Merge branch 'repo_update' into ci_update

.github/PULL_REQUEST_TEMPLATE.md

@@ -4,3 +4,4 @@ FOR CONTRIBUTOR:
 * [ ] - This PR adds a new tool or tool collection
 * [ ] - This PR updates an existing tool or tool collection
 * [ ] - This PR does something else (explain below)
+* [ ] - Tools added/updated by this PR (if any) comply with the [Naming and Annotation Conventions for Tools in the Image Community in Galaxy](https://github.com/elixir-europe/biohackathon-projects-2023/blob/main/16/conventions.md) (or please explain why they do not)

README.md

@@ -1,6 +1,7 @@
-[![Build Status](https://travis-ci.org/BMCV/galaxy-image-analysis.svg?branch=master)](https://travis-ci.org/BMCV/galaxy-image-analysis)
+[![Galaxy Tool Linting and Tests for push and PR](https://github.com/BMCV/galaxy-image-analysis/actions/workflows/pr.yaml/badge.svg?branch=master)](https://github.com/BMCV/galaxy-image-analysis/actions/workflows/pr.yaml?query=branch:master)
 [![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.jbiotec.2017.07.019-blue)](https://doi.org/10.1016/j.jbiotec.2017.07.019)
 [![Chat on matrix](https://img.shields.io/badge/chat_on-matrix-green)](https://matrix.to/#/#galaxyproject_imaging:matrix.org)
+[![European Galaxy server](https://img.shields.io/badge/usegalaxy-.eu-brightgreen?logo=data:image/png;base64,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)](https://imaging.usegalaxy.eu)
 
 # Galaxy Image Analysis
 

tools/overlay_images/overlay_images.xml

@@ -1,4 +1,4 @@
-<tool id="ip_overlay_images" name="Overlay images" version="0.0.3-2" profile="20.05">
+<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>
@@ -15,7 +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 $method_option.alpha
@@ -54,38 +59,43 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="tiff" name="out" from_work_dir="output.tif" />
+        <data format="tiff" name="out_tiff" from_work_dir="output.tif" label="${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>