Mercurial > repos > imgteam > 2d_auto_threshold

diff auto_threshold.xml @ 0:d4da97f51700 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:27:36 -0500
parents
children 4853fc2b50bf
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/auto_threshold.xml	Sat Feb 09 14:27:36 2019 -0500
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+<tool id="ip_threshold" name="Auto Threshold" version="0.0.3">
+   <description>applies a standard threshold algorithm to an image</description>
+   <requirements>
+        <requirement type="package" version="0.14.2">scikit-image</requirement>
+        <requirement type="package" version="1.15.4">numpy</requirement>
+        <requirement type="package" version="5.3.0">pillow</requirement>
+        <requirement type="package" version="0.15.1">tifffile</requirement>
+   </requirements>
+   <command detect_errors="aggressive">
+   <![CDATA[
+   python '$__tool_directory__/auto_threshold.py' '$input' '$output' $thresh_type $dark_background
+   ]]>
+   </command>
+   <inputs>
+        <param name="input" type="data" format="tiff" label="Source file" />
+        <param name="thresh_type" type="select" label="Threshold Algorithm">
+          <option value="otsu" selected="True">Otsu</option>
+          <option value="li">Li’s Minimum Cross Entropy</option>
+          <option value="isodata">Isodata</option>
+          <option value="gaussian_adaptive">Adaptive (Gauss)</option>
+          <option value="mean_adaptive">Adaptive (Mean)</option>
+          <option value="yen">Yen</option>
+        </param>
+        <param name="dark_background" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Dark Background" />
+    </inputs>
+    <outputs>
+       <data format="tiff" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="sample.tif"/>
+            <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
+            <param name="thresh_type" value="gaussian_adaptive"/>
+            <param name="dark_backgroud" value="True"/>
+        </test>
+        <test>
+            <param name="input" value="sample.tif"/>
+            <output name="output" value="out2.tif" ftype="tiff" compare="sim_size"/>
+            <param name="thresh_type" value="otsu"/>
+            <param name="dark_backgroud" value="True"/>
+        </test>
+    </tests>
+    <help>
+        Applies a standard threshold algorithm to an image.
+    </help>
+    <citations>
+        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
+    </citations>
+</tool>