Mercurial > repos > imgteam > 2d_auto_threshold

annotate auto_threshold.xml @ 5:7db4fc31dbee draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
author imgteam
date Mon, 11 Mar 2024 17:12:33 +0000
parents 3df9f0a4bf34
children 8bccb36e055a
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5
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
imgteam
parents: 4
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1 <tool id="ip_threshold" name="Threshold image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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2 <description>with scikit-image</description>
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7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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3 <macros>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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4 <token name="@TOOL_VERSION@">0.18.1</token>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
imgteam
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5 <token name="@VERSION_SUFFIX@">0</token>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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6 </macros>
4
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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7 <edam_operations>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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8 <edam_operation>operation_3443</edam_operation>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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9 </edam_operations>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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10 <xrefs>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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11 <xref type="bio.tools">scikit-image</xref>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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12 <xref type="biii">scikit-image</xref>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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13 </xrefs>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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14 <requirements>
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15 <requirement type="package" version="0.18.1">scikit-image</requirement>
0c777d708acc "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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16 <requirement type="package" version="2020.10.1">tifffile</requirement>
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3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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17 </requirements>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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18 <command detect_errors="aggressive">
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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19 <![CDATA[
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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20 python '$__tool_directory__/auto_threshold.py'
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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21 '$input'
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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22 ./out.tif
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7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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23 '$th_method.method_id'
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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24 '$th_method.block_size'
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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25 '$th_method.threshold'
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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26 '$invert_output'
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3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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27 ]]>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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28 </command>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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29 <inputs>
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0c777d708acc "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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30 <param name="input" type="data" format="tiff,png" label="Input image" />
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7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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31 <conditional name="th_method">
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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32 <param name="method_id" type="select" label="Thresholding method">
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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33 <option value="manual">Manual</option>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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34 <option value="otsu" selected="True">Globally adaptive / Otsu</option>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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35 <option value="li">Globally adaptive / Li's Minimum Cross Entropy</option>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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36 <option value="isodata">Globally adaptive / Isodata</option>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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37 <option value="yen">Globally adaptive / Yen</option>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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38 <option value="loc_gaussian">Locally adaptive / Gaussian</option>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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39 <option value="loc_median">Locally adaptive / Median</option>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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40 <option value="loc_mean">Locally adaptive / Mean</option>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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41 </param>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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42 <when value="manual">
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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43 <param name="threshold" type="float" value="0" label="Threshold value" />
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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44 <param name="block_size" type="hidden" value="0" />
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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45 </when>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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46 <when value="otsu">
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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47 <param name="threshold" type="hidden" value="0" />
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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48 <param name="block_size" type="hidden" value="0" />
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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49 </when>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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50 <when value="li">
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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51 <param name="threshold" type="hidden" value="0" />
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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52 <param name="block_size" type="hidden" value="0" />
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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53 </when>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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54 <when value="isodata">
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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55 <param name="threshold" type="hidden" value="0" />
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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56 <param name="block_size" type="hidden" value="0" />
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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57 </when>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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58 <when value="yen">
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59 <param name="threshold" type="hidden" value="0" />
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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60 <param name="block_size" type="hidden" value="0" />
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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61 </when>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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62 <when value="loc_gaussian">
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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63 <param name="threshold" type="hidden" value="0" />
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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64 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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65 </when>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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66 <when value="loc_median">
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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67 <param name="threshold" type="hidden" value="0" />
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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68 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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69 </when>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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70 <when value="loc_mean">
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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71 <param name="threshold" type="hidden" value="0" />
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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72 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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73 </when>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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74 </conditional>
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75 <param name="invert_output" type="boolean" checked="false" truevalue="True" falsevalue="False" label="Invert output labels" help="Pixels are usually assigned the label 0 if the pixel value is below (or equal to) the threshold, and 255 if it is above the threshold. If this option is activated, pixels are assigned the label 255 if the pixel value is below (or equal to) the threshold, and 0 if it is above the threshold." />
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d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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76 </inputs>
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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77 <outputs>
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78 <data format="tiff" name="output" from_work_dir="out.tif" />
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79 </outputs>
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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80 <tests>
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81 <test>
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82 <param name="input" value="sample.tif"/>
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83 <output name="output" value="out.tif" ftype="tiff" compare="sim_size" delta="10"/>
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84 <param name="method_id" value="loc_gaussian"/>
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85 <param name="block_size" value="3"/>
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86 <param name="invert_output" value="False"/>
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87 </test>
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88 <test>
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89 <param name="input" value="sample.tif"/>
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90 <output name="output" value="out2.tif" ftype="tiff" compare="sim_size" delta="10"/>
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91 <param name="method_id" value="otsu"/>
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92 <param name="block_size" value="5"/>
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93 <param name="invert_output" value="False"/>
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94 </test>
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95 <test>
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96 <param name="input" value="sample.tif"/>
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97 <output name="output" value="out3.tif" ftype="tiff" compare="sim_size" delta="10"/>
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98 <param name="method_id" value="manual"/>
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99 <param name="threshold" value="64"/>
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100 <param name="invert_output" value="True"/>
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101 </test>
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102 </tests>
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103 <help>
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104 Applies a standard thresholding algorithm to an image.
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105
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106 The thresholding algorithm automatically determines a threshold value (unless manual thresholding is used).
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107 The input image is then thresholded, by assigning white (pixel value 255) to image regions above the determined threshold,
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108 and black (pixel value 0) to image regions below or equal to the determined threshold.
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109
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110 The assignment of black and white to image regions below and above the threshold is inverted, if the corresponding option is set.
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111 </help>
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112 <citations>
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113 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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114 </citations>
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115 </tool>