diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
new file mode 100644
index 0000000..cd67886
--- /dev/null
+++ b/.github/workflows/ci.yaml
@@ -0,0 +1,165 @@
+name: Weekly global Tool Linting and Tests
+on:
+  schedule:
+    # Run at midnight every monday
+    - cron: '0 0 * * 1'
+  repository_dispatch:
+    types: [run-all-tool-tests-command]
+env:
+  GALAXY_RELEASE: release_20.09
+jobs:
+  setup:
+    name: Setup cache
+    if: github.repository_owner == 'computational-metabolomics'
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7]
+    steps:
+    - name: Add reaction
+      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      uses: peter-evans/create-or-update-comment@v1
+      with:
+        token: ${{ secrets.PAT }}
+        repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
+        comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
+        reaction-type: hooray
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_${{ matrix.python-version }}_${{ env.GALAXY_RELEASE }}
+    # Install the `wheel` package so that when installing other packages which
+    # are not available as wheels, pip will build a wheel for them, which can be cached.
+    - name: Install wheel
+      run: pip install wheel
+    - name: Install Planemo
+      run: pip install planemo
+    - name: Fake a planemo run to update cache
+      run: |
+        touch tool.xml
+        PIP_QUIET=1 planemo test --galaxy_python_version ${{ matrix.python-version }} --no_conda_auto_init --galaxy_branch $GALAXY_RELEASE
+  test:
+    name: Test tools
+    # This job runs on Linux
+    runs-on: ubuntu-latest
+    needs: setup
+    strategy:
+      fail-fast: false
+      matrix:
+        chunk: [0,1,2,3]
+        python-version: [3.7]
+    services:
+      postgres:
+        image: postgres:11
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+    # checkout the repository
+    # and use it as the current working directory
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_${{ matrix.python-version }}_${{ env.GALAXY_RELEASE }}
+    - name: Install Planemo
+      run: pip install planemo
+    - name: Planemo ci_find_tools
+      run: planemo ci_find_tools --chunk_count 4 --chunk ${{ matrix.chunk  }} --exclude test_repositories --exclude packages --exclude deprecated --exclude_from .tt_skip --exclude_from .tt_biocontainer_skip --group_tools --output tool.list
+    - name: Show repo list
+      run: cat tool.list
+    - name: Planemo test tools
+      run: |
+           mkdir json_output/
+           while read -r TOOLS; do
+               if grep -qf .tt_biocontainer_skip <(echo $TOOLS); then
+                   PLANEMO_OPTIONS=""
+               else
+                   PLANEMO_OPTIONS="--biocontainers --no_dependency_resolution --no_conda_auto_init"
+               fi
+               json=$(mktemp -u -p json_output --suff .json)
+               PIP_QUIET=1 planemo test --database_connection postgresql://postgres:postgres@localhost:5432/galaxy $PLANEMO_OPTIONS --galaxy_branch $GALAXY_RELEASE  --galaxy_python_version ${{ matrix.python-version }} --test_output_json $json $TOOLS || true
+               docker system prune --all --force --volumes || true
+           done < tool.list
+    - name: Merge tool_test_output.json files
+      run: planemo merge_test_reports json_output/*.json tool_test_output.json
+    - name: Create tool_test_output.html
+      run: planemo test_reports tool_test_output.json --test_output tool_test_output.html
+    - name: Copy artifacts into place
+      run: |
+        mkdir upload
+        mv tool_test_output.json tool_test_output.html upload/
+    - uses: actions/upload-artifact@v2.0.1
+      with:
+        name: 'Tool test output ${{ matrix.chunk  }}'
+        path: upload
+
+  combine_outputs:
+    name: Combine chunked test results
+    needs: test
+    strategy:
+      matrix:
+        python-version: [3.7]
+    # This job runs on Linux
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/download-artifact@v2
+      with:
+        path: artifacts
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install Planemo
+      run: pip install planemo
+    - name: Install jq
+      run: sudo apt-get install jq
+    - name: Combine outputs
+      run: find artifacts -name tool_test_output.json -exec sh -c 'planemo merge_test_reports "$@" tool_test_output.json' sh {} +
+    - name: Create tool_test_output.html
+      run: planemo test_reports tool_test_output.json --test_output tool_test_output.html
+    - name: Copy artifacts into place
+      run: |
+        mkdir upload
+        mv tool_test_output.json tool_test_output.html upload/
+    - uses: actions/upload-artifact@v2.0.1
+      with:
+        name: 'All tool test results'
+        path: upload
+
+    - name: Create URL to the run output
+      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      id: vars
+      run: echo ::set-output name=run-url::https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID
