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annotate overlay_segmentation_mask.xml @ 1:8077f714ad94 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit b2acc1845a25828181597fe5b6982fe116a7796d
author imgteam
date Mon, 22 Jul 2019 04:58:02 -0400
parents 9e67f52b3eaf
children 4c01cc565771
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8077f714ad94 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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1 <tool id="ip_overlay_segmentation" name="Overlay Segmentation Mask" version="0.0.6">
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9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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2 <description>Overlay Segmentation Mask</description>
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3 <requirements>
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8077f714ad94 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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4 <requirement type="package" version="0.14.2">scikit-image</requirement>
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9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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5 <requirement type="package" version="3.0.2">matplotlib</requirement>
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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6 <requirement type="package" version="5.3.0">pillow</requirement>
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8077f714ad94 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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7 <requirement type="package" version="0.15.1">tifffile</requirement>
8077f714ad94 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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8 <requirement type="package" version="1.16.0">numpy</requirement>
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9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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9 </requirements>
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10 <command detect_errors="aggressive"><![CDATA[
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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11 python '$__tool_directory__/overlay_segmentation_mask.py'
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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12 $greyscale
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13 #if str($label_option.label) == '--label'
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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14 --label --label_color '$label_option.label_color'
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15 #end if
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16 --thickness $thickness
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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17 --stroke_color '$stroke_color'
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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18 '$input_image' '$input_mask' ./tmp.png
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19 ]]>
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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20 </command>
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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21 <inputs>
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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22 <param name="input_image" type="data" label="Image Source File" format="tif,bmp,jpg,png"/>
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23 <param name="input_mask" type="data" label="Mask Source File" format="tif,bmp,jpg,png"/>
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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24 <param name="greyscale" type="boolean" checked='true' truevalue='--grey' falsevalue='' label="Image Is Greyscale" />
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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25 <param name="thickness" size="4" type="float" value="0.3" label="Thickness" />
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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26 <param name="stroke_color" type="color" value="#ff0000" label="Stroke Color"/>
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 <conditional name="label_option">
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28 <param name="label" type="boolean" checked='false' truevalue='--label' falsevalue='' label="Plot Labels" />
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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29 <when value=""> </when>
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 <when value="--label">
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31 <param name="label_color" type="color" value="#ffff00" label="Label Color"/>
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32 </when>
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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33 </conditional>
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34 </inputs>
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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35 <outputs>
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36 <data format="png" name="output" from_work_dir="tmp.png" />
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37 </outputs>
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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38 <tests>
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39 <test>
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40 <conditional name="label_option">
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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41 <param name="label" value="--label"/>
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42 <param name="label_color" value="#ffff00"/>
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43 </conditional>
9e67f52b3eaf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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44 <param name="stroke_color" value="#ffaa00"/>
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45 <param name="label_option['label']" value="--label"/>
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46 <param name="input_image" value="sample.tif"/>
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47 <param name="input_mask" value="sample_seg.tif"/>
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48 <param name="greyscale" value="--grey"/>
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49 <output name="output" value="outt.png" ftype="png" compare="sim_size"/>
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50 </test>
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51 </tests>
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52 <help>
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53 **What it does**
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54
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55 This tool overlays a segmentation mask over an image.
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56 </help>
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57 <citations>
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58 <citation type="doi">10.7717/peerj.453</citation>
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59 </citations>
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60 </tool>