diff --git a/.github/styler.R b/.github/styler.R
new file mode 100755
index 0000000..c5c0cb5
--- /dev/null
+++ b/.github/styler.R
@@ -0,0 +1,36 @@
+#!/usr/bin/env Rscript
+
+library("argparse")
+library("styler")
+
+parser <- ArgumentParser(description = "Call styler")
+parser$add_argument("dir",
+    metavar = "DIR", type = "character",
+    help = "File to parse"
+)
+parser$add_argument("--dry",
+    choices = c("off", "on"), default = "on"
+)
+args <- parser$parse_args()
+
+file_info <- file.info(args$dir)
+is_directory <- file_info$isdir
+
+if (is_directory) {
+    captured_output <- capture.output({
+        result <- style_dir(args$dir, indent_by = 4, dry = args$dry, recursive = TRUE)
+    })
+} else {
+    captured_output <- capture.output({
+        result <- style_file(args$dir, indent_by = 4, dry = args$dry)
+    })
+}
+
+n <- nrow(subset(result, changed == TRUE))
+if (n > 0) {
+    if (args$dry == "off") {
+        print(paste("Changed", n, "files"))
+    } else {
+        stop(paste("Linting failed for", n, "files"))
+    }
+}
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
new file mode 100644
index 0000000..fa0c51a
--- /dev/null
+++ b/.github/workflows/ci.yaml
@@ -0,0 +1,232 @@
+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_24.0
+  MAX_CHUNKS: 40
+jobs:
+  setup:
+    name: Setup cache and determine changed repositories
+    if: ${{ github.repository_owner == 'computational-metabolomics' }}
+    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: ${{ github.event.client_payload.github.payload.comment.id }}
+        reaction-type: hooray
+    - name: Set galaxy fork and branch
+      id: get-fork-branch
+      run: |
+        TMP="${{ github.event.client_payload.slash_command.args.named.fork }}"
+        echo "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: Check for missing containers
+    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
+        repository-list: ${{ needs.setup.outputs.repository-list }}
+        tool-list: ${{ needs.setup.outputs.tool-list }}
+        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:
+        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
+    - 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]: ${{ steps.vars.outputs.run-url }}
+    - name: Check outputs
+      uses: galaxyproject/planemo-ci-action@v1
+      id: check
+      with:
+        mode: check
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index d8d282a..3b6a512 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -1,13 +1,26 @@
 name: Galaxy Tool Linting and Tests for push and PR
-on: [push, pull_request]
+on:
+  pull_request:
+    paths-ignore:
+      - 'deprecated/**'
+      - 'docs/**'
+      - '*'
+  push:
+    branches:
+      - main
+      - master
+    paths-ignore:
+      - 'deprecated/**'
+      - 'docs/**'
+      - '*'
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_21.09
+  GALAXY_BRANCH: release_24.0
   MAX_CHUNKS: 4
   MAX_FILE_SIZE: 1M
 concurrency:
-  # group runs by PR, but keep runs on master separate
-  # because we do not want to cancel toolshed uploads
+  # Group runs by PR, but keep runs on the default branch separate
+  # because we do not want to cancel ToolShed uploads
   group: pr-${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main') && github.run_number || github.ref }}
   cancel-in-progress: true
 jobs:
@@ -30,7 +43,7 @@ jobs:
       commit-range: ${{ steps.discover.outputs.commit-range }}
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
     - name: Print github context properties
       run: |
@@ -43,18 +56,18 @@ jobs:
         echo 'event.after: ${{ github.event.after }}'
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
-      run: echo "::set-output name=galaxy-head-sha::$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)"
-    - uses: actions/setup-python@v1
+      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: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
     - name: Cache .planemo
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       id: cache-planemo
       with:
         path: ~/.planemo
@@ -65,7 +78,7 @@ jobs:
       run: pip install wheel
     - name: Install flake8
       run: pip install flake8 flake8-import-order
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
@@ -96,30 +109,38 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
-    # checkout the repository
-    # and use it as the current working directory
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v1
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+
+    - name: Set fail level for pull request
+      if: ${{ github.event_name == 'pull_request' }}
+      run:
+        echo "FAIL_LEVEL=warn" >> "$GITHUB_ENV"
+    - name: Set fail level for merge
+      if: ${{ github.event_name != 'pull_request' }}
+      run:
+        echo "FAIL_LEVEL=error" >> "$GITHUB_ENV"
     - name: Planemo lint
       uses: galaxyproject/planemo-ci-action@v1
       id: lint
       with:
         mode: lint
+        fail-level: ${{ env.FAIL_LEVEL }}
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'Tool linting output'
@@ -129,21 +150,21 @@ jobs:
   flake8:
     name: Lint Python scripts
     needs: setup
-    if: ${{ needs.setup.outputs.repository-list != '' }}
+    if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v1
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -152,7 +173,7 @@ jobs:
       run: pip install flake8 flake8-import-order
     - name: Flake8
       run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --output-file pylint_report.txt --tee