+
+    - name: Create comment
+      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      uses: peter-evans/create-or-update-comment@v1
+      with:
+        token: ${{ secrets.PAT }}
+        repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
+        issue-number: ${{ github.event.client_payload.github.payload.issue.number }}
+        body: |
+          [Find all tool test results here][1]
+
+          [1]: ${{ steps.vars.outputs.run-url }}
+    - name: Check status of combined outputs
+      run: |
+        if jq '.["tests"][]["data"]["status"]' upload/tool_test_output.json | grep -v "success"; then
+            echo "Unsuccessful tests found, inspect the 'All tool test results' artifact for details."
+            exit 1
+        fi
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
new file mode 100644
index 0000000..ce60228
--- /dev/null
+++ b/.github/workflows/pr.yaml
@@ -0,0 +1,427 @@
+name: Galaxy Tool Linting and Tests for push and PR
+on: [push, pull_request]
+env:
+  GALAXY_REPO: https://github.com/galaxyproject/galaxy
+  GALAXY_RELEASE: release_20.09
+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
+    strategy:
+      matrix:
+        python-version: [3.7]
+    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 }}'
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Determine latest galaxy commit
+      run: echo "GALAXY_HEAD_SHA=$(git ls-remote ${{ env.GALAXY_REPO }} refs/heads/${{ env.GALAXY_RELEASE }} | cut -f1)" >> $GITHUB_ENV
+    - name: Save latest galaxy commit to artifact file
+      run: echo $GALAXY_HEAD_SHA > galaxy.sha
+    - uses: actions/upload-artifact@v2
+      with:
+        name: Workflow artifacts
+        path: galaxy.sha
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
+    - name: Cache .planemo
+      uses: actions/cache@v2
+      id: cache-planemo
+      with:
+        path: ~/.planemo
+        key: planemo_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
+    # Install the `wheel` package so that when installing other packages which
+    # are not available as wheels, pip will build a wheel for them, which can be cached.
+    - name: Install wheel
+      run: pip install wheel
+    - name: Install Planemo and flake8
+      run: pip install planemo flake8 flake8-import-order
+    - name: Fake a Planemo run to update cache
+      if: steps.cache-pip.outputs.cache-hit != 'true' || steps.cache-planemo.outputs.cache-hit != 'true'
+      run: |
+        touch tool.xml
+        PIP_QUIET=1 planemo test --galaxy_python_version ${{ matrix.python-version }} --no_conda_auto_init --galaxy_source $GALAXY_REPO --galaxy_branch $GALAXY_RELEASE
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+    # The range of commits to check for changes is:
+    # - `origin/master...` for all events happening on a feature branch
+    # - for events on the master branch we compare against the sha before the event
+    #   (note that this does not work for feature branch events since we want all
+    #   commits on the feature branch and not just the commits of the last event)
+    # - for pull requests we compare against the 1st ancestor, given the current
+    #   HEAD is the merge between the PR branch and the base branch
+    - name: Set commit range (push to the feature branch)
+      if: github.ref != 'refs/heads/master' && github.event_name == 'push'
+      run: |
+        git fetch origin master
+        echo "COMMIT_RANGE=origin/master..." >> $GITHUB_ENV
+    - name: Set commit range (push to the master branch, e.g. merge)
+      if: github.ref == 'refs/heads/master' && github.event_name == 'push'
+      run: echo "COMMIT_RANGE=${{ github.event.before }}.." >> $GITHUB_ENV
+    - name: Set commit range (pull request)
+      if: github.event_name == 'pull_request'
+      run: echo "COMMIT_RANGE=HEAD~.." >> $GITHUB_ENV
+    - name: Planemo ci_find_repos
+      run: planemo ci_find_repos --changed_in_commit_range $COMMIT_RANGE --exclude packages --exclude deprecated --exclude_from .tt_skip --output changed_repositories.list
+    - name: Show repo list
+      run: cat changed_repositories.list
+    - uses: actions/upload-artifact@v2.0.1
+      with:
+        name: Workflow artifacts
+        path: changed_repositories.list
+
+  # Planemo lint the changed repositories
+  lint:
+    name: Lint tools
+    needs: setup
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.7]
+    steps:
+    # checkout the repository
+    # and use it as the current working directory
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - uses: actions/download-artifact@v2
+      with:
+        name: Workflow artifacts
+        path: ../workflow_artifacts/
+    - name: Determine latest galaxy commit
+      run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
+    - name: Install Planemo
+      run: pip install planemo
+    - name: Planemo lint
+      run: |
+        set -e
