diff --git a/.flake8_requirements b/.flake8_requirements
new file mode 100644
index 0000000..90225d0
--- /dev/null
+++ b/.flake8_requirements
@@ -0,0 +1,2 @@
+flake8
+flake8-import-order
diff --git a/.github/workflows/tools.yaml b/.github/workflows/tools.yaml
index 7a34ded..fe5552b 100644
--- a/.github/workflows/tools.yaml
+++ b/.github/workflows/tools.yaml
@@ -19,7 +19,7 @@ jobs:
       chunk-list: ${{ steps.discover.outputs.chunk-list }}
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: ['3.7']
     steps:
     - name: Print github context properties
       run: |
@@ -85,198 +85,90 @@ jobs:
 
   setup-ci-tools:
     name: Setup as in CI for tools
+    if: ${{ github.repository_owner == 'galaxyproject' }}
+    uses: ./.github/workflows/wf_setup.yaml
+    with:
+      # default-galaxy-fork: galaxyproject
+      # default-galaxy-branch: release_22.05
+      max-chunks: 40
+      github-event-name-override: 'schedule'
+    secrets:
+      PAT: ${{ secrets.PAT }}
+
+  check-setup-ci-tools:
+    name: Check setup
+    needs: setup-ci-tools
     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: ${{ steps.discover.outputs.chunk-list }}
-    strategy:
-      matrix:
-        python-version: [3.7]
     steps:
-    - name: Determine latest commit in the Galaxy repo
-      id: get-galaxy-sha
-      run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)" >> $GITHUB_OUTPUT
-    - uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Cache .cache/pip
-      uses: actions/cache@v3
-      id: cache-pip
-      with:
-        path: ~/.cache/pip
-        key: pip_cache_py_${{ 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@v3
-      with:
-        fetch-depth: 1
-    - name: Artificially exclude workflows (because ci_find_repos discovers tool and workflow repos)
-      run: echo 'test/workflows/' > .tt_skip
-    - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
-      uses: ./
-      id: discover
-      env:
-        GITHUB_EVENT_NAME: schedule
-      with:
-        create-cache: true
-        galaxy-fork: ${{ env.GALAXY_FORK }}
-        galaxy-branch: ${{ env.GALAXY_BRANCH }}
-        max-chunks: ${{ env.MAX_CHUNKS }}
-        python-version: ${{ matrix.python-version }}
-        github-event-name-override: 'schedule'
     - name: Check for empty commit range
-      run: if [ -n "${{ steps.discover.outputs.commit-range }}" ]; then exit 1; fi
+      run: if [ -n "${{ needs.setup-ci-tools.outputs.commit-range }}" ]; then exit 1; fi
     # note: ci_find_repos will find all tools and workflows
     - name: Check that all tools an workflows are in the repository list
       run: |
-        if ! grep -q "tool1" <<<$(echo "${{ steps.discover.outputs.repository-list }}"); then echo "tool1 must be in the repo list"; exit 1; fi
-        if ! grep -q "tool2" <<<$(echo "${{ steps.discover.outputs.repository-list }}"); then echo "tool2 must be in the repo list"; exit 1; fi
-        if grep -q "example3" <<<$(echo "${{ steps.discover.outputs.repository-list }}"); then echo "example3 must not be in the repo list"; exit 1; fi
-        if grep -q "example4" <<<$(echo "${{ steps.discover.outputs.repository-list }}"); then echo "example4 must not be in the repo list"; exit 1; fi
+        if ! grep -q "tool1" <<<$(echo "${{ needs.setup-ci-tools.outputs.repository-list }}"); then echo "tool1 must be in the repo list"; exit 1; fi
+        if ! grep -q "tool2" <<<$(echo "${{ needs.setup-ci-tools.outputs.repository-list }}"); then echo "tool2 must be in the repo list"; exit 1; fi
+        if grep -q "example3" <<<$(echo "${{ needs.setup-ci-tools.outputs.repository-list }}"); then echo "example3 must not be in the repo list"; exit 1; fi
+        if grep -q "example4" <<<$(echo "${{ needs.setup-ci-tools.outputs.repository-list }}"); then echo "example4 must not be in the repo list"; exit 1; fi
     # note: ci_find_tools will find onlytools
     - name: Check that all tools are in the tool list
       run: |
-        if ! grep -q "tool1.xml" <<<$(echo "${{ steps.discover.outputs.tool-list }}"); then echo "tool1.xml must be in the repo list"; exit 1; fi