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'Python linting output'
@@ -166,52 +187,32 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-20.04]
-        r-version: ['4.0.1']
+        r-version: ['release']
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: r-lib/actions/setup-r@master
+    - uses: r-lib/actions/setup-r@v2
       with:
         r-version: ${{ matrix.r-version }}
     - name: Cache R packages
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       with:
         path: ${{ env.R_LIBS_USER }}
         key: r_cache_${{ matrix.os }}_${{ matrix.r-version }}
-    - name: Install non-R lintr dependencies
-      run: sudo apt-get install libcurl4-openssl-dev
-    - name: Install lintr
-      run: |
-        install.packages('remotes')
-        remotes::install_cran("lintr")
-      shell: Rscript {0}
-    - name: Save repositories to file
-      run: echo '${{ needs.setup.outputs.repository-list }}' > repository_list.txt
+    - name: Install packages
+      uses: r-lib/actions/setup-r-dependencies@v2
+      with:
+        packages: |
+          any::argparse 
+          any::styler
     - name: lintr
       run: |
-        library(lintr)
-        linters <- with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL)
-        con <- file("repository_list.txt", "r")
-        status <- 0
-        while (TRUE) {
-          repo <- readLines(con, n = 1)
-          if (length(repo) == 0) {
-             break
-          }
-          lnt <- lint_dir(repo, relative_path=T, linters=linters)
-          if (length(lnt) > 0) {
-            status <- 1
-            for (l in lnt) {
-              rel_path <- paste(repo, l$filename, sep="/")
-              write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message), stderr())
-              write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message), "rlint_report.txt", append=TRUE)
-            }
-          }
-        }
-        quit(status = status)
-      shell: Rscript {0}
-    - uses: actions/upload-artifact@v2
+        set -eo pipefail
+        echo '${{ 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'
@@ -222,10 +223,8 @@ jobs:
     needs: setup
     if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
     runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Check file sizes
@@ -240,7 +239,7 @@ jobs:
           cat file_size_report.txt
           exit 1
         fi
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'File size report'
@@ -257,7 +256,7 @@ jobs:
       fail-fast: false
       matrix:
         chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }}
-        python-version: ['3.7']
+        python-version: ['3.11']
     services:
       postgres:
         image: postgres:11
@@ -268,26 +267,29 @@ jobs:
         ports:
           - 5432:5432
     steps:
-    # checkout the repository
-    # and use it as the current working directory
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v1
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Cache .planemo
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       id: cache-planemo
       with:
         path: ~/.planemo
         key: planemo_cache_py_${{ 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
@@ -298,7 +300,10 @@ jobs:
         galaxy-branch: ${{ env.GALAXY_BRANCH }}
         chunk: ${{ matrix.chunk }}
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
-    - uses: actions/upload-artifact@v2
+        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
@@ -307,63 +312,70 @@ jobs:
   #   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
-#  SEEMS TO BE FAILING ON CONDA - UNABLE TO FIX
-#  combine_outputs:
-#    name: Combine chunked test results
-#    needs: [setup, test]
-#    if: ${{ needs.setup.outputs.repository-list != '' }}
-#    runs-on: ubuntu-latest
-#    strategy:
-#      matrix:
-#        python-version: ['3.7']
-#    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: Combine outputs
-#      uses: galaxyproject/planemo-ci-action@v1
-#      id: combine
-#      with:
-#        mode: combine
-#        html-report: true
-#    - uses: actions/upload-artifact@v2
-#      with:
-#        name: 'All tool test results'
-#        path: upload
-#    - name: Check outputs
-#      uses: galaxyproject/planemo-ci-action@v1
-#      id: check
-#      with:
-#        mode: check
+  #   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, flake8, lintr]
+    needs: [setup, lint, combine_outputs]
     if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'computational-metabolomics' }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v1
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -384,9 +396,31 @@ jobs:
         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 == ' computational-metabolomics' }}
+    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]
+    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:
@@ -402,6 +436,6 @@ jobs:
     - 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
\ No newline at end of file
+    - 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/.github/workflows/slash.yaml b/.github/workflows/slash.yaml
new file mode 100644
index 0000000..838257c
--- /dev/null
+++ b/.github/workflows/slash.yaml
@@ -0,0 +1,15 @@
+name: Slash Command Dispatch
+on:
+  issue_comment:
+    types: [created]
+jobs:
+  slashCommandDispatch:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Slash Command Dispatch
+        if: github.repository_owner == 'galaxyproject'
+        uses: peter-evans/slash-command-dispatch@v3
+        with:
+          token: ${{ secrets.PAT }}
+          commands: |
+            run-all-tool-tests