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annotate auto_local_threshold.xml @ 0:a20c14eb5f98 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
author imgteam
date Thu, 18 Jul 2019 09:22:07 -0400
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a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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1 <tool id="ip_localthreshold" name="Local Threshold" version="0.0.1">
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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2 <description>applies a local threshold algorithm to an image</description>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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3 <requirements>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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4 <requirement type="package" version="0.14.2">scikit-image</requirement>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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5 <requirement type="package" version="1.15.4">numpy</requirement>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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6 <requirement type="package" version="5.3.0">pillow</requirement>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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7 <requirement type="package" version="0.15.1">tifffile</requirement>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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8 </requirements>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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9 <command detect_errors="aggressive">
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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10 <![CDATA[
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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11 python '$__tool_directory__/auto_local_threshold.py' '$input' '$output' $block_size $thresh_type $dark_background
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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12 ]]>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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13 </command>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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14 <inputs>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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15 <param name="input" type="data" format="tiff" label="Source file" />
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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16 <param name="thresh_type" type="select" label="Threshold Algorithm">
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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17 <option value="gaussian" selected="True">Gaussian</option>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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18 <option value="median">Median</option>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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19 <option value="mean">Mean</option>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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20 </param>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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21 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood which is used to calculate the threshold value" />
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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22 <param name="dark_background" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Dark Background" />
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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23 </inputs>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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24 <outputs>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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25 <data format="tiff" name="output" />
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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26 </outputs>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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27 <tests>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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28 <test>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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29 <param name="input" value="sample.tif"/>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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30 <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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31 <param name="thresh_type" value="gaussian"/>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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32 <param name="block_size" value="429"/>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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33 <param name="dark_backgroud" value="True"/>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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34 </test>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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35 </tests>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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36 <help>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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37 Applies a local threshold algorithm to an image.
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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38 </help>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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39 <citations>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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40 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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41 </citations>
a20c14eb5f98 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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42 </tool>