-        if ! grep -q "tool2.xml" <<<$(echo "${{ steps.discover.outputs.tool-list }}"); then echo "tool2.xml must be in the repo list"; exit 1; fi
+        if ! grep -q "tool1.xml" <<<$(echo "${{ needs.setup-ci-tools.outputs.tool-list }}"); then echo "tool1.xml must be in the repo list"; exit 1; fi
+        if ! grep -q "tool2.xml" <<<$(echo "${{ needs.setup-ci-tools.outputs.tool-list }}"); then echo "tool2.xml must be in the repo list"; exit 1; fi
     # chunk-count will only consider tools/workflows depending on the workflow input to the action
     - name: Check that the number of chunks is three, i.e. the number of tools
-      run: if [ "${{ steps.discover.outputs.chunk-count }}" != "3" ]; then exit 1; fi
+      run: if [ "${{ needs.setup-ci-tools.outputs.chunk-count }}" != "3" ]; then exit 1; fi
 
   lint:
-    name: Test linting of tools
-    needs: [setup-ci-tools]
+    name: Lint
+    needs: setup-ci-tools
+    uses: ./.github/workflows/wf_lint.yaml
+    with:
+      repository-list: ${{ needs.setup-ci-tools.outputs.repository-list }}
+      tool-list: ${{ needs.setup-ci-tools.outputs.tool-list }}
+      galaxy-head-sha: ${{ needs.setup-ci-tools.outputs.galaxy-head-sha }}
+      commit-range: ${{ needs.setup-ci-tools.outputs.commit-range }}
+      planemo-version: ${{ needs.setup-ci-tools.outputs.planemo-version }}
+      fail-level: error
+
+  check-lint:
+    name: Check linting results
+    needs: lint
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.7]
-    steps:
-    - uses: actions/checkout@v3
-      with:
-        fetch-depth: 1
-    - uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Cache .cache/pip
-      uses: actions/cache@v3
-      id: cache-pip
-      with:
-        path: ~/.cache/pip
-        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup-ci-tools.outputs.galaxy-head-sha }}
-    - name: Install wheel
-      run: pip install wheel
-    - name: Planemo lint tools
-      uses: ./
+    steps:  
+    - uses: actions/download-artifact@v3
       with:
-        mode: lint
-        report-level: all
-        fail-level: error
-        repository-list: ${{ needs.setup-ci-tools.outputs.repository-list }}
-        tool-list: ${{ needs.setup-ci-tools.outputs.tool-list }}
-        additional-planemo-options: --report_level all
-      continue-on-error: true
+        path: lint_report.txt
+    # TODO check result of lint job (ie make sure it failed)
     - name: check if all test tools were linted
       run: |
         grep tool1 lint_report.txt
         grep tool2 lint_report.txt
         grep "ERROR: Error 'HTTPConnectionPool" lint_report.txt
         grep "Applying linter tests... CHECK" lint_report.txt
+
   test-tools:
-    name: Test testing of tools
-    needs: [setup-ci-tools]
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        chunk: ${{ fromJson(needs.setup-ci-tools.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@v3
-      with:
-        fetch-depth: 1
-    - uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Cache .cache/pip
-      uses: actions/cache@v3
-      id: cache-pip
-      with:
-        path: ~/.cache/pip
-        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup-ci-tools.outputs.galaxy-head-sha }}
-    - name: Get number of CPU cores
-      uses: SimenB/github-actions-cpu-cores@v1
-      id: cpu-cores
-    - name: Planemo test tools
-      uses: ./
-      id: test-tools
-      with:
-        mode: test
-        repository-list: ${{ needs.setup-ci-tools.outputs.repository-list }}
-        galaxy-fork: ${{ env.GALAXY_FORK }}
-        galaxy-branch: ${{ env.GALAXY_BRANCH }}
-        chunk: ${{ matrix.chunk }}
-        chunk-count: ${{ needs.setup-ci-tools.outputs.chunk-count }}
-        additional-planemo-options: --simultaneous_uploads --check_uploads_ok
-        galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
-    - uses: actions/upload-artifact@v3
-      with:
-        name: 'Tool test output ${{ matrix.chunk }}'
-        path: upload
+    name: Test tools
+    needs: setup-ci-tools
+    uses: ./.github/workflows/wf_test.yaml
+    with:
+      galaxy-fork: ${{ needs.setup-ci-tools.outputs.galaxy-fork }}