+        while read -r DIR; do
+            planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive "$DIR";
+        done < ../workflow_artifacts/changed_repositories.list
+
+  # flake8 of Python scripts in the changed repositories
+  flake8:
+    name: Lint Python scripts
+    needs: setup
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.7]
+    steps:
+    # checkout the repository to master
+    # and use it as the current working directory
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - uses: actions/download-artifact@v2
+      with:
+        name: Workflow artifacts
+        path: ../workflow_artifacts/
+    - name: Determine latest galaxy commit
+      run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
+    - name: Install flake8
+      run: pip install flake8 flake8-import-order
+    - name: Flake8
+      run: |
+        if [ -s ../workflow_artifacts/changed_repositories.list ]; then
+            flake8 $(cat ../workflow_artifacts/changed_repositories.list)
+        fi
+
+  lintr:
+    name: Lint R scripts
+    needs: setup
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        r-version: [4.0.1]
+    steps:
+    # checkout the repository to master
+    # and use it as the current working directory
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 1
+    - uses: actions/download-artifact@v2
+      with:
+        name: Workflow artifacts
+        path: ../workflow_artifacts/
+    - uses: r-lib/actions/setup-r@master
+      with:
+        r-version: ${{ matrix.r-version }}
+    - name: Cache R packages
+      uses: actions/cache@v2
+      with:
+        path: ${{ env.R_LIBS_USER }}
+        key: r_cache_1${{ 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", force=TRUE)
+      shell: Rscript {0}
+    - name: lintr
+      run: |
+        library(lintr)
+        linters <- with_defaults(line_length_linter = NULL, 
+                                 object_name_linter = NULL,
+                                 object_usage_linter = NULL,
+                                 cyclocomp_linter(complexity_limit = 25))
+        con <- file("../workflow_artifacts/changed_repositories.list", "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())
+            }
+          }
+        }
+        quit(status = status)
+      shell: Rscript {0}
+
+  # Planemo test the changed repositories, each chunk creates an artifact
+  # containing HTML and JSON reports for the executed tests
+  test:
+    name: Test tools
+    # This job runs on Linux
+    runs-on: ubuntu-latest
+    needs: setup
+    strategy:
+      fail-fast: false
+      matrix:
+        chunk: [0]
+        python-version: [3.7]
+    services:
+      postgres:
+        image: postgres:11
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+    # checkout the repository
+    # and use it as the current working directory
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - uses: actions/download-artifact@v2
+      with:
+        name: Workflow artifacts
+        path: ../workflow_artifacts/
+    - name: Determine latest galaxy commit
+      run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
+    - name: Cache .planemo
+      uses: actions/cache@v2
+      id: cache-planemo
+      with:
+        path: ~/.planemo
+        key: planemo_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
+    - name: Install Planemo
+      run: pip install planemo
+    - name: Planemo ci_find_tools
+      run: |
+        touch changed_repositories_chunk.list changed_tools_chunk.list
+        if [ -s ../workflow_artifacts/changed_repositories.list ]; then
+            if [ $(wc -l < ../workflow_artifacts/changed_repositories.list) -eq 1 ]; then
+                planemo ci_find_tools --chunk_count 1 --chunk ${{ matrix.chunk }} \
+                               --output changed_tools_chunk.list \
+                               $(cat ../workflow_artifacts/changed_repositories.list)
+            else
+                planemo ci_find_repos --chunk_count 1 --chunk ${{ matrix.chunk }} \
+                               --output changed_repositories_chunk.list \
+                               $(cat ../workflow_artifacts/changed_repositories.list)
+            fi
+        fi
+    - name: Show changed tools/repositories chunk list
+      run: cat changed_tools_chunk.list changed_repositories_chunk.list
+    - name: Planemo test tools
+      run: |
+        if grep -lqf .tt_biocontainer_skip changed_tools_chunk.list changed_repositories_chunk.list; then
+                PLANEMO_OPTIONS=""
+        else
+                PLANEMO_OPTIONS="--biocontainers --no_dependency_resolution --no_conda_auto_init"
+        fi
+        if [ -s changed_tools_chunk.list ]; then
+            PIP_QUIET=1 planemo test --database_connection postgresql://postgres:postgres@localhost:5432/galaxy $PLANEMO_OPTIONS --galaxy_source $GALAXY_REPO --galaxy_branch $GALAXY_RELEASE --galaxy_python_version ${{ matrix.python-version }} --test_output_json tool_test_output.json $(cat changed_tools_chunk.list) || true
