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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
author thomaswollmann
date Mon, 07 Jan 2019 04:57:18 -0500
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568e9a4e05e5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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1 <?xml version="1.0"?>
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2 <tool name="Overlay Segmentation Mask" id="ip_overlay_segmentation" version="0.0.6">
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3 <description>Overlay Segmentation Mask</description>
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4 <requirements>
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5 <requirement type="package" version="0.14.0">scikit-image</requirement>
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6 <requirement type="package" version="3.0.2">matplotlib</requirement>
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7 <requirement type="package" version="5.3.0">pillow</requirement>
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8 <requirement type="package" version="0.10.0">tifffile</requirement>
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9 </requirements>
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10 <stdio>
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11 <exit_code level="fatal" range="1:"/>
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12 </stdio>
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13 <command interpreter="python"><![CDATA[overlay_segmentation_mask.py
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14 $greyscale
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15 #if str($label_option.label) == '--label'
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16 --label --label_color '$label_option.label_color'
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17 #end if
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18 --thickness $thickness
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19 --stroke_color '$stroke_color'
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20 '$input_image' '$input_mask' ./tmp.png
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21 && mv ./tmp.png '$output'
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22 ]]>
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23 </command>
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24 <inputs>
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25 <param name="input_image" type="data" label="Image Source File" format="tif,bmp,jpg,png"/>
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26 <param name="input_mask" type="data" label="Mask Source File" format="tif,bmp,jpg,png"/>
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27 <param name="greyscale" type="boolean" checked='true' truevalue='--grey' falsevalue='' label="Image Is Greyscale" />
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28 <param name="thickness" size="4" type="float" value="0.3" label="Thickness" />
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29 <param name="stroke_color" type="color" value="#ff0000" label="Stroke Color"/>
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30 <conditional name="label_option">
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31 <param name="label" type="boolean" checked='false' truevalue='--label' falsevalue='' label="Plot Labels" />
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32 <when value=""> </when>
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33 <when value="--label">
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34 <param name="label_color" type="color" value="#ffff00" label="Label Color"/>
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35 </when>
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36 </conditional>
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37 </inputs>
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38 <outputs>
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39 <data format="png" name="output" />
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40 </outputs>
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41 <tests>
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42 <test>
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43 <conditional name="label_option">
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44 <param name="label" value="--label"/>
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45 <param name="label_color" value="#ffff00"/>
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46 </conditional>
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47 <param name="stroke_color" value="#ffaa00"/>
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48 <param name="label_option['label']" value="--label"/>
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49 <param name="input_image" value="sample.tif"/>
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50 <param name="input_mask" value="sample_seg.tif"/>
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51 <param name="greyscale" value="--grey"/>
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52 <output name="output" value="outt.png" ftype="png" compare="sim_size"/>
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53 </test>
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54 </tests>
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55 <help>
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56 This tool overlays a segmentation mask over an image.
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57 </help>
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58 <citations>
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59 <citation type="doi">10.7717/peerj.453</citation>
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60 </citations>
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61 </tool>