Mercurial > repos > imgteam > 2d_local_threshold

diff 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
parents
children c90b91f4a07b
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/auto_local_threshold.xml	Thu Jul 18 09:22:07 2019 -0400
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+<tool id="ip_localthreshold" name="Local Threshold" version="0.0.1">
+   <description>applies a local 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 '$__tool_directory__/auto_local_threshold.py' '$input' '$output' $block_size $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="gaussian" selected="True">Gaussian</option>
+          <option value="median">Median</option>
+          <option value="mean">Mean</option>
+        </param>        
+        <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood which is used to calculate the threshold value" />
+        <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"/>
+            <param name="block_size" value="429"/>
+            <param name="dark_backgroud" value="True"/>
+        </test>
+    </tests>
+    <help>
+        Applies a local threshold algorithm to an image.
+    </help>
+    <citations>
+        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
+    </citations>
+</tool>