+      galaxy-branch: ${{ needs.setup-ci-tools.outputs.galaxy-branch }}
+      planemo-version: ${{ needs.setup-ci-tools.outputs.planemo-version }}
+      repository-list: ${{ needs.setup-ci-tools.outputs.repository-list }}
+      chunk-count: ${{ needs.setup-ci-tools.outputs.chunk-count }}
+      chunk-list: ${{ needs.setup-ci-tools.outputs.chunk-list }}
+      galaxy-head-sha: ${{ needs.setup-ci-tools.outputs.galaxy-head-sha }}
+      # set these values if you want to use different values than the IUC defaults
+      # test-timeout: 900
 
-  combine_outputs:
-    name: Test combining 'chunked' test results
+  check-test:
+    name: Check testing results
     needs: [setup-ci-tools, test-tools]
-    strategy:
-      matrix:
-        python-version: [3.7]
-    # This job runs on Linux
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-      with:
-        fetch-depth: 1
-    - uses: actions/download-artifact@v3
-      with:
-        path: artifacts
-    - uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Cache .cache/pip
-      uses: actions/cache@v3
-      id: cache-pip
-      with:
-        path: ~/.cache/pip
-        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup-ci-tools.outputs.galaxy-head-sha }}
-    - name: Combine outputs
-      uses: ./
-      id: combine
-      with:
-        mode: combine
-        html-report: true
     - name: Check statistics
-      run: if ! grep -q "3\s\+success" <<<$(echo ${{ steps.combine.outputs.statistics }}); then echo "wrong statistics"; exit 1; fi
+      run: if ! grep -q "3\s\+success" <<<$(echo ${{ needs.test-tools.outputs.statistics }}); then echo "wrong statistics"; exit 1; fi
     - uses: actions/upload-artifact@v3
       with:
         name: 'All tool test results'
         path: upload
-    - name: Check outputs
-      uses: ./
-      id: check
-      with:
-        mode: check
diff --git a/.github/workflows/wf_deploy.yaml b/.github/workflows/wf_deploy.yaml
new file mode 100644
index 0000000..fb4ce76
--- /dev/null
+++ b/.github/workflows/wf_deploy.yaml
@@ -0,0 +1,89 @@
+name: Deploy Tools
+on:
+  workflow_call:
+    inputs:
+      galaxy-head-sha:
+        description: 'hash of the latest commit in the Galaxy repo'
+        required: true
+        type: string
+      repository-list:
+        description: 'list of repositories to deploy'
+        required: true
+        type: string
+      python-version-list:
+        description: 'Python versions (stringified JSON array)'
+        default: "[\"3.7\"]"
+        required: false
+        type: string
+      planemo-version:
+        description: 'Planemo version to use'
+        default: "planemo"
+        required: false
+        type: string
+    secrets:
+      TTS_API_KEY:
+        required: true
+      TS_API_KEY:
+        required: true
+
+jobs:
+  # deploy the tools to the toolsheds (first TTS for testing)
+  deploy:
+    name: Deploy
+    if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ${{ fromJson(inputs.python-version-list) }}
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v3
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ inputs.galaxy-head-sha }}_planemo_${{ steps.get-galaxy-sha.outputs.planemo-version }}
+    - name: Deploy on testtoolshed
+      uses: ./
+      with:
+        mode: deploy
+        repository-list: ${{ inputs.repository-list }}
+        shed-target: testtoolshed
+        shed-key: ${{ secrets.TTS_API_KEY }}
+        planemo-version: ${{ inputs.planemo-version }}
+      continue-on-error: true
+    - name: Deploy on toolshed
+      uses: ./
+      with:
+        mode: deploy
+        repository-list: ${{ inputs.repository-list }}
+        shed-target: toolshed
+        shed-key: ${{ secrets.TS_API_KEY }}
+        planemo-version: ${{ inputs.planemo-version }}
+
+  deploy-report:
+    name: Report deploy status
+    needs: [deploy]
+    if: ${{ always() && needs.deploy.result != 'success' && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) }}
+    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@v2
+      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 }}
\ No newline at end of file
diff --git a/.github/workflows/wf_lint.yaml b/.github/workflows/wf_lint.yaml