+            docker system prune --all --force --volumes || true
+        elif [ -s changed_repositories_chunk.list ]; then
+            while read -r DIR; do
+                if [[ "$DIR" =~ ^data_managers.* ]]; then
+                    TESTPATH=$(planemo ci_find_tools "$DIR")
+                else
+                    TESTPATH="$DIR"
+                fi
+                PIP_QUIET=1 planemo test --database_connection postgresql://postgres:postgres@localhost:5432/galaxy $PLANEMO_OPTIONS --galaxy_source $GALAXY_REPO --galaxy_branch $GALAXY_RELEASE --galaxy_python_version ${{ matrix.python-version }} --test_output_json "$DIR"/tool_test_output.json "$TESTPATH" || true
+                docker system prune --all --force --volumes || true
+            done < changed_repositories_chunk.list
+        else
+            echo '{"tests":[]}' > tool_test_output.json
+        fi
+    - name: Merge tool_test_output.json files
+      run: find . -name tool_test_output.json -exec sh -c 'planemo merge_test_reports "$@" tool_test_output.json' sh {} +
+    - name: Create tool_test_output.html
+      run: planemo test_reports tool_test_output.json --test_output tool_test_output.html
+    - name: Copy artifacts into place
+      run: |
+        mkdir upload
+        mv tool_test_output.json tool_test_output.html upload/
+    - uses: actions/upload-artifact@v2.0.1
+      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
+    strategy:
+      matrix:
+        python-version: [3.7]
+    # This job runs on Linux
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/download-artifact@v2
+      with:
+        path: artifacts
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Determine latest galaxy commit
+      run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
+    - name: Install Planemo
+      run: pip install planemo
+    - name: Install jq
+      run: sudo apt-get install jq
+    - name: Combine outputs
+      run: find artifacts/ -name tool_test_output.json -exec sh -c 'planemo merge_test_reports "$@" tool_test_output.json' sh {} +
+    - name: Create tool_test_output.html
+      run: planemo test_reports tool_test_output.json --test_output tool_test_output.html
+    - name: Copy artifacts into place
+      run: |
+        mkdir upload
+        mv tool_test_output.json tool_test_output.html upload/
+    - uses: actions/upload-artifact@v2.0.1
+      with:
+        name: 'All tool test results'
+        path: upload
+    - name: Check status of combined status
+      run: |
+        if jq '.["tests"][]["data"]["status"]' upload/tool_test_output.json | grep -v "success"; then
+            echo "Unsuccessful tests found, inspect the 'All tool test results' artifact for details."
+            exit 1
+        fi
+
+  # deploy the tools to the toolsheds (first TTS for testing)
+  deploy:
+    name: Deploy
+    needs: [lint,flake8,lintr,combine_outputs]
+    strategy:
+      matrix:
+        python-version: [3.7]
+    runs-on: ubuntu-latest
+    if: github.ref == 'refs/heads/master' && github.repository_owner == 'computational-metabolomics'
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - uses: actions/download-artifact@v2
+      with:
+        name: Workflow artifacts
+        path: ../workflow_artifacts/
+    - name: Determine latest galaxy commit
+      run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
+    - name: Cache .cache/pip
+      uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_$GALAXY_HEAD_SHA
+    - name: Install Planemo
+      run: pip install planemo
+    - name: Deploy on testtoolshed
+      env:
+        SHED_KEY: ${{ secrets.tts_api_key }}
+      run: |
+        while read -r DIR; do
+            planemo shed_update --shed_target testtoolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" || exit 1;
+        done < ../workflow_artifacts/changed_repositories.list
+      continue-on-error: true
+    - name: Deploy on toolshed
+      env:
+        SHED_KEY: ${{ secrets.ts_api_key }}
+      run: |
+        while read -r DIR; do
+            planemo shed_update --shed_target toolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" || exit 1;
+        done < ../workflow_artifacts/changed_repositories.list
diff --git a/.github/workflows/slash.yaml b/.github/workflows/slash.yaml
new file mode 100644
index 0000000..918e645
--- /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 == 'computational-metabolomics'
+        uses: peter-evans/slash-command-dispatch@v2
+        with:
+          token: ${{ secrets.PAT }}
+          commands: |
+            run-all-tool-tests
diff --git a/.tt_skip b/.tt_skip
new file mode 100644
index 0000000..e69de29
diff --git a/README.rst b/README.rst
index 972669c..1cf7fbf 100644
--- a/README.rst
+++ b/README.rst
@@ -3,13 +3,13 @@ msPurity for Galaxy
 |Build Status (Travis)| |Git| |Bioconda| |License|
 
