diff spot_detection_2d.xml @ 1:859dd1c11ac0 draft

"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"

--- a/spot_detection_2d.xml	Wed Jul 21 19:59:00 2021 +0000
+++ b/spot_detection_2d.xml	Sat Feb 19 20:43:29 2022 +0000
@@ -1,21 +1,22 @@
-<tool id="ip_spot_detection_2d" name="Spot Detection" version="0.0.1" profile="20.05"> 
-    <description>based on local intensity maxima</description>
+<tool id="ip_spot_detection_2d" name="Spot Detection" version="0.0.2" profile="20.05"> 
+    <description>in a 2D image (sequence)</description>
     <requirements>
         <requirement type="package" version="2.9.0">imageio</requirement>
         <requirement type="package" version="1.20.2">numpy</requirement>
         <requirement type="package" version="1.2.4">pandas</requirement>
         <requirement type="package" version="0.18.1">scikit-image</requirement>
     </requirements>
-    <command>
+    <command detect_errors="aggressive">
     <![CDATA[
          python '$__tool_directory__/spot_detection_2d.py'
          '$fn_in'
          '$fn_out'
          '$frame_1st'
          '$frame_end'
-         '$typ_intens'
+         '$filter'
+         '$ssig'
          '$thres'
-         '$ssig'
+         '$typ_intens'
          '$bndy'
     ]]>
     </command>
@@ -23,13 +24,17 @@
         <param name="fn_in" type="data" format="tiff" label="Image sequence (stack)" />
         <param name="frame_1st" type="integer" value="1" label="Starting time point (1 for the first frame of the stack)" />
         <param name="frame_end" type="integer" value="0" label="Ending time point (0 for the last frame of the stack)" />
+        <param name="filter" type="select" label="Choose a detection filter">
+            <option value="Gauss" selected="True">Gaussian</option>
+            <option value="LoG">Laplacian-of-Gaussian, LoG (more accurate when spots have similar sizes)</option>
+        </param>
+        <param name="ssig" type="float" value="1.0" min="0.5" max="10" label="Sigma of the Gaussian (for noise suppression)" />
+        <param name="thres" type="float" value="10.0" min="0" max="100" label="Percentage of the global maximal as the threshold for candidate spots" />
         <param name="typ_intens" type="select" label="How to measure the intensities">
             <option value="smoothed" selected="True">Smoothed</option>
             <option value="robust">Robust</option>
         </param>
-        <param name="thres" type="float" value="10" label="Percentage of the global maximal intensity as the threshold for candidate spots" />
-        <param name="ssig" type="float" value="1" label="Sigma of the Gaussian filter for noise suppression" />
-        <param name="bndy" type="integer" value="10" label="Number of pixels (Spots within n-pixel image boundaries will be ignored)" />
+        <param name="bndy" type="integer" value="10" min="0" max="50" label="Width (in pixel) of image boundaries where spots will be ignored" />
     </inputs>
     <outputs>
         <data format="tabular" name="fn_out" />
@@ -39,9 +44,10 @@
             <param name="fn_in" value="test_img1.tif"/>
             <param name="frame_1st" value="1"/>
             <param name="frame_end" value="0"/>
-            <param name="typ_intens" value="smoothed"/>
+            <param name="filter" value="Gauss"/>
+            <param name="ssig" value="1"/>
             <param name="thres" value="10"/>
-            <param name="ssig" value="1"/>
+            <param name="typ_intens" value="smoothed"/>
             <param name="bndy" value="10"/>
             <output name="fn_out" value="spots_detected.tsv" ftype="tabular" />
         </test>
@@ -49,6 +55,8 @@
     <help>
     **What it does**
 
-    This tool detects spots and measures the intensities in a 2D image sequence based on local intensity maxima.
+    This tool detects spots and measures the intensities in a 2D image (sequence).
     </help>
+    <citations>
+    </citations>
 </tool>