new file mode 100644
index 0000000..5bca14e
--- /dev/null
+++ b/.github/workflows/wf_lint.yaml
@@ -0,0 +1,234 @@
+name: Lint
+on:
+  workflow_call:
+    inputs:
+      repository-list:
+        description: 'list of repositories to lint'
+        default: ''
+        required: false
+        type: string
+      tool-list:
+        description: 'list of tools to lint'
+        default: ''
+        required: false
+        type: string
+      report-level: 
+        description: 'Tool lint report level'
+        default: 'all'
+        required: false
+        type: string
+      fail-level: 
+        description: 'Tool lint fail level'
+        default: 'warn'
+        required: false
+        type: string 
+      galaxy-head-sha:
+        description: 'hash of the latest commit in the Galaxy repo'
+        required: true
+        type: string
+      commit-range:
+        description: 'commit range to test'
+        default: ''
+        required: false
+        type: string
+      max-file-size:
+        description: 'maximum file size'
+        default: "1M"
+        required: false
+        type: string
+      python-version-list:
+        description: 'stringified JSON array of Python versions'
+        default: "[\"3.7\"]"
+        required: false
+        type: string
+      r-version-list:
+        description: 'stringified JSON array of R versions'
+        default: "[\"release\"]"
+        required: false
+        type: string
+      os-version-list:
+        description: 'stringified JSON array of OS versions'
+        default: "[\"ubuntu-20.04\"]"
+        required: false
+        type: string
+      planemo-version:
+        description: 'Planemo version to use'
+        default: "planemo"
+        required: false
+        type: string
+    outputs:
+      result:
+        description: "Result of the lint jobs"
+        value: ${{ jobs.lint-success.result }}
+
+jobs:
+  lint:
+    name: Tools
+    if: ${{ inputs.repository-list != '' || inputs.tool-list != '' }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ${{ fromJson(inputs.python-version-list) }}
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v3
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ inputs.galaxy-head-sha }}_planemo_${{ steps.get-galaxy-sha.outputs.planemo-version }}
+    - name: Planemo lint
+      uses: ./
+      id: lint
+      with:
+        mode: lint
+        report-level: ${{ inputs.report-level }}
+        fail-level: ${{ inputs.fail-level }}
+        repository-list: ${{ inputs.repository-list }}
+        tool-list: ${{ inputs.tool-list }}
+        planemo-version: ${{ inputs.planemo-version }}
+    - uses: actions/upload-artifact@v3
+      if: ${{ failure() }}
+      with:
+        name: 'Tool linting output'
+        path: lint_report.txt
+
+  flake8:
+    name: Python scripts
+    if: ${{ inputs.repository-list != '' }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ${{ fromJson(inputs.python-version-list) }}
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v3
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ inputs.galaxy-head-sha }}_planemo_${{ steps.get-galaxy-sha.outputs.planemo-version }}
+    - name: Install flake8
+      run: pip install -r .flake8_requirements
+    - name: Flake8
+      run: echo '${{ inputs.repository-list }}' | xargs -d '\n' flake8 --output-file pylint_report.txt --tee
+    - uses: actions/upload-artifact@v3
+      if: ${{ failure() }}
+      with:
+        name: 'Python linting output'
+        path: pylint_report.txt
+
+  lintr:
+    name: R scripts
+    if: ${{ inputs.repository-list != '' }}
+    strategy:
+      matrix:
+        os: ${{ fromJson(inputs.os-version-list) }}
+        r-version: ${{ fromJson(inputs.r-version-list) }}
+    runs-on: ${{ matrix.os }}
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 1
+    - uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: ${{ matrix.r-version }}
+    - name: Cache R packages
+      uses: actions/cache@v3
+      with:
+        path: ${{ env.R_LIBS_USER }}
+        key: r_cache_${{ matrix.os }}_${{ matrix.r-version }}
