Mercurial > repos > imgteam > 2d_auto_threshold

comparison auto_threshold.xml @ 4:3df9f0a4bf34 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
author imgteam
date Fri, 10 Nov 2023 14:23:07 +0000
parents 0c777d708acc
children 7db4fc31dbee
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3:0c777d708acc 4:3df9f0a4bf34
1 <tool id="ip_threshold" name="Auto Threshold" version="0.0.5" profile="20.05"> 1 <tool id="ip_threshold" name="Threshold image" version="0.0.5-2" profile="20.05">
2 <description>applies a standard thresholding algorithm to an image</description> 2 <description>with scikit-image</description>
3 <requirements> 3 <edam_operations>
4 <edam_operation>operation_3443</edam_operation>
5 </edam_operations>
6 <xrefs>
7 <xref type="bio.tools">scikit-image</xref>
8 <xref type="biii">scikit-image</xref>
9 </xrefs>
10 <requirements>
4 <requirement type="package" version="0.18.1">scikit-image</requirement> 11 <requirement type="package" version="0.18.1">scikit-image</requirement>
5 <requirement type="package" version="2020.10.1">tifffile</requirement> 12 <requirement type="package" version="2020.10.1">tifffile</requirement>
6 </requirements> 13 </requirements>
7 <command detect_errors="aggressive"> 14 <command detect_errors="aggressive">
8 <![CDATA[ 15 <![CDATA[
9 python '$__tool_directory__/auto_threshold.py' 16 python '$__tool_directory__/auto_threshold.py'
10 '$input' 17 '$input'
11 ./out.tif 18 ./out.tif
12 '$th_method' 19 '$th_method'
13 '$block_size' 20 '$block_size'
14 '$dark_bg' 21 '$dark_bg'
15 ]]> 22 ]]>
16 </command> 23 </command>
17 <inputs> 24 <inputs>
18 <param name="input" type="data" format="tiff,png" label="Input image" /> 25 <param name="input" type="data" format="tiff,png" label="Input image" />
19 <param name="th_method" type="select" label="Thresholding method"> 26 <param name="th_method" type="select" label="Thresholding method">
20 <option value="otsu" selected="True">Otsu</option> 27 <option value="otsu" selected="True">Otsu</option>
21 <option value="li">Li's Minimum Cross Entropy</option> 28 <option value="li">Li's Minimum Cross Entropy</option>
22 <option value="isodata">Isodata</option> 29 <option value="isodata">Isodata</option>