diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
new file mode 100644
index 0000000..aa15865
--- /dev/null
+++ b/.github/workflows/ci.yaml
@@ -0,0 +1,234 @@
+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_FORK: galaxyproject
+  GALAXY_BRANCH: release_24.2
+  MAX_CHUNKS: 40
+jobs:
+  setup:
+    name: Setup cache and determine changed repositories
+    if: ${{ github.repository_owner == 'arpcard' }}
+    runs-on: ubuntu-latest
+    outputs:
+      galaxy-head-sha: ${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
+      fork: ${{ steps.get-fork-branch.outputs.fork }}
+      branch: ${{ steps.get-fork-branch.outputs.branch }}
+      repository-list: ${{ steps.discover.outputs.repository-list }}
+      chunk-count: ${{ steps.discover.outputs.chunk-count }}
+      chunk-list: ${{ steps.discover.outputs.chunk-list }}
+    strategy:
+      matrix:
+        python-version: ['3.11']
+    steps:
+    - name: Add reaction
+      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      uses: peter-evans/create-or-update-comment@v4
+      with:
+        token: ${{ secrets.PAT }}
+        repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
+        comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
+        reactions: hooray
+    - name: Set galaxy fork and branch
+      id: get-fork-branch
+      run: |
+        TMP="${{ github.event.client_payload.slash_command.args.named.fork }}"
+        echo "fork=${TMP:-$GALAXY_FORK}" >> $GITHUB_OUTPUT
+        TMP="${{ github.event.client_payload.slash_command.args.named.branch }}"
+        echo "branch=${TMP:-$GALAXY_BRANCH}" >> $GITHUB_OUTPUT
+    - name: Determine latest commit in the Galaxy repo
+      id: get-galaxy-sha
+      run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)" >> $GITHUB_OUTPUT
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v4
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ 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
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 1
+    - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
+      uses: galaxyproject/planemo-ci-action@v1
+      id: discover
+      with:
+        create-cache: ${{ steps.cache-pip.outputs.cache-hit != 'true' || steps.cache-planemo.outputs.cache-hit != 'true' }}
+        galaxy-fork: ${{ steps.get-fork-branch.outputs.fork }}
+        galaxy-branch: ${{ steps.get-fork-branch.outputs.branch }}
+        max-chunks: ${{ env.MAX_CHUNKS }}
+        python-version: ${{ matrix.python-version }}
+    - name: Show repository list
+      run: echo '${{ steps.discover.outputs.repository-list }}'
+    - name: Show chunks
+      run: |
+        echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})'
+
+  lint:
+    name: Lint tool-list
+    needs: setup
+    if: ${{ needs.setup.outputs.repository-list != '' || needs.setup.outputs.tool-list != '' }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.11']
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v4
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+    - name: Planemo lint
+      uses: galaxyproject/planemo-ci-action@v1
+      id: lint
+      with:
+        mode: lint
+        fail-level: warn
+        repository-list: ${{ needs.setup.outputs.repository-list }}
+        tool-list: ${{ needs.setup.outputs.tool-list }}
+        additional-planemo-options: --biocontainers
+    - uses: actions/upload-artifact@v4
+      if: ${{ failure() }}
+      with:
+        name: 'Tool linting output'
+        path: lint_report.txt
+
+  test:
+    name: Test tools
+    # This job runs on Linux
+    runs-on: ubuntu-latest
+    needs: setup
+    if: ${{ needs.setup.outputs.repository-list != '' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }}
+        python-version: ['3.11']
+    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@v4
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v4
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+    - name: Get number of CPU cores
+      uses: SimenB/github-actions-cpu-cores@v2
+      id: cpu-cores
+    - name: Clean dotnet folder for space
