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annotate auto_threshold.xml @ 2:f40e5d11eb47 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 09:55:34 +0000
parents 7f2962f619e3
children 5224cc463a97
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7f2962f619e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit 8a2a5763d1ac38b3c7974bd7c2da4d5c1101a0a9
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1 <tool id="ip_threshold" name="Auto Threshold" version="0.0.4">
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6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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2 <description>applies a standard threshold algorithm to an image</description>
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7f2962f619e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit 8a2a5763d1ac38b3c7974bd7c2da4d5c1101a0a9
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3 <requirements>
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4 <requirement type="package" version="0.14.2">scikit-image</requirement>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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5 <requirement type="package" version="1.15.4">numpy</requirement>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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6 <requirement type="package" version="5.3.0">pillow</requirement>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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7 <requirement type="package" version="0.15.1">tifffile</requirement>
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8 </requirements>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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9 <command detect_errors="aggressive">
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10 <![CDATA[
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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11 python '$__tool_directory__/auto_threshold.py' '$input' '$output' $thresh_type $dark_background
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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12 ]]>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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13 </command>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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14 <inputs>
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15 <param name="input" type="data" format="tiff" label="Source file" />
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16 <param name="thresh_type" type="select" label="Threshold Algorithm">
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17 <option value="otsu" selected="True">Otsu</option>
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18 <option value="li">Li’s Minimum Cross Entropy</option>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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19 <option value="isodata">Isodata</option>
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20 <option value="gaussian_adaptive">Adaptive (Gauss)</option>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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21 <option value="mean_adaptive">Adaptive (Mean)</option>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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22 <option value="yen">Yen</option>
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23 </param>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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24 <param name="dark_background" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Dark Background" />
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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25 </inputs>
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26 <outputs>
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27 <data format="tiff" name="output" />
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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28 </outputs>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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29 <tests>
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30 <test>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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31 <param name="input" value="sample.tif"/>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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32 <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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33 <param name="thresh_type" value="gaussian_adaptive"/>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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34 <param name="dark_backgroud" value="True"/>
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35 </test>
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36 <test>
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37 <param name="input" value="sample.tif"/>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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38 <output name="output" value="out2.tif" ftype="tiff" compare="sim_size"/>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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39 <param name="thresh_type" value="otsu"/>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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40 <param name="dark_backgroud" value="True"/>
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41 </test>
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42 </tests>
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43 <help>
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44 Applies a standard threshold algorithm to an image.
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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45 </help>
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46 <citations>
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47 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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48 </citations>
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49 </tool>