Merge branch 'master' into fix_boolean_to_select_transition

galaxyproteomics · Apr 27, 2024 · e980a63 · e980a63
2 parents e06e673 + 00029e8
commit e980a63
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Showing 4 changed files with 34 additions and 14 deletions.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -7,7 +7,7 @@ on:
     types: [run-all-tool-tests-command]
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_23.2
+  GALAXY_BRANCH: release_24.0
   MAX_CHUNKS: 40
 jobs:
   setup:
@@ -103,7 +103,7 @@ jobs:
         mode: lint
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
-        additional-planemo-options: --biocontainers -s tests,output,inputs,help,general,command,citations,tool_xsd,xml_order,tool_urls,shed_metadata
+        additional-planemo-options: --biocontainers -s stdio,tests,output,inputs,help,general,command,citations,tool_xsd,xml_order,tool_urls,shed_metadata,urls,readme,shed_yaml,repository_dependencies,tool_dependencies_actions,tool_dependencies_sha256sum,tool_dependencies_xsd,expansion
     - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
@@ -204,6 +204,7 @@ jobs:
       with:
         name: 'All tool test results'
         path: upload
+    - run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY
     - name: Create URL to the run output
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
       id: vars

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
@@ -2,7 +2,6 @@ name: Galaxy Tool Linting and Tests for push and PR
 on:
   pull_request:
     paths-ignore:
-      - '.github/**'
       - 'deprecated/**'
       - 'docs/**'
       - '*'
@@ -11,13 +10,12 @@ on:
       - main
       - master
     paths-ignore:
-      - '.github/**'
       - 'deprecated/**'
       - 'docs/**'
       - '*'
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_23.2
+  GALAXY_BRANCH: release_24.0
   MAX_CHUNKS: 4
   MAX_FILE_SIZE: 1M
 concurrency:
@@ -401,7 +399,7 @@ jobs:
   deploy-report:
     name: Report deploy status
     needs: [deploy]
-    if: ${{ always() && needs.deploy.result != 'success' && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'galaxyproject' }}
+    if: ${{ always() && needs.deploy.result != 'success' && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'galaxyproteomics' }}
     runs-on: ubuntu-latest
     steps:
     # report to the PR if deployment failed

diff --git a/tools/qupath_roi_splitter/qupath_roi_splitter.py b/tools/qupath_roi_splitter/qupath_roi_splitter.py
@@ -25,20 +25,22 @@ def draw_roi(input_roi, input_img, fill):
             # Polygon with holes
             if not isinstance(sub_roi[0][0], list):
                 if first_roi:
-                    input_img = draw_poly(sub_roi, input_img, fill=fill)
                     first_roi = False
+                    col = (0, 0, 0)
                 else:
                     # holes in ROI
-                    input_img = draw_poly(sub_roi, input_img, col=(255, 255, 255), fill=fill)
+                    col = (255, 255, 255) if not fill else (0, 0, 0)
+                input_img = draw_poly(sub_roi, input_img, col=col, fill=fill)
             else:
                 # MultiPolygon with holes
                 for sub_coord in sub_roi:
                     if first_roi:
-                        input_img = draw_poly(sub_coord, input_img, fill=fill)
                         first_roi = False
+                        col = (0, 0, 0)
                     else:
                         # holes in ROI
-                        input_img = draw_poly(sub_coord, input_img, col=(255, 255, 255), fill=fill)
+                        col = (255, 255, 255) if not fill else (0, 0, 0)
+                    input_img = draw_poly(sub_coord, input_img, col=col, fill=fill)
 
     return input_img
 
@@ -89,13 +91,18 @@ def split_qupath_roi(in_roi):
 
         coords_df.to_csv("{}_{}.txt".format(tma_name, cell_type), sep='\t', index=False)
 
+        # img save
+        if args.img:
+            cv2.imwrite("{}_{}.png".format(tma_name, cell_type), img)
+
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Split ROI coordinates of QuPath TMA annotation by cell type (classfication)")
     parser.add_argument("--qupath_roi", default=False, help="Input QuPath annotation (GeoJSON file)")
     parser.add_argument("--fill", action="store_true", required=False, help="Fill pixels in ROIs")
     parser.add_argument('--version', action='version', version='%(prog)s 0.1.0')
     parser.add_argument("--all", action="store_true", required=False, help="Extracts all ROIs")
+    parser.add_argument("--img", action="store_true", required=False, help="Generates image of ROIs")
     args = parser.parse_args()
 
     if args.qupath_roi:

diff --git a/tools/qupath_roi_splitter/qupath_roi_splitter.xml b/tools/qupath_roi_splitter/qupath_roi_splitter.xml
@@ -1,36 +1,42 @@
 <tool id="qupath_roi_splitter" name="QuPath ROI Splitter" version="@VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Split ROI coordinates of QuPath TMA annotation by cell type (classification)</description>
     <macros>
-        <token name="@VERSION@">0.2.0</token>
+        <token name="@VERSION@">0.2.1</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
         <requirement type="package" version="3.0.1">geojson</requirement>
         <requirement type="package" version="1.24.2">numpy</requirement>
         <requirement type="package" version="4.7.0">opencv</requirement>
-        <requirement type="package" version="2.0.0">pandas</requirement>        
+        <requirement type="package" version="2.0.0">pandas</requirement>
     </requirements>
      <command detect_errors="exit_code"><![CDATA[
         #for $input in $input_collection
             python3 '$__tool_directory__/qupath_roi_splitter.py'
                 --qupath_roi '$input'
                 $optional.fill
                 $optional.all
+                $optional.img
              &&
         #end for
         mkdir out
         && mv *.txt out/
+        && mv *.png out/
     ]]></command>
     <inputs>
         <param name="input_collection" type="data_collection" format="geojson" label="Input QuPath annotation" help="Collection containing GeoJSON files"/>
         <section name="optional" title="Optional">
             <param name="fill" type="boolean" truevalue="--fill" falsevalue="" checked="false" label="Fill ROIs" help="Fill pixels in ROIs"/>
             <param name="all" type="boolean" truevalue="--all" falsevalue="" checked="false" label="Extract all" help="Extracts all ROIs"/>
+            <param name="img" type="boolean" truevalue="--img" falsevalue="" checked="false" label="Generate image" help="Generates image from ROIs"/>
         </section>
     </inputs>
     <outputs>
         <collection name="output_txts" type="list" label="${tool.name} on ${on_string}: ROI data">
-            <discover_datasets pattern="__name_and_ext__" directory="out" visible="false" format="txt"/>
+            <discover_datasets pattern="(?P&lt;name&gt;.*\.txt)" directory="out" visible="false" ext="txt"/>
+        </collection>
+        <collection name="output_imgs" type="list" label="${tool.name} on ${on_string}: Images of ROIs">
+            <discover_datasets pattern="(?P&lt;name&gt;.*\.png)" directory="out" visible="false" ext="png"/>
         </collection>
     </outputs>
     <tests>
@@ -43,9 +49,10 @@
             </param>
             <section name="optional">
                 <param name="fill" value="true"/>
+                <param name="img" value="true"/>
             </section>
             <output_collection name="output_txts" type="list" count="4">
-                <element name="F-5_Stroma">
+                <element name="F-5_Stroma.txt">
                     <assert_contents>
                         <has_text text="x"/>
                         <has_text text="y"/>
@@ -54,6 +61,13 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <output_collection name="output_imgs" type="list" count="4">
+                <element name="E-5_Tumor.png">
+                    <assert_contents>
+                        <has_size value="1309478"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
         </test>
     </tests>
     <help><![CDATA[