+    - name: Install non-R lintr dependencies
+      run: sudo apt-get install libcurl4-openssl-dev
+    - name: Install lintr
+      run: |
+        install.packages('remotes')
+        remotes::install_cran("lintr")
+      shell: Rscript {0}
+    - name: Save repositories to file
+      run: echo '${{ inputs.repository-list }}' > repository_list.txt
+    - name: lintr
+      run: |
+        library(lintr)
+        linters <- 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, paste("(", l$line, ")")), stderr())
+              write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message, paste("(", l$line, ")")), "rlint_report.txt", append=TRUE)
+            }
+          }
+        }
+        quit(status = status)
+      shell: Rscript {0}
+    - uses: actions/upload-artifact@v3
+      if: ${{ failure() }}
+      with:
+        name: 'R linting output'
+        path: rlint_report.txt
+
+  file_sizes:
+    name: Check file sizes
+    if: ${{ github.event_name == 'pull_request' && inputs.repository-list != '' }}
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+    - name: Check file sizes
+      run: |
+        touch file_size_report.txt
+        git diff --diff-filter=d --name-only ${{ inputs.commit-range }} > git.diff
+        while read line; do
+          find "$line" -type f -size +${{ inputs.max-file-size }} >> file_size_report.txt
+        done < git.diff
+        if [[ -s file_size_report.txt ]]; then
+          echo "Files larger than ${{ inputs.max-file-size }} found"
+          cat file_size_report.txt
+          exit 1
+        fi
+    - uses: actions/upload-artifact@v3
+      if: ${{ failure() }}
+      with:
+        name: 'File size report'
+        path: file_size_report.txt
+
+  lint-success:
+    name: Determine lint success
+    needs: [lint, flake8, lintr, file_sizes]
+    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
diff --git a/.github/workflows/wf_setup.yaml b/.github/workflows/wf_setup.yaml
new file mode 100644
index 0000000..bba67ae
--- /dev/null
+++ b/.github/workflows/wf_setup.yaml
@@ -0,0 +1,181 @@
+name: Setup tool tests
+on:
+  workflow_call:
+    inputs:
+      default-galaxy-fork:
+        description: 'Default Galaxy fork to use'
+        default: 'galaxyproject'
+        required: false
+        type: string
+      default-galaxy-branch:
+        description: 'Default Galaxy branch to use'
+        default: 'release_22.05'
+        required: false
+        type: string
+      default-planemo-version:
+        description: 'Default planemo version to use'
+        default: 'planemo'
+        required: false
+        type: string
+      max-chunks:
+        description: 'maximum number of chunks to use'
+        required: true
+        type: number
+      fetch-depth:
+        description: 'Number of commits to fetch. 0 indicates all history for all branches and tags'
+        default: 1
+        required: false 
+        type: number
+      python-version-list:
+        description: 'Python versions (stringified JSON array)'
+        default: "[\"3.7\"]"
+        required: false
+        type: string
+      ## supposed to be used in internal testing only
+      github-event-name-override:
+        description: 'ONLY FOR TESTING: override GITHUB_EVENT_NAME'
+        default: ''
+        required: false
+        type: string
+      github-ref-override:
+        description: 'ONLY FOR TESTING: override GITHUB_REF'
+        default: ''
+        required: false
+        type: string
+    secrets:
+      PAT:
+        required: false
+    outputs:
+      galaxy-head-sha:
+        description: "hash of the latest commit in the Galaxy repo"
+        value: ${{ jobs.setup.outputs.galaxy-head-sha }}
+      repository-list:
+        description: "list of repositories to test"
+        value: ${{ jobs.setup.outputs.repository-list }}
+      tool-list:
+        description: "list of tools to test"
+        value: ${{ jobs.setup.outputs.tool-list }}
+      chunk-count:
+        description: "number of chunks"
+        value: ${{ jobs.setup.outputs.chunk-count }}
+      chunk-list:
+        description: "list of chunks (stringified JSON array)"
