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.github/PULL_REQUEST_TEMPLATE.md

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+FOR CONTRIBUTOR:
+* [ ] - I have read the [CONTRIBUTING.md](https://github.com/galaxyproject/tools-iuc/blob/master/CONTRIBUTING.md) document and this tool is appropriate for the tools-iuc repo.
+* [ ] - License permits unrestricted use (educational + commercial)
+* [ ] - 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)

.github/workflows/ci.yaml

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+name: Weekly global Tool Linting and Tests
+on:
+  schedule:
+    # Run at midnight every monday
+    - cron: '0 0 * * 1'
+  repository_dispatch:
+    types: [run-all-tool-tests-command]
+env:
+  GALAXY_RELEASE: release_20.09
+  GALAXY_FORK: galaxyproject
+  MAX_CHUNKS: 40
+jobs:
+  setup:
+    name: Setup cache
+    if: github.repository_owner == 'ASaiM'
+    runs-on: ubuntu-latest
+    outputs:
+      branch: ${{ steps.get-fork-branch.outputs.branch }}
+      fork: ${{ steps.get-fork-branch.outputs.fork }}
+      galaxy_head_sha: ${{ steps.get-galaxy-sha.outputs.galaxy_head_sha }}
+      nchunks: ${{ steps.get-chunks.outputs.nchunks }}
+      chunk_list: ${{ steps.get-chunks.outputs.chunk_list }}
+    strategy:
+      matrix:
+        python-version: [3.7]
+    steps:
+    - name: Add reaction
+      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      uses: peter-evans/create-or-update-comment@v1
+      with:
+        token: ${{ secrets.PAT }}
+        repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
+        comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
+        reaction-type: hooray
+    - name: Set galaxy fork and branch
+      id: get-fork-branch
+      run: |
+        TMP="${{ github.event.client_payload.slash_command.args.named.fork }}"
+        echo "::set-output name=fork::${TMP:-$GALAXY_FORK}"
+        TMP="${{ github.event.client_payload.slash_command.args.named.branch }}"
+        echo "::set-output name=branch::${TMP:-$GALAXY_RELEASE}"
+    - name: Determine latest commit in the Galaxy repo
+      id: get-galaxy-sha
+      run: echo "::set-output name=galaxy_head_sha::$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)"
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy_head_sha }}
+    # Install the `wheel` package so that when installing other packages which
+    # are not available as wheels, pip will build a wheel for them, which can be cached.
+    - name: Install wheel
+      run: pip install wheel
+    - name: Install Planemo
+      run: pip install planemo
+    - name: Fake a Planemo run to update cache
+      if: steps.cache-pip.outputs.cache-hit != 'true'
+      run: |
+        touch tool.xml
+        PIP_QUIET=1 planemo test --galaxy_python_version ${{ matrix.python-version }} --no_conda_auto_init --galaxy_source 'https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy' --galaxy_branch "${{ steps.get-fork-branch.outputs.branch }}" --galaxy_python_version ${{ matrix.python-version }}
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 1
+    - name: Planemo ci_find_repos
+      run: planemo ci_find_repos --exclude packages --exclude deprecated --exclude_from .tt_skip --output repository_list.txt
+    - name: Show repository list
+      run: cat repository_list.txt
+    - name: Planemo ci_find_tools for the repository list
+      run: planemo ci_find_tools --output tool_list.txt $(cat repository_list.txt)
+    - name: Show tool list
+      run: cat tool_list.txt
+    - name: Compute chunks
+      id: get-chunks
+      run: |
+        nchunks=$(wc -l < tool_list.txt)
+        if [ "$nchunks" -gt "$MAX_CHUNKS" ]; then
+            nchunks=$MAX_CHUNKS
+        elif [ "$nchunks" -eq 0 ]; then
+            nchunks=1
+        fi
+        echo "::set-output name=nchunks::$nchunks"
+        echo "::set-output name=chunk_list::[$(seq -s ", " 0 $(($nchunks - 1)))]"
+    - name: Show chunks
+      run: |
+        echo 'Using ${{ steps.get-chunks.outputs.nchunks }} chunks (${{ steps.get-chunks.outputs.chunk_list }})'
+
+  test:
+    name: Test tools
+    # This job runs on Linux
+    runs-on: ubuntu-latest
+    needs: setup
+    strategy:
+      fail-fast: false
+      matrix:
+        chunk: ${{ fromJson(needs.setup.outputs.chunk_list) }}
+        python-version: [3.7]
+    services:
+      postgres:
+        image: postgres:11
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+    # checkout the repository
+    # and use it as the current working directory
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
+    - name: Install Planemo
+      run: pip install planemo
