Merge branch 'master' into master

ivelet · Jul 10, 2024 · 2b97988 · 2b97988
2 parents b889e8d + b7f4b9b
commit 2b97988
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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_24.1
   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_24.1
   MAX_CHUNKS: 4
   MAX_FILE_SIZE: 1M
 concurrency:

diff --git a/tools/ear/.shed.yml b/tools/ear/.shed.yml
@@ -0,0 +1,11 @@
+name: erga_ear
+owner: bgruening
+description: "A tool to compile assembly reports and stastics from assembly pipeline"
+homepage_url: https://github.com/ERGA-consortium/EARs/tree/main
+long_description: |
+      A tool that compiles various statistics and reports generated from Assembly pipeline tools and compiles them in to a summarized PDF document for reporting.
+remote_repository_url: https://github.com/ERGA-consortium/EARs/tree/main
+type: unrestricted
+categories:
+- Sequence Analysis
+- Assembly
diff --git a/tools/ear/macros.xml b/tools/ear/macros.xml
@@ -0,0 +1,24 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.0.0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@PROFILE@">23.2</token>
+    <xml name="creator">
+        <creator>
+            <organization name="Galaxy EU" url="https://galaxyproject.org/eu/"/>
+        </creator>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @misc{github_EAR,
+                    author = {Deigo De Panis},
+                    title = {EAR: A tool for compiling statistics and reports from Assembly pipeline for assembly review process},
+                    year = {2024},
+                    publisher = {GitHub},
+                    journal = {GitHub repository},
+                    url = {https://github.com/ERGA-consortium/EARs/tree/main}
+                }
+            </citation>
+        </citations>
+    </xml>
+</macros>