 
-Version v1.12.2+galaxy3
-------
+Version v1.16.2+galaxy0
+------------------------
 
   - msPurity
-     - bioconductor-mspurity v1.12.2
+     - bioconductor-mspurity v1.16.2
   - Galaxy tools
-     - v3
+     - v0
 
 About
 ------
@@ -35,17 +35,17 @@ Use the following links for more details of the msPurity R package:
 
 
 Dependencies
-------
-Dependencies for these Galaxy tools should be handled by CONDA. The most recent version of the msPurity R package can found on channel  `tomnl <https://anaconda.org/tomnl/bioconductor-mspurity>`_ on `anaconda <https://anaconda.org/tomnl/bioconductor-mspurity>`_. Warning this will be a different version of the package compared to the BICONDA bioconductor-mspurity.
+------------------
+Dependencies for these Galaxy tools should be handled by CONDA.
 
 
 Galaxy
-------
+------------------
 `Galaxy <https://galaxyproject.org>`_ is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
 
 
 Authors, contributors & contacts
--------------------------
+-------------------------------------
 
 - Thomas N. Lawson (t.n.lawson@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_
 - Ralf J. M. Weber (r.j.weber@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_
@@ -55,6 +55,12 @@ Authors, contributors & contacts
 
 Changes
 -------------------------
+v1.16.2-galaxy0
+  - Version bump
+  - Fix for intra spectral matching
+  - Fix for typo https://github.com/computational-metabolomics/mspurity-galaxy/pull/43
+  - Lint fixes
+
 v1.12.2-galaxy3
   - Bug fix reference to offsets in conditional #41
 
@@ -73,7 +79,7 @@ v1.12.2-galaxy0
   - Update to version v1.12.2 of `msPurity <https://github.com/computational-metabolomics/msPurity/pull/71>`_
   - Optional summary output for combineAnnotations (for very large output)
   - Extra column added to flagRemove output
-  - Hide probmetab input 
+  - Hide probmetab input
   - Make dimsPredictPuritySingle more compatible with "simple workflow inputs"
 
 
@@ -86,7 +92,7 @@ v1.12.0-galaxy1
   - Username updated in Toolshed yaml
 
 v1.12.0-galaxy0
-  - Updates for Bioconductor stable msPurity v1.12.0 release 
+  - Updates for Bioconductor stable msPurity v1.12.0 release
   - Additional columns added for spectral matching (for msnpy use case)
   - Merge of v1.11.4-galaxy1
 
diff --git a/tools/msPurity/.shed.yml b/tools/msPurity/.shed.yml
index db0dece..7885fcd 100644
--- a/tools/msPurity/.shed.yml
+++ b/tools/msPurity/.shed.yml
@@ -6,6 +6,7 @@ description: "[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precu
 auto_tool_repositories:
   name_template: "{{ tool_id }}"
   description_template: "[Metabolomics][LC-MS][DIMS][MS/MS] msPurity - {{ tool_name }} {{description}}"
+  long_description_template: "[Metabolomics][LC-MS][DIMS][MS/MS] msPurity - {{ tool_name }} {{description}}"
 suite:
   name: "suite_mspurity"
   description: "wrapper for msPurity R package"
diff --git a/tools/msPurity/averageFragSpectra.R b/tools/msPurity/averageFragSpectra.R
index 13a488c..81cc843 100644
--- a/tools/msPurity/averageFragSpectra.R
+++ b/tools/msPurity/averageFragSpectra.R
@@ -4,33 +4,33 @@ library(xcms)
 print(sessionInfo())
 
 
-get_av_spectra <- function(x){
+get_av_spectra <- function(x) {
 
-  if (length(x$av_intra)>0){
+  if (length(x$av_intra) > 0) {
     av_intra_df <- plyr::ldply(x$av_intra)
 
-    if (nrow(av_intra_df)==0){
+    if (nrow(av_intra_df) == 0) {
       av_intra_df <- NULL
     }else{
-      av_intra_df$method <- 'intra'
+      av_intra_df$method <- "intra"
     }
 
   }else{
     av_intra_df <- NULL
   }
 
-  if ((is.null(x$av_inter)) || (nrow(x$av_inter)==0)){
+  if ((is.null(x$av_inter)) || (nrow(x$av_inter) == 0)) {
     av_inter_df <- NULL
   }else{
     av_inter_df <- x$av_inter
-    av_inter_df$method <- 'inter'
+    av_inter_df$method <- "inter"
   }
 
-  if ((is.null(x$av_all)) || (nrow(x$av_all)==0)){
+  if ((is.null(x$av_all)) || (nrow(x$av_all) == 0)) {
     av_all_df <- NULL
   }else{
     av_all_df <- x$av_all
-    av_all_df$method <- 'all'
+    av_all_df$method <- "all"
   }
 
   combined <- plyr::rbind.fill(av_intra_df, av_inter_df, av_all_df)
@@ -40,126 +40,116 @@ get_av_spectra <- function(x){
 
 
 option_list <- list(
-  make_option("--out_rdata", type="character"),
-  make_option("--out_peaklist", type="character"),
-  make_option("--pa", type="character"),
-
-  make_option("--av_level", type="character"),
-
-  make_option("--minfrac", default=0.5),
-  make_option("--minnum", default=1),
-  make_option("--ppm", default=5.0),
-
-  make_option("--snr", default=0),
-
-  make_option("--ra", default=0),
-
-  make_option("--av", default="median", type="character"),
-  make_option("--sumi", action="store_true"),
-
-  make_option("--rmp", action="store_true"),
-  make_option("--cores", default=1)
+  make_option("--out_rdata", type = "character"),
+  make_option("--out_peaklist", type = "character"),
+  make_option("--pa", type = "character"),
+  make_option("--av_level", type = "character"),
+  make_option("--minfrac", default = 0.5),
+  make_option("--minnum", default = 1),
+  make_option("--ppm", default = 5.0),
+  make_option("--snr", default = 0),
+  make_option("--ra", default = 0),
+  make_option("--av", default = "median", type = "character"),
+  make_option("--sumi", action = "store_true"),
+  make_option("--rmp", action = "store_true"),
+  make_option("--cores", default = 1)
 )
 