+        value: ${{ jobs.setup.outputs.chunk-list }}
+      commit-range:
+        description: "commit range to test"
+        value: ${{ jobs.setup.outputs.commit-range }}
+      galaxy-fork:
+        description: "The determined galaxy fork to use"
+        value: ${{ jobs.fork-branch.outputs.galaxy-fork }}
+      galaxy-branch:
+        description: "The determined galaxy branch to use"
+        value: ${{ jobs.fork-branch.outputs.galaxy-branch }}
+      planemo-version:
+        description: "The determined planemo version to use"
+        value: ${{ jobs.fork-branch.outputs.planemo-version }}
+jobs:
+  fork-branch:
+    name: Determine Galaxy fork and branch to use
+    runs-on: ubuntu-latest
+    outputs:
+      galaxy-fork: ${{ steps.get-fork-branch.outputs.fork }}
+      galaxy-branch: ${{ steps.get-fork-branch.outputs.branch }}
+      planemo-version: ${{ steps.get-fork-branch.outputs.planemo-version }}
+    steps:
+    - name: Add reaction
+      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      uses: peter-evans/create-or-update-comment@v2
+      with:
+        token: ${{ secrets.PAT }}
+        repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
+        comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
+        reaction-type: hooray
+    - name: Set galaxy fork and branch
+      id: get-fork-branch
+      run: |
+        SLASH_FORK="${{ github.event.client_payload.slash_command.args.named.fork }}"
+        DEFAULT_FORK="${{ inputs.default-galaxy-fork }}"
+        echo "fork=${SLASH_FORK:-$DEFAULT_FORK}" >> $GITHUB_OUTPUT
+        SLASH_BRANCH="${{ github.event.client_payload.slash_command.args.named.branch }}"
+        DEFAULT_BRANCH="${{ inputs.default-galaxy-branch }}"
+        echo "branch=${SLASH_BRANCH:-$DEFAULT_BRANCH}" >> $GITHUB_OUTPUT
+        SLASH_PLANEMO="${{ github.event.client_payload.slash_command.args.named.planemo-version }}"
+        DEFAULT_PLANEMO="${{ inputs.default-planemo-version }}"
+        echo "planemo-version=${SLASH_PLANEMO:-$DEFAULT_PLANEMO}" >> $GITHUB_OUTPUT
+    - name: Print used Galaxy fork and branch and planemo version
+      run: |
+        echo 'fork: ${{ steps.get-fork-branch.outputs.fork }}'
+        echo 'branch: ${{ steps.get-fork-branch.outputs.branch }}'
+        echo 'planemo-version: ${{ steps.get-fork-branch.outputs.planemo-version }}'
+  setup:
+    name: Setup cache and determine changed repositories
+    needs: fork-branch
+    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: ${{ fromJson(inputs.python-version-list) }}
+    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/${{ needs.fork-branch.outputs.galaxy-fork }}/galaxy refs/heads/${{ needs.fork-branch.outputs.galaxy-branch }} | cut -f1)" >> $GITHUB_OUTPUT
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v3
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}_planemo_${{ steps.get-galaxy-sha.outputs.planemo-version }}
+    - name: Cache .planemo
+      uses: actions/cache@v3
+      id: cache-planemo
+      with:
+        path: ~/.planemo
+        key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}_planemo_${{ steps.get-galaxy-sha.outputs.planemo-version }}
+    # 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@v3
+      with:
+        fetch-depth: ${{ inputs.fetch-depth }}
+    - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
+      uses: ./
+      id: discover
+      with:
+        create-cache: ${{ steps.cache-pip.outputs.cache-hit != 'true' || steps.cache-planemo.outputs.cache-hit != 'true' }}
+        galaxy-fork: ${{ needs.fork-branch.outputs.galaxy-fork }}
+        galaxy-branch: ${{ needs.fork-branch.outputs.galaxy-branch }}
+        max-chunks: ${{ inputs.max-chunks }}
+        python-version: ${{ matrix.python-version }}
+        planemo-version: ${{ needs.fork-branch.outputs.planemo-version }}
+        github-event-name-override: ${{ inputs.github-event-name-override }}
+        github-ref-override: ${{ inputs.github-ref-override }}
+    - name: Show commit range
+      run: echo '${{ 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 }})'
\ No newline at end of file