+      run: rm -Rf /usr/share/dotnet
+    - name: Planemo test
+      uses: galaxyproject/planemo-ci-action@v1
+      id: test
+      with:
+        mode: test
+        repository-list: ${{ needs.setup.outputs.repository-list }}
+        galaxy-fork: ${{ needs.setup.outputs.fork }}
+        galaxy-branch: ${{ needs.setup.outputs.branch }}
+        chunk: ${{ matrix.chunk }}
+        chunk-count: ${{ needs.setup.outputs.chunk-count }}
+        galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
+        # Limit each test to 15 minutes
+        test_timeout: 900
+    - uses: actions/upload-artifact@v4
+      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: ['3.11']
+    # This job runs on Linux
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/download-artifact@v4
+      with:
+        path: artifacts
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v4
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+    - name: Combine outputs
+      uses: galaxyproject/planemo-ci-action@v1
+      id: combine
+      with:
+        mode: combine
+        html-report: true
+        markdown-report: true
+    - uses: actions/upload-artifact@v4
+      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: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      id: vars
+      run: echo "run-url=https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID" >> $GITHUB_OUTPUT
+
+    - name: Create comment
+      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      uses: peter-evans/create-or-update-comment@v4
+      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.combine.outputs.statistics }}
+
+          [Find all tool test results here][1]
+
+          [1]: ${{ steps.vars.outputs.run-url }}
+    - name: Check outputs
+      uses: galaxyproject/planemo-ci-action@v1
+      id: check
+      with:
+        mode: check
diff --git a/.github/workflows/main-shed.yml b/.github/workflows/main-shed.yml
deleted file mode 100644
index 378080e..0000000
--- a/.github/workflows/main-shed.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-name: Autobuild
-
-on:
-  push:
-    branches: 
-      - master
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v1
-      with:
-        python-version: '3.x'
-    - name: Cache pip
-      uses: actions/cache@v1
-      with:
-        path: ~/.cache/pip # This path is specific to Ubuntu
-        # Look to see if there is a cache hit for the corresponding requirements file
-        key: ${{ runner.os }}-pip-planemo-0.74.9
-        restore-keys: |
-          ${{ runner.os }}-pip-
-          ${{ runner.os }}-
-    - name: Install dependencies
-      run: python -m pip install --upgrade pip setuptools wheel 'planemo==0.74.9'
-    - name: planemo shed_update
-      env: 
-        SHED_KEY: ${{ secrets.SHED_KEY }}
-      run: planemo shed_update -r -t toolshed --check_diff --force_repository_creation --shed_key_from_env SHED_KEY
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
new file mode 100644
index 0000000..7b81d8d
--- /dev/null
+++ b/.github/workflows/pr.yaml
@@ -0,0 +1,432 @@
+name: Galaxy Tool Linting and Tests for push and PR
+on:
+  pull_request:
+    paths-ignore:
+      - 'deprecated/**'
+      - 'docs/**'
+      - '*'
+  push:
+    branches:
+      - main
+      - master
+    paths-ignore:
+      - 'deprecated/**'
+      - 'docs/**'
+      - '*'
+env:
+  GALAXY_FORK: galaxyproject
+  GALAXY_BRANCH: release_24.2
+  MAX_CHUNKS: 4
+  MAX_FILE_SIZE: 1M
+concurrency:
+  # Group runs by PR, but keep runs on the default branch separate
+  # because we do not want to cancel ToolShed uploads
+  group: pr-${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main') && github.run_number || github.ref }}
+  cancel-in-progress: true
+jobs:
+  # the setup job does two things:
+  # 1. cache the pip cache and .planemo
+  # 2. determine the list of changed repositories
+  # it produces one artifact which contains
+  # - a file with the latest SHA from the chosen branch of the Galaxy repo
+  # - a file containing the list of changed repositories
+  # which are needed in subsequent steps.