-opt <- parse_args(OptionParser(option_list=option_list))
+opt <- parse_args(OptionParser(option_list = option_list))
 print(opt)
 
 
-loadRData <- function(rdata_path, name){
-#loads an RData file, and returns the named xset object if it is there
+load_r_data <- function(rdata_path, name) {
+    #loads an RData file, and returns the named xset object if it is there
     load(rdata_path)
     return(get(ls()[ls() %in% name]))
 }
 
 # Requires
-pa <- loadRData(opt$pa, 'pa')
+pa <- load_r_data(opt$pa, "pa")
 
 pa@cores <- opt$cores
 
-if(is.null(opt$rmp)){
-  rmp = FALSE
+if (is.null(opt$rmp)) {
+  rmp <- FALSE
 }else{
-  rmp = TRUE
+  rmp <- TRUE
 }
 
-if(is.null(opt$sumi)){
-
-  sumi = FALSE
+if (is.null(opt$sumi)) {
+  sumi <- FALSE
 }else{
-  sumi = TRUE
-
+  sumi <- TRUE
 }
 
-
-if(opt$av_level=="intra"){
-
+if (opt$av_level == "intra") {
   pa <- msPurity::averageIntraFragSpectra(pa,
-                                      minfrac=opt$minfrac,
-                                      minnum=opt$minnum,
-                                      ppm=opt$ppm,
-                                      snr=opt$snr,
-                                      ra=opt$ra,
-                                      av=opt$av,
-                                      sumi=sumi,
-                                      rmp=rmp,
-                                      cores=opt$cores)
-
-} else if(opt$av_level=="inter"){
+                                          minfrac = opt$minfrac,
+                                          minnum = opt$minnum,
+                                          ppm = opt$ppm,
+                                          snr = opt$snr,
+                                          ra = opt$ra,
+                                          av = opt$av,
+                                          sumi = sumi,
+                                          rmp = rmp,
+                                          cores = opt$cores)
+
+} else if (opt$av_level == "inter") {
 
   pa <- msPurity::averageInterFragSpectra(pa,
-                                      minfrac=opt$minfrac,
-                                      minnum=opt$minnum,
-                                      ppm=opt$ppm,
-                                      snr=opt$snr,
-                                      ra=opt$ra,
-                                      av=opt$av,
-                                      sumi=sumi,
-                                      rmp=rmp,
-                                      cores=opt$cores)
-} else if(opt$av_level=="all"){
+                                          minfrac = opt$minfrac,
+                                          minnum = opt$minnum,
+                                          ppm = opt$ppm,
+                                          snr = opt$snr,
+                                          ra = opt$ra,
+                                          av = opt$av,
+                                          sumi = sumi,
+                                          rmp = rmp,
+                                          cores = opt$cores)
+} else if (opt$av_level == "all") {
 
   pa <- msPurity::averageAllFragSpectra(pa,
-                                        minfrac=opt$minfrac,
-                                        minnum=opt$minnum,
-                                        ppm=opt$ppm,
-                                        snr=opt$snr,
-                                        ra=opt$ra,
-                                        av=opt$av,
-                                        sumi=sumi,
-                                        rmp=rmp,
-                                        cores=opt$cores)
-
+                                        minfrac = opt$minfrac,
+                                        minnum = opt$minnum,
+                                        ppm = opt$ppm,
+                                        snr = opt$snr,
+                                        ra = opt$ra,
+                                        av = opt$av,
+                                        sumi = sumi,
+                                        rmp = rmp,
+                                        cores = opt$cores)
 }
 
 print(pa)
-save(pa, file=opt$out_rdata)
-
+save(pa, file = opt$out_rdata)
 
-if (length(pa)>0){
+if (length(pa) > 0) {
 
   av_spectra <- plyr::ldply(pa@av_spectra, get_av_spectra)
 
-  if (nrow(av_spectra)==0){
-    message('No average spectra available')
-  } else{
-    colnames(av_spectra)[1] <- 'grpid'
+  if (nrow(av_spectra) == 0) {
+    message("No average spectra available")
+  } else {
+    colnames(av_spectra)[1] <- "grpid"
     av_spectra$grpid <- names(pa@av_spectra)[av_spectra$grpid]
-    
-    if((length(pa@av_intra_params)>0) || (length(pa@av_inter_params)>0) ){
-        # Add some extra info (only required if av_intra or av_inter performed)
-        colnames(av_spectra)[2] <- 'fileid'
-        av_spectra$avid <- 1:nrow(av_spectra)
-        
-        filenames <- sapply(av_spectra$fileid, function(x) names(pa@fileList)[as.integer(x)])
-        # filenames_galaxy <- sapply(av_spectra$fileid, function(x) basename(pa@fileList[as.integer(x)]))
-        
-        av_spectra = as.data.frame(append(av_spectra, list(filename = filenames), after=2))
+
+    if ((length(pa@av_intra_params) > 0) || (length(pa@av_inter_params) > 0)) {
+      # Add some extra info (only required if av_intra or av_inter performed)
+      colnames(av_spectra)[2] <- "fileid"
+      av_spectra$avid <- seq_len(nrow(av_spectra))
+
+      filenames <- sapply(av_spectra$fileid,
+                          function(x) names(pa@fileList)[as.integer(x)])
+      # filenames_galaxy <- sapply(
+      #    av_spectra$fileid, function(x) basename(pa@fileList[as.integer(x)]))
+
+        av_spectra <- as.data.frame(
+          append(av_spectra, list(filename = filenames), after = 2))
     }
 