diff --git a/.github/workflows/wf_test.yaml b/.github/workflows/wf_test.yaml
new file mode 100644
index 0000000..6d6e6ba
--- /dev/null
+++ b/.github/workflows/wf_test.yaml
@@ -0,0 +1,198 @@
+name: Test tools
+on:
+  workflow_call:
+    inputs:
+      python-version-list:
+        description: 'Python versions (stringified JSON array)'
+        default: "[\"3.7\"]"
+        required: false
+        type: string
+      chunk-count:
+        description: 'number of chunks'
+        required: true
+        type: string
+      chunk-list:
+        description: 'list of chunks (stringified JSON array)'
+        required: true
+        type: string
+      repository-list:
+        description: 'list of repositories to test'
+        required: true
+        type: string
+      galaxy-head-sha:
+        description: 'hash of the latest commit in the Galaxy repo'
+        required: true
+        type: string
+      galaxy-fork:
+        description: 'Galaxy fork to use'
+        required: true
+        type: string
+      galaxy-branch:
+        description: 'Galaxy branch to use'
+        required: true
+        type: string
+      cache-planemo:
+        description: 'cache the .planemo directory'
+        default: true
+        required: false
+        type: boolean
+      test-timeout:
+        description: 'Timeout in seconds per test'
+        default: 900
+        required: false
+        type: number
+      planemo-version:
+        description: 'Planemo version to use'
+        default: "planemo"
+        required: false
+        type: string
+    secrets:
+      PAT:
+        required: false
+    outputs:
+      result:
+        description: "Result of the testing"
+        value: ${{ jobs.test-success.result }}
+      statistics:
+        description: "Statistics of the test results"
+        value: "${{ jobs.combine_outputs.outputs.statistics }}"
+jobs:
+  # Planemo test the changed repositories, each chunk creates an artifact
+  # containing HTML and JSON reports for the executed tests
+  test:
+    name: Test tools
+    if: ${{ inputs.repository-list != '' }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        chunk: ${{ fromJson(inputs.chunk-list) }}
+        python-version: ${{ fromJson(inputs.python-version-list) }} 
+    services:
+      postgres:
+        image: postgres:11
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v3
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ inputs.galaxy-head-sha }}_planemo_${{ steps.get-galaxy-sha.outputs.planemo-version }}
+    - name: Cache .planemo
+      if: ${{ inputs.cache-planemo }}
+      uses: actions/cache@v3
+      id: cache-planemo
+      with:
+        path: ~/.planemo
+        key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ inputs.galaxy-head-sha }}_planemo_${{ steps.get-galaxy-sha.outputs.planemo-version }}
+    - name: Get number of CPU cores
+      uses: SimenB/github-actions-cpu-cores@v1
+      id: cpu-cores
+    - name: Clean dotnet folder for space
+      run: rm -Rf /usr/share/dotnet
+    - name: Planemo test
+      uses: ./
+      id: test
+      with:
+        mode: test
+        repository-list: ${{ inputs.repository-list }}
+        galaxy-fork: ${{ inputs.galaxy-fork }}
+        galaxy-branch: ${{ inputs.galaxy-branch }}
+        chunk: ${{ matrix.chunk }}
+        chunk-count: ${{ inputs.chunk-count }}
+        galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
+        # Limit each test to 15 minutes
+        test_timeout: ${{ inputs.test-timeout }}
+        planemo-version: ${{ inputs.planemo-version }}
+    - uses: actions/upload-artifact@v3
+      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: test
+    runs-on: ubuntu-latest
+    outputs:
+      galaxy-fork: ${{ steps.combine.outputs.statistics }}
+    strategy:
+      matrix:
+        python-version: ${{ fromJson(inputs.python-version-list) }}
+    steps:
+    - uses: actions/download-artifact@v3
+      with:
+        path: artifacts
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v3
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ inputs.galaxy-head-sha }}_planemo_${{ steps.get-galaxy-sha.outputs.planemo-version }}