+    - name: Planemo ci_find_tools, chunked
+      run: planemo ci_find_tools --chunk_count ${{ needs.setup.outputs.nchunks }} --chunk ${{ matrix.chunk }} --exclude test_repositories --exclude packages --exclude deprecated --exclude_from .tt_skip --group_tools --output tool_list_chunk.txt
+    - name: Show tool list chunk
+      run: cat tool_list_chunk.txt
+    - name: Planemo test tools
+      run: |
+        mkdir json_output
+        while read -r TOOL_GROUP; do
+            # Check if any of the lines in .tt_biocontainer_skip is a substring of $TOOL_GROUP
+            if echo $TOOL_GROUP | grep -qf .tt_biocontainer_skip; then
+                PLANEMO_OPTIONS=""
+            else
+                PLANEMO_OPTIONS="--biocontainers --no_dependency_resolution --no_conda_auto_init"
+            fi
+            json=$(mktemp -u -p json_output --suff .json)
+            PIP_QUIET=1 planemo test --database_connection postgresql://postgres:postgres@localhost:5432/galaxy $PLANEMO_OPTIONS --galaxy_source "https://github.com/${{ needs.setup.outputs.fork }}/galaxy" --galaxy_branch "${{ needs.setup.outputs.branch }}" --galaxy_python_version ${{ matrix.python-version }} --test_output_json "$json" $TOOL_GROUP || true
+            docker system prune --all --force --volumes || true
+        done < tool_list_chunk.txt
+        if [ ! -s tool_list_chunk.txt ]; then
+            echo '{"tests":[]}' > "$(mktemp -u -p json_output --suff .json)"
+        fi
+    - name: Merge tool_test_output.json files
+      run: planemo merge_test_reports json_output/*.json tool_test_output.json
+    - name: Create tool_test_output.html
+      run: planemo test_reports tool_test_output.json --test_output tool_test_output.html
+    - name: Copy artifacts into place
+      run: |
+        mkdir upload
+        mv tool_test_output.json tool_test_output.html upload/
+    - uses: actions/upload-artifact@v2
+      with:
+        name: 'Tool test output ${{ matrix.chunk }}'
+        path: upload
+
+  # - combine the results of the test chunks (which will never fail due
+  #   to `|| true`) and create a global test report as json and html which
+  #   is provided as artifact
+  # - check if any tool test actually failed (by lookup in the combined json)
+  #   and fail this step if this is the case
+  combine_outputs:
+    name: Combine chunked test results
+    needs: [setup, test]
+    strategy:
+      matrix:
+        python-version: [3.7]
+    # This job runs on Linux
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/download-artifact@v2
+      with:
+        path: artifacts
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
+    - name: Install Planemo
+      run: pip install planemo
+    - name: Install jq
+      run: sudo apt-get install jq
+    - name: Combine outputs
+      run: find artifacts/ -name tool_test_output.json -exec sh -c 'planemo merge_test_reports "$@" tool_test_output.json' sh {} +
+    - name: Create tool_test_output.html
+      run: planemo test_reports tool_test_output.json --test_output tool_test_output.html
+    - name: Copy artifacts into place
+      run: |
+        mkdir upload
+        mv tool_test_output.json tool_test_output.html upload/
+    - uses: actions/upload-artifact@v2
+      with:
+        name: 'All tool test results'
+        path: upload
+
+    - name: Create URL to the run output
+      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      id: vars
+      run: echo ::set-output name=run-url::https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID
+
+    - name: Gather statistics
+      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      id: stats
+      run: echo ::set-output name=statistics::$(jq '.["tests"][]["data"]["status"]' upload/tool_test_output.json | sed 's/"//g' | sort | uniq -c)
+
+    - name: Create comment
+      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      uses: peter-evans/create-or-update-comment@v1
+      with:
+        token: ${{ secrets.PAT }}
+        repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
+        issue-number: ${{ github.event.client_payload.github.payload.issue.number }}
+        body: |
+          Summary:
+
+          ${{ steps.stats.outputs.statistics }}
+
+          [Find all tool test results here][1]
+
+          [1]: ${{ steps.vars.outputs.run-url }}
+    - name: Check status of combined outputs
+      run: |
+        if jq '.["tests"][]["data"]["status"]' upload/tool_test_output.json | grep -v "success"; then
+            echo "Unsuccessful tests found, inspect the 'All tool test results' artifact for details."
+            exit 1
+        fi