 
     print(head(av_spectra))
-    write.table(av_spectra, opt$out_peaklist, row.names=FALSE, sep='\t')
+    write.table(av_spectra, opt$out_peaklist, row.names = FALSE, sep = "\t")
 
   }
 }
-
diff --git a/tools/msPurity/combineAnnotations.R b/tools/msPurity/combineAnnotations.R
index 5a83939..04f7aa3 100644
--- a/tools/msPurity/combineAnnotations.R
+++ b/tools/msPurity/combineAnnotations.R
@@ -4,115 +4,120 @@ print(sessionInfo())
 
 # Get the parameter
 option_list <- list(
-  make_option(c("-s","--sm_resultPth"),type="character"),
-  make_option(c("-m","--metfrag_resultPth"),type="character"),
-  make_option(c("-c","--sirius_csi_resultPth"),type="character"),
-  make_option(c("-p","--probmetab_resultPth"),type="character"),
-  make_option(c("-l","--ms1_lookup_resultPth"),type="character"),
-
-  make_option("--ms1_lookup_checkAdducts", action="store_true"),
-  make_option("--ms1_lookup_keepAdducts", type="character", default=NA),
-  make_option("--ms1_lookup_dbSource", type="character", default="hmdb"),
-
-  make_option("--sm_weight", type="numeric"),
-  make_option("--metfrag_weight", type="numeric"),
-  make_option("--sirius_csi_weight", type="numeric"),
-  make_option("--probmetab_weight", type="numeric"),
-  make_option("--ms1_lookup_weight", type="numeric"),
-  make_option("--biosim_weight", type="numeric"),
-  
-  make_option("--summaryOutput", action="store_true"),
-  
-  make_option("--create_new_database", action="store_true"),
-  make_option("--outdir", type="character", default="."),
-
-  make_option("--compoundDbType", type="character", default="sqlite"),
-  make_option("--compoundDbPth", type="character", default=NA),
-  make_option("--compoundDbHost", type="character", default=NA)
+  make_option(c("-s", "--sm_resultPth"), type = "character"),
+  make_option(c("-m", "--metfrag_resultPth"), type = "character"),
+  make_option(c("-c", "--sirius_csi_resultPth"), type = "character"),
+  make_option(c("-p", "--probmetab_resultPth"), type = "character"),
+  make_option(c("-l", "--ms1_lookup_resultPth"), type = "character"),
+
+  make_option("--ms1_lookup_checkAdducts", action = "store_true"),
+  make_option("--ms1_lookup_keepAdducts", type = "character", default = NA),
+  make_option("--ms1_lookup_dbSource", type = "character", default = "hmdb"),
+
+  make_option("--sm_weight", type = "numeric"),
+  make_option("--metfrag_weight", type = "numeric"),
+  make_option("--sirius_csi_weight", type = "numeric"),
+  make_option("--probmetab_weight", type = "numeric"),
+  make_option("--ms1_lookup_weight", type = "numeric"),
+  make_option("--biosim_weight", type = "numeric"),
+
+  make_option("--summaryOutput", action = "store_true"),
+
+  make_option("--create_new_database", action = "store_true"),
+  make_option("--outdir", type = "character", default = "."),
+
+  make_option("--compoundDbType", type = "character", default = "sqlite"),
+  make_option("--compoundDbPth", type = "character", default = NA),
+  make_option("--compoundDbHost", type = "character", default = NA)
 )
-opt <- parse_args(OptionParser(option_list=option_list))
+opt <- parse_args(OptionParser(option_list = option_list))
 
 print(opt)
 
-if (!is.null(opt$create_new_database)){
-  sm_resultPth <-  file.path(opt$outdir, 'combined_annotations.sqlite')
+if (!is.null(opt$create_new_database)) {
+  sm_resultPth <- file.path(opt$outdir, "combined_annotations.sqlite")
   file.copy(opt$sm_resultPth, sm_resultPth)
 }else{
   sm_resultPth <- opt$sm_resultPth
 }
 
