param name="im" value="test.png"/> |
3cbb8ae57f5b
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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31 <param name="white_obj" value="true"/> |
3cbb8ae57f5b
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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32 <output name="pixel_table" value="table.csv" ftype="tabular"/> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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33 </test> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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34 <test> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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35 <param name="im" value="test.png"/> |
3cbb8ae57f5b
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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36 <param name="white_obj" value="true"/> |
3cbb8ae57f5b
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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37 <param name="offset_x" value="1"/> |
3cbb8ae57f5b
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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38 <param name="offset_y" value="2"/> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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39 <output name="pixel_table" value="table2.csv" ftype="tabular"/> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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40 </test> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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41 </tests> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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42 <help> |
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43 This tool creates a table containing the pixelcoordinates of the Region of Interest (ROI). |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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44 </help> |
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45 <citations> |
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46 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> |
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47 </citations> |
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48 </tool> |