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annotate coordinates_of_roi.xml @ 0:0d30ffea8874 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:33:43 -0500
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0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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1 <tool id="ip_coordinates_of_roi" name="Coordinates of ROI" version="0.0.3">
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="0.14.2">scikit-image</requirement>
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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5 <requirement type="package" version="0.23.4">pandas</requirement>
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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6 </requirements>
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7 <command detect_errors="aggressive">
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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8 <![CDATA[
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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9 python '$__tool_directory__/coordinates_of_roi.py'
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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10 '$im'
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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11 '$pixel_table'
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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12 $offset_x $offset_y
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 $white_obj
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14 --threshold $threshold
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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15 ]]>
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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16 </command>
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17 <inputs>
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18 <param name="im" type="data" format="png" label="Source file" />
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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19 <param name="white_obj" type="boolean" truevalue="--white_obj" falsevalue="" checked="false"
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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20 label="Set to Yes if object is white and background black, otherwise set to No" />
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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21 <param name="threshold" type="float" value="0.5" label="Threshold value" />
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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22 <param name="offset_x" type="integer" value="0" label="Added offset in x direction (=width direction)" />
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23 <param name="offset_y" type="integer" value="0" label="Added offset in y direction (=height direction)" />
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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24 </inputs>
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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25 <outputs>
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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26 <data format="tabular" name="pixel_table" />
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 </outputs>
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28 <tests>
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29 <test>
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 <param name="im" value="test.png"/>
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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31 <param name="white_obj" value="true"/>
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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32 <output name="pixel_table" value="table.tsv" ftype="tabular"/>
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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33 </test>
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34 <test>
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35 <param name="im" value="test.png"/>
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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36 <param name="white_obj" value="true"/>
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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37 <param name="offset_x" value="1"/>
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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38 <param name="offset_y" value="2"/>
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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39 <output name="pixel_table" value="table2.tsv" ftype="tabular"/>
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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40 </test>
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41 </tests>
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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42 <help>
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43 **What it does**
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44
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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45 This tool creates a table containing the pixelcoordinates of the Region of Interest (ROI).
0d30ffea8874 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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46 </help>
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47 <citations>
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48 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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49 </citations>
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50 </tool>