+  setup:
+    name: Setup cache and determine changed repositories
+    runs-on: ubuntu-latest
+    outputs:
+      galaxy-head-sha: ${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
+      repository-list: ${{ steps.discover.outputs.repository-list }}
+      tool-list: ${{ steps.discover.outputs.tool-list }}
+      chunk-count: ${{ steps.discover.outputs.chunk-count }}
+      chunk-list: ${{ steps.discover.outputs.chunk-list }}
+      commit-range: ${{ steps.discover.outputs.commit-range }}
+    strategy:
+      matrix:
+        python-version: ['3.11']
+    steps:
+    - name: Print github context properties
+      run: |
+        echo 'event: ${{ github.event_name }}'
+        echo 'sha: ${{ github.sha }}'
+        echo 'ref: ${{ github.ref }}'
+        echo 'head_ref: ${{ github.head_ref }}'
+        echo 'base_ref: ${{ github.base_ref }}'
+        echo 'event.before: ${{ github.event.before }}'
+        echo 'event.after: ${{ github.event.after }}'
+    - name: Determine latest commit in the Galaxy repo
+      id: get-galaxy-sha
+      run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)" >> $GITHUB_OUTPUT
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v4
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
+    - name: Cache .planemo
+      uses: actions/cache@v4
+      id: cache-planemo
+      with:
+        path: ~/.planemo
+        key: planemo_cache_py_${{ 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 flake8
+      run: pip install flake8 flake8-import-order
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
+      uses: galaxyproject/planemo-ci-action@v1
+      id: discover
+      with:
+        create-cache: ${{ steps.cache-pip.outputs.cache-hit != 'true' || steps.cache-planemo.outputs.cache-hit != 'true' }}
+        galaxy-fork: ${{ env.GALAXY_FORK }}
+        galaxy-branch: ${{ env.GALAXY_BRANCH }}
+        max-chunks: ${{ env.MAX_CHUNKS }}
+        python-version: ${{ matrix.python-version }}
+    - name: Show commit range
+      run: echo '${{ steps.discover.outputs.commit-range }}'
+    - name: Show repository list
+      run: echo '${{ steps.discover.outputs.repository-list }}'
+    - name: Show tool list
+      run: echo '${{ steps.discover.outputs.tool-list }}'
+    - name: Show chunks
+      run: |
+        echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})'
+
+  # Planemo lint the changed repositories
+  lint:
+    name: Lint tool-list
+    needs: setup
+    if: ${{ needs.setup.outputs.repository-list != '' || needs.setup.outputs.tool-list != '' }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.11']
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v4
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+    - name: Planemo lint
+      uses: galaxyproject/planemo-ci-action@v1
+      id: lint
+      with:
+        mode: lint
+        fail-level: warn
+        repository-list: ${{ needs.setup.outputs.repository-list }}
+        tool-list: ${{ needs.setup.outputs.tool-list }}
+    - uses: actions/upload-artifact@v4
+      if: ${{ failure() }}
+      with:
+        name: 'Tool linting output'
+        path: lint_report.txt
+
+  # flake8 of Python scripts in the changed repositories
+  flake8:
+    name: Lint Python scripts
+    needs: setup
+    if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.11']
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v4
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+    - name: Install flake8
+      run: pip install flake8 flake8-import-order
+    - name: Flake8
+      run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --output-file pylint_report.txt --tee
+    - uses: actions/upload-artifact@v4
+      if: ${{ failure() }}
+      with:
+        name: 'Python linting output'
+        path: pylint_report.txt
+
+  lintr:
+    name: Lint R scripts
+    needs: setup
+    if: ${{ needs.setup.outputs.repository-list != '' }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-24.04]
+        r-version: ['release']
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 1
+    - uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: ${{ matrix.r-version }}
+    - name: Cache R packages
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.R_LIBS_USER }}
+        key: r_cache_${{ matrix.os }}_${{ matrix.r-version }}
+    - name: Install packages
+      uses: r-lib/actions/setup-r-dependencies@v2
+      with:
+        packages: |
+          any::argparse 
+          any::styler
+    - name: lintr
+      run: |
+        set -eo pipefail
+        echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' -n 1 ./.github/styler.R --dry off
+        git status
+        git diff --exit-code | tee rlint_report.txt
+    - uses: actions/upload-artifact@v4
+      if: ${{ failure() }}
+      with:
+        name: 'R linting output'
