diff overlay_images.xml @ 3:22ff7c705a83 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 8cd85b185acbfaa9ee6f4e9a389abc1f7b7c44bb

--- a/overlay_images.xml	Thu Aug 10 07:29:34 2023 +0000
+++ b/overlay_images.xml	Wed Nov 08 19:57:15 2023 +0000
@@ -1,5 +1,11 @@
-<tool id="ip_overlay_images" name="Overlay Images" version="0.0.3" profile="20.05"> 
-    <description>for visualization</description>
+<tool id="ip_overlay_images" name="Overlay images" version="0.0.3-3" profile="20.05">
+    <description></description>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">galaxy_image_analysis</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="0.18.1">scikit-image</requirement> 
         <requirement type="package" version="3.3.4">matplotlib</requirement>
@@ -9,7 +15,12 @@
     <command detect_errors="aggressive">
     <![CDATA[
         python '$__tool_directory__/overlay_images.py'
-        '$method_option.im1' '$method_option.im2' ./output.tif
+        '$method_option.im1' '$method_option.im2'
+        #if $method_option.method == "seg_contour"
+            ./output.png
+        #else
+            ./output.tif
+        #end if
         --method $method_option.method
         #if $method_option.method == "blending"
             --alpha $method_option.alpha
@@ -48,38 +59,43 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="tiff" name="out" from_work_dir="output.tif" />
+        <data format="tiff" name="out_tiff" from_work_dir="output.tif" label="${tool.name} on ${on_string} output:tiff">
+            <filter>method_option['method'] != 'seg_contour'</filter>
+        </data>
+        <data format="png" name="out_png" from_work_dir="output.png" label="${tool.name} on ${on_string} output:png">
+            <filter>method_option['method'] == 'seg_contour'</filter>
+        </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="im1" value="mask1.tif"/>
             <param name="im2" value="mask1r.tif"/>
             <param name="method" value="coloc_vis"/>
-            <output name="out" value="test1.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
+            <output name="out_tiff" value="test1.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="im1" value="mask1.tif"/>
             <param name="im2" value="mask1r.tif"/>
             <param name="method" value="blending"/>
             <param name="alpha" value="0.3"/>
-            <output name="out" value="test2.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
+            <output name="out_tiff" value="test2.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="im1" value="sample1.tif"/>
             <param name="im2" value="mask1.tif"/>
             <param name="method" value="seg_contour"/>
             <param name="thickness" value="2"/>
             <param name="color" value="#ff0000"/>
             <param name="show_label" value="--show_label"/>
-            <output name="out" value="test3.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
+            <output name="out_png" value="test3.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="im1" value="sample1.tif"/>
             <param name="im2" value="mask2.tif"/>
             <param name="method" value="seg_contour"/>
             <param name="thickness" value="2"/>
             <param name="color" value="#ff0000"/>
-            <output name="out" value="test4.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
+            <output name="out_png" value="test4.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
         </test>
     </tests>
     <help>