diff auto_threshold.xml @ 3:0c777d708acc draft

"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"

--- a/auto_threshold.xml	Wed Dec 18 05:00:41 2019 -0500
+++ b/auto_threshold.xml	Sat Feb 19 15:17:40 2022 +0000
@@ -1,47 +1,54 @@
-<tool id="ip_threshold" name="Auto Threshold" version="0.0.4">
-   <description>applies a standard threshold algorithm to an image</description>
+<tool id="ip_threshold" name="Auto Threshold" version="0.0.5" profile="20.05">
+   <description>applies a standard thresholding 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>
+        <requirement type="package" version="0.18.1">scikit-image</requirement>
+        <requirement type="package" version="2020.10.1">tifffile</requirement>
    </requirements>
    <command detect_errors="aggressive">
    <![CDATA[
-   python '$__tool_directory__/auto_threshold.py' '$input' '$output' $thresh_type $dark_background
+   python '$__tool_directory__/auto_threshold.py'
+   '$input'
+   ./out.tif
+   '$th_method'
+   '$block_size'
+   '$dark_bg'
    ]]>
    </command>
    <inputs>
-        <param name="input" type="data" format="tiff" label="Source file" />
-        <param name="thresh_type" type="select" label="Threshold Algorithm">
+        <param name="input" type="data" format="tiff,png" label="Input image" />
+        <param name="th_method" type="select" label="Thresholding method">
           <option value="otsu" selected="True">Otsu</option>
-          <option value="li">Li’s Minimum Cross Entropy</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>
+          <option value="loc_gaussian">Adaptive (Gaussian)</option>
+          <option value="loc_median">Adaptive (Median)</option>
+          <option value="loc_mean">Adaptive (Mean)</option>
         </param>
-        <param name="dark_background" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Dark Background" />
+        <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold (only valid for adaptive thresholding methods)" />
+        <param name="dark_bg" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Dark Background" />
     </inputs>
     <outputs>
-       <data format="tiff" name="output" />
+       <data format="tiff" name="output" from_work_dir="out.tif" />
     </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"/>
+            <param name="th_method" value="loc_gaussian"/>
+            <param name="block_size" value="3"/>
+            <param name="dark_bg" 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"/>
+            <param name="th_method" value="otsu"/>
+            <param name="block_size" value="5"/>
+            <param name="dark_bg" value="True"/>
         </test>
     </tests>
     <help>
-        Applies a standard threshold algorithm to an image.
+        Applies a standard thresholding algorithm to an image.
     </help>
     <citations>
         <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>