+        path: rlint_report.txt
+
+  file_sizes:
+    name: Check file sizes
+    needs: setup
+    if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Check file sizes
+      run: |
+        touch file_size_report.txt
+        git diff --diff-filter=d --name-only ${{ needs.setup.outputs.commit-range }} > git.diff
+        while read line; do
+          find "$line" -type f -size +${{ env.MAX_FILE_SIZE }} >> file_size_report.txt
+        done < git.diff
+        if [[ -s file_size_report.txt ]]; then
+          echo "Files larger than ${{ env.MAX_FILE_SIZE }} found"
+          cat file_size_report.txt
+          exit 1
+        fi
+    - uses: actions/upload-artifact@v4
+      if: ${{ failure() }}
+      with:
+        name: 'File size report'
+        path: file_size_report.txt
+
+  # Planemo test the changed repositories, each chunk creates an artifact
+  # containing HTML and JSON reports for the executed tests
+  test:
+    name: Test tools
+    needs: setup
+    if: ${{ needs.setup.outputs.repository-list != '' }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }}
+        python-version: ['3.11']
+    services:
+      postgres:
+        image: postgres:11
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v4
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+    - name: Cache .planemo
+      uses: actions/cache@v4
+      id: cache-planemo
+      with:
+        path: ~/.planemo
+        key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+    - name: Get number of CPU cores
+      uses: SimenB/github-actions-cpu-cores@v2
+      id: cpu-cores
+    - name: Clean dotnet folder for space
+      run: rm -Rf /usr/share/dotnet
+    - name: Planemo test
+      uses: galaxyproject/planemo-ci-action@v1
+      id: test
+      with:
+        mode: test
+        repository-list: ${{ needs.setup.outputs.repository-list }}
+        galaxy-fork: ${{ env.GALAXY_FORK }}
+        galaxy-branch: ${{ env.GALAXY_BRANCH }}
+        chunk: ${{ matrix.chunk }}
+        chunk-count: ${{ needs.setup.outputs.chunk-count }}
+        galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
+        # Limit each test to 15 minutes
+        test_timeout: 1800
+    - uses: actions/upload-artifact@v4
+      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]
+    if: ${{ always() && needs.setup.outputs.repository-list != '' }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11']
+    steps:
+    - uses: actions/download-artifact@v4
+      with:
+        path: artifacts
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v4
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+    - name: Combine outputs
+      uses: galaxyproject/planemo-ci-action@v1
+      id: combine
+      with:
+        mode: combine
+        html-report: true
+        markdown-report: true
+    - uses: actions/upload-artifact@v4
+      with:
+        name: 'All tool test results'
+        path: upload
+    - run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY
+    - name: Check outputs
+      uses: galaxyproject/planemo-ci-action@v1
+      id: check
+      with:
+        mode: check
+    - name: Check if all test chunks succeeded
+      run: |
+        NFILES=$(ls artifacts/ | grep "Tool test output" | wc -l)
+        if [[ "${{ needs.setup.outputs.chunk-count }}" != "$NFILES" ]]; then
+          exit 1
+        fi
+
+  # deploy the tools to the toolsheds (first TTS for testing)
+  deploy:
+    name: Deploy
+    needs: [setup, lint, combine_outputs]
+    if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'arpcard' }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11']
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v4
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+    - name: Deploy on testtoolshed
+      uses: galaxyproject/planemo-ci-action@v1
+      with:
+        mode: deploy
+        repository-list: ${{ needs.setup.outputs.repository-list }}
+        shed-target: testtoolshed
+        shed-key: ${{ secrets.TTS_API_KEY }}
+      continue-on-error: true
+    - name: Deploy on toolshed
+      uses: galaxyproject/planemo-ci-action@v1
+      with:
+        mode: deploy
+        repository-list: ${{ needs.setup.outputs.repository-list }}
+        shed-target: toolshed
+        shed-key: ${{ secrets.TS_API_KEY }}
+
+  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' }}
+    runs-on: ubuntu-latest
+    steps:
+    # report to the PR if deployment failed
+    - name: Get PR object
+      uses: 8BitJonny/gh-get-current-pr@2.2.0
+      id: getpr
+      with:
+        sha: ${{ github.event.after }}
+    - name: Create comment
+      uses: peter-evans/create-or-update-comment@v4
+      with:
+        token: ${{ secrets.PAT }}
+        issue-number: ${{ steps.getpr.outputs.number }}
+        body: |
+          Attention: deployment ${{ needs.deploy.result }}!