+    - name: Combine outputs
+      uses: ./
+      id: combine
+      with:
+        mode: combine
+        planemo-version: ${{ inputs.planemo-version }}
+        html-report: true
+    - uses: actions/upload-artifact@v3
+      with:
+        name: 'All tool test results'
+        path: upload
+    - name: Create URL to the run output
+      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      id: vars
+      run: echo "run-url=https://github.com/$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@v2
+      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]: ${{ steps.vars.outputs.run-url }}
+    - name: Print statistics
+      run: |
+        echo "${{ steps.combine.outputs.statistics }}"
+    - name: Check outputs
+      uses: ./
+      id: check
+      with:
+        mode: check
+
+  test-success:
+    name: Determine test success
+    needs: [combine_outputs]
+    if: ${{ always() && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/main' }}
+    runs-on: ubuntu-latest
+    steps:
+    - name: Check tool test status
+      if: ${{ needs.combine_outputs.result != 'success' && needs.combine_outputs.result != 'skipped' }}
+      run: exit 1
diff --git a/.github/workflows/workflows.yaml b/.github/workflows/workflows.yaml
index bc506be..635a75a 100644
--- a/.github/workflows/workflows.yaml
+++ b/.github/workflows/workflows.yaml
@@ -117,8 +117,6 @@ jobs:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 1
-    - name: Artificially exclude tools (because ci_find_repos discovers tool and workflow repos)
-      run: echo 'test/tools/' > .tt_skip
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
       uses: ./
       id: discover
diff --git a/.tt_skip b/.tt_skip
new file mode 100644
index 0000000..e1b4e62
--- /dev/null
+++ b/.tt_skip
@@ -0,0 +1 @@
+test/workflows/
\ No newline at end of file
diff --git a/.wt_skip b/.wt_skip
new file mode 100644
index 0000000..300b835
--- /dev/null
+++ b/.wt_skip
@@ -0,0 +1 @@
+test/tools/
\ No newline at end of file
diff --git a/planemo_ci_actions.sh b/planemo_ci_actions.sh
index 3370892..986779b 100755
--- a/planemo_ci_actions.sh
+++ b/planemo_ci_actions.sh
@@ -19,12 +19,18 @@ fi
 GITHUB_EVENT_NAME=${GITHUB_EVENT_NAME_OVERRIDE:-$GITHUB_EVENT_NAME}
 GITHUB_REF=${GITHUB_REF_OVERRIDE:-$GITHUB_REF}
 
+if [ "$WORKFLOWS" == "true" ]; then
+  SKIP_FILE=".wt_skip"
+else
+  SKIP_FILE=".tt_skip"
+fi
+
 # setup mode
 # - get commit range (for push and pull_request events) .. 
 #   not set for sheduled and repository_dispatch events
 # - get list of relevant tools and repositories
 #   - tools/repos in the commit range (if set)
-#   - tools/repos not listed in .tt_skip or contained in 
+#   - tools/repos not listed in .tt_skip (resp .wt_skip) or contained in 
 #     `packages/` or `deprecated/`
 # - determine chunk count as linear function of the number
 #   of tools (limited by MAX_CHUNK)
@@ -66,13 +72,13 @@ if [ "$REPOSITORIES" == "" ] && [ "$MODE" == "setup" ]; then
     PLANEMO_COMMIT_RANGE=("--changed_in_commit_range" "$COMMIT_RANGE")
   fi
   
-  touch .tt_skip
-  planemo ci_find_repos "${PLANEMO_COMMIT_RANGE[@]}" --exclude packages --exclude deprecated --exclude_from .tt_skip --output repository_list.txt
+  touch "$SKIP_FILE"
+  planemo ci_find_repos "${PLANEMO_COMMIT_RANGE[@]}" --exclude packages --exclude deprecated --exclude_from "$SKIP_FILE" --output repository_list.txt
   REPOSITORIES=$(cat repository_list.txt)
 
   touch tool_list.txt
   if [ "$WORKFLOWS" != "true" ]; then
-    planemo ci_find_tools "${PLANEMO_COMMIT_RANGE[@]}" --exclude packages --exclude deprecated --exclude_from .tt_skip --output tool_list.txt
+    planemo ci_find_tools "${PLANEMO_COMMIT_RANGE[@]}" --exclude packages --exclude deprecated --exclude_from "$SKIP_FILE" --output tool_list.txt
     TOOLS=$(cat tool_list.txt)
   fi
 
diff --git a/test/tools/galaxy_slots/.shed.yml b/test/tools/galaxy_slots/.shed.yml
index 7ff5cd8..a6bd43a 100644
--- a/test/tools/galaxy_slots/.shed.yml
+++ b/test/tools/galaxy_slots/.shed.yml
@@ -1,4 +1,4 @@
-categories: [Sequence Analysis]
+categories: [Testing]
 description: test setting GALAXY_SLOTS
 name: galaxy_slots
 owner: adent