+
+          https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}
+
+  determine-success:
+    name: Check workflow success
+    needs: [setup, lint, flake8, lintr, file_sizes, combine_outputs]
+    if: ${{ always() && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/main' }}
+    runs-on: ubuntu-latest
+    steps:
+    - name: Check tool lint status
+      if: ${{ needs.lint.result != 'success' && needs.flake8.result != 'skipped' }}
+      run: exit 1
+    - name: Indicate Python script lint status
+      if: ${{ needs.flake8.result != 'success' && needs.flake8.result != 'skipped' }}
+      run: exit 1
+    - name: Indicate R script lint status
+      if: ${{ needs.lintr.result != 'success' && needs.lintr.result != 'skipped' }}
+      run: exit 1
+    - name: Indicate file size check status
+      if: ${{ needs.file_sizes.result != 'success' && needs.file_sizes.result != 'skipped' }}
+      run: exit 1
+    - name: Check tool test status
+      if: ${{ needs.combine_outputs.result != 'success' && needs.combine_outputs.result != 'skipped' }}
+      run: exit 1
diff --git a/.github/workflows/pr_without_tool_change.yaml b/.github/workflows/pr_without_tool_change.yaml
new file mode 100644
index 0000000..edff410
--- /dev/null
+++ b/.github/workflows/pr_without_tool_change.yaml
@@ -0,0 +1,15 @@
+name: Fallback
+# Fallback workflow that provides a succeeding "Check workflow success" job
+# as this is a requirement for being able to merge a PR
+# see https://docs.github.com/en/repositories/configuring-branches-and-merges-in-your-repository/defining-the-mergeability-of-pull-requests/troubleshooting-required-status-checks#handling-skipped-but-required-checks
+on:
+  pull_request:
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  determine-success:
+    name: Check workflow success
+    runs-on: ubuntu-latest
+    steps:
+      -  run: 'echo "No tool tests required for this PR"'
diff --git a/.shed.yml b/tools/rgi/.shed.yml
similarity index 100%
rename from .shed.yml
rename to tools/rgi/.shed.yml
diff --git a/README.rst b/tools/rgi/README.rst
similarity index 100%
rename from README.rst
rename to tools/rgi/README.rst
diff --git a/rgi.xml b/tools/rgi/rgi.xml
similarity index 63%
rename from rgi.xml
rename to tools/rgi/rgi.xml
index d65a095..4cc14b9 100644
--- a/rgi.xml
+++ b/tools/rgi/rgi.xml
@@ -1,45 +1,50 @@
-<tool id="rgi" name="Resistance Gene Identifier (RGI)" profile="18.09" version="5.2.1">
+<tool id="rgi" name="Resistance Gene Identifier (RGI)" profile="18.09" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>This tool predicts resistome(s) from protein or nucleotide data based on homology and SNP models.</description>
+    <macros>
+        <token name="@TOOL_VERSION@">6.0.3</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="5.2.1">rgi</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">rgi</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
+        <regex source="both" match="ERROR" level="fatal" description="Tool output contained text ERROR"/>
     </stdio>
+    <version_command>rgi main --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-#if $db_opts.db_opts_selector == "default":
-    export DB_PATH='${__tool_data_path__}/rgi_databases/_default' &&
-    export DATA_PATH="\$_GALAXY_JOB_TMP_DIR" &&
-    mkdir -p "\$DB_PATH" &&
-#end if
-
-#if $db_opts.db_opts_selector != "default":
-    rgi load
-        #if $db_opts.db_opts_selector == "local":
-            -i "${__tool_data_path__}/rgi_databases/$db_opts.rgi_db_local/card.json" 
-        #else:
-            -i "$db_opts.rgi_db_hist"
-        #end if
-        --local
+export DB_PATH='$rgi_db_local.fields.path' &&
+export DATA_PATH="\$_GALAXY_JOB_TMP_DIR" &&
+
+rgi load
+    -i '$rgi_db_local.fields.path'/card.json 
+    --local
     &&
-#end if
+
+## symlink input sequence otherwise tool will try to write to input dir
+## and not fail with exit code != 0
+ln -s '$input_sequence' sequence &&
 
 rgi main
-    -i '$input_sequence'
-    -o out
-    -t $input_type
-    -a $alignment_tool
-    -n "\${GALAXY_SLOTS:-1}"
+    --input_sequence sequence
+    --output_file out
+    --input_type $input_type
+    --alignment_tool $alignment_tool
+    --num_threads "\${GALAXY_SLOTS:-1}"
     $include_loose
+    $include_nudge
     $low_quality
-    -d $data
-
-#if $db_opts.db_opts_selector != "default":
+    --data $data
     --local
-#end if
-       ]]></command>
+    --orf_finder $orf_finder 
+    ]]></command>
     <inputs>
-        <param argument="--input_sequence" type="data" format="fastq,fasta" label="Input sequence" help="input file must be in either FASTA (contig and protein) or gzip format e.g myFile.fasta, myFasta.fasta.gz"/>
+        <param name="rgi_db_local" type="select" multiple="false" label="RGI database">
+            <options from_data_table="rgi_databases">
+                <validator type="no_options" message="No databases are available built-in"/>
+            </options>
+        </param>
+        <param argument="--input_sequence" type="data" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Input sequence" help="input file must be in either FASTA (contig and protein) or gzip format e.g myFile.fasta, myFasta.fasta.gz"/>
         <param argument="--input_type" type="select" multiple="false" label="Input type" help="specify data input type (default = contig)">
             <option value="contig" selected="true">CONTIG (Nucleotide Sequence)</option>
             <option value="protein">PROTEIN (Protein Sequence)</option>
@@ -48,7 +53,8 @@ rgi main
             <option value="blast" selected="true">BLAST</option>
             <option value="diamond">DIAMOND</option>
         </param>
-        <param argument="--include_loose" type="boolean" checked="false" truevalue="--include_loose" falsevalue="" label="Include loose hits" help="include loose hits in addition to strict and perfect hits"/>
+        <param argument="--include_loose" type="boolean" checked="false" truevalue="--include_loose" falsevalue="" label="Include loose hits" help="Include loose hits in addition to strict and perfect hits"/>
+        <param argument="--include_nudge" type="boolean" checked="false" truevalue="--include_nudge" falsevalue="" label="Include loose hits" help="Include hits nudged from loose to strict hits"/>
         <param argument="--low_quality" type="boolean" checked="false" truevalue="--low_quality" falsevalue="" label="Low quality" help="use for short contigs to predict partial genes"/>
         <param argument="--data" type="select" multiple="false" label="Data type" help="specify a data-type (default = NA)">
             <option value="wgs">WGS</option>
@@ -56,29 +62,10 @@ rgi main
             <option value="chromosome">CHROMOSOME</option>
             <option value="NA" selected="true">NA</option>
         </param>
-        <conditional name="db_opts">
-            <param name="db_opts_selector" type="select" label="Select an RGI database">
-                <option value="default" selected="true">Default RGI database</option>
-                <option value="local">Locally installed RGI database</option>
-                <option value="hist">RGI database from your history</option>
-            </param>
-            <when value="default">
-                <param name="rgi_db_local" type="hidden" value="" /> 
-                <param name="rgi_db_hist" type="hidden" value="" />
-            </when>
-            <when value="local">
-                <param name="rgi_db_local" type="select" multiple="false" label="Locally installed RGI database">
-                    <options from_data_table="rgi_databases">
-                        <validator type="no_options" message="No databases are available built-in"/>
-                    </options>
-                </param>
-                <param name="rgi_db_hist" type="hidden" value="" />
-            </when>
-            <when value="hist">
-                <param name="rgi_db_local" type="hidden" value="" />
-                <param name="rgi_db_hist" type="data" format="json" label="RGI database from your history" />
-            </when>
-        </conditional>
+        <param argument="--orf_finder" type="select" multiple="false" label="ORF finding tool">
+            <option value="PRODIGAL">PRODIGAL</option>
+            <option value="PYRODIGAL">PYRODIGAL</option>
+        </param>
     </inputs>
     <outputs>
         <data name="report" format="json" from_work_dir="out.json" label="${tool.name} on ${on_string}: report.json"/>
@@ -92,9 +79,7 @@ rgi main
             <param name="include_loose" value="false" />
             <param name="low_quality" value="false" />
             <param name="data" value="NA" />
-            <conditional name="db_opts">
-                <param name="db_opts_selector" value="default" />
-            </conditional>
+            <param name="rgi_db_local" value="3.2.7"/>
             <output name="summary">
                 <assert_contents>
                     <has_text text="AY123251" />
@@ -142,41 +127,6 @@ report.json
 
 A json version of summary.txt.
 
-Help
-----
-
-**usage:**
-    ``rgi main [-h] -i INPUT_SEQUENCE -o OUTPUT_FILE [-t {read,contig,protein,wgs}] [-a {DIAMOND,BLAST}] [-n THREADS] [--include_loose] [--local] [--clean] [--debug] [--low_quality] [-d {wgs,plasmid,chromosome,NA}] [-v]``
-
-**optional arguments:**
-
-- ``-h, --help``
-    show this help message and exit
-- ``-i INPUT_SEQUENCE, --input_sequence INPUT_SEQUENCE``
-    input file must be in either FASTA (contig and protein) or gzip format e.g myFile.fasta, myFasta.fasta.gz
-- ``-o OUTPUT_FILE, --output_file OUTPUT_FILE``
-    output folder and base filename
-- ``-t {read,contig,protein,wgs}, --input_type {read,contig,protein,wgs}``
-    specify data input type (default = contig)
-- ``-a {DIAMOND,BLAST}, --alignment_tool {DIAMOND,BLAST}``
-    specify alignment tool (default = BLAST)
-- ``-n THREADS, --num_threads THREADS``
-    number of threads (CPUs) to use in the BLAST search (default=8)
-- ``--include_loose``
-    include loose hits in addition to strict and perfect hits
-- ``--local``
-    use local database (default: uses database in executable directory)
-- ``--clean``
-    removes temporary files
-- ``--debug``
-    debug mode
-- ``--low_quality``
-    use for short contigs to predict partial genes
-- ``-d {wgs,plasmid,chromosome,NA}, --data {wgs,plasmid,chromosome,NA}``
-    specify a data-type (default = NA)
-- ``-v, --version``
-    prints software version number
-
 Links
 -----
 
diff --git a/test-data/test1.fasta b/tools/rgi/test-data/test1.fasta
similarity index 100%
rename from test-data/test1.fasta
rename to tools/rgi/test-data/test1.fasta