-if (is.null(opt$ms1_lookup_checkAdducts)){
+if (is.null(opt$ms1_lookup_checkAdducts)) {
   opt$ms1_lookup_checkAdducts <- FALSE
 }
-if (!is.null(opt$ms1_lookup_keepAdducts)){
+if (!is.null(opt$ms1_lookup_keepAdducts)) {
     opt$ms1_lookup_keepAdducts <- gsub("__ob__", "[", opt$ms1_lookup_keepAdducts)
     opt$ms1_lookup_keepAdducts <- gsub("__cb__", "]", opt$ms1_lookup_keepAdducts)
     ms1_lookup_keepAdducts <- strsplit(opt$ms1_lookup_keepAdducts, ",")[[1]]
 }
 
-weights <-list('sm'=opt$sm_weight,
-               'metfrag'=opt$metfrag_weight,
-               'sirius_csifingerid'= opt$sirius_csi_weight,
-               'probmetab'=opt$probmetab_weight,
-               'ms1_lookup'=opt$ms1_lookup_weight,
-               'biosim'=opt$biosim_weight
+weights <- list("sm" = opt$sm_weight,
+               "metfrag" = opt$metfrag_weight,
+               "sirius_csifingerid" = opt$sirius_csi_weight,
+               "probmetab" = opt$probmetab_weight,
+               "ms1_lookup" = opt$ms1_lookup_weight,
+               "biosim" = opt$biosim_weight
                )
 print(weights)
 
-if (is.null(opt$probmetab_resultPth)){
-  opt$probmetab_resultPth = NA
+if (is.null(opt$probmetab_resultPth)) {
+  opt$probmetab_resultPth <- NA
 }
 
-if (round(!sum(unlist(weights),0)==1)){
-  stop(paste0('The weights should sum to 1 not ', sum(unlist(weights))))
+if (round(!sum(unlist(weights), 0) == 1)) {
+  stop(paste0("The weights should sum to 1 not ", sum(unlist(weights))))
 }
 
-if (is.null(opt$summaryOutput)){
-  summaryOutput = FALSE
+if (is.null(opt$summaryOutput)) {
+  summaryOutput <- FALSE
 }else{
- summaryOutput = TRUE
+ summaryOutput <- TRUE
 }
 
-if (opt$compoundDbType=='local_config'){
+if (opt$compoundDbType == "local_config") {
   # load in compound config
   # Soure local function taken from workflow4metabolomics
-  source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
+  source_local <- function(fname) {
+    argv <- commandArgs(trailingOnly = FALSE)
+    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+    source(paste(base_dir, fname, sep = "/"))
+  }
   source_local("dbconfig.R")
 }else{
-  compoundDbPth = opt$compoundDbPth
-  compoundDbType = opt$compoundDbType
-  compoundDbName = NA
-  compoundDbHost = NA
-  compoundDbPort = NA
-  compoundDbUser = NA
-  compoundDbPass = NA
+  compoundDbPth <- opt$compoundDbPth
+  compoundDbType <- opt$compoundDbType
+  compoundDbName <- NA
+  compoundDbHost <- NA
+  compoundDbPort <- NA
+  compoundDbUser <- NA
+  compoundDbPass <- NA
 }
 
 summary_output <- msPurity::combineAnnotations(
-                            sm_resultPth = sm_resultPth,
-                            compoundDbPth = compoundDbPth,
-                            metfrag_resultPth = opt$metfrag_resultPth,
-                            sirius_csi_resultPth = opt$sirius_csi_resultPth,
-                            probmetab_resultPth = opt$probmetab_resultPth,
-                            ms1_lookup_resultPth = opt$ms1_lookup_resultPth,
-                            ms1_lookup_keepAdducts = ms1_lookup_keepAdducts,
-                            ms1_lookup_checkAdducts = opt$ms1_lookup_checkAdducts,
-
-                            compoundDbType = compoundDbType,
-                            compoundDbName = compoundDbName,
-                            compoundDbHost = compoundDbHost,
-                            compoundDbPort = compoundDbPort,
-                            compoundDbUser = compoundDbUser,
-                            compoundDbPass = compoundDbPass,
-                            weights = weights,
-                            summaryOutput = summaryOutput)
-if (summaryOutput){
-  write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)
+                          sm_resultPth = sm_resultPth,
+                          compoundDbPth = compoundDbPth,
+                          metfrag_resultPth = opt$metfrag_resultPth,
+                          sirius_csi_resultPth = opt$sirius_csi_resultPth,
+                          probmetab_resultPth = opt$probmetab_resultPth,
+                          ms1_lookup_resultPth = opt$ms1_lookup_resultPth,
+                          ms1_lookup_keepAdducts = ms1_lookup_keepAdducts,
+                          ms1_lookup_checkAdducts = opt$ms1_lookup_checkAdducts,
+
+                         compoundDbType = compoundDbType,
+                         compoundDbName = compoundDbName,
+                         compoundDbHost = compoundDbHost,
+                         compoundDbPort = compoundDbPort,
+                         compoundDbUser = compoundDbUser,
+                         compoundDbPass = compoundDbPass,
+                         weights = weights,
+                         summaryOutput = summaryOutput)
+if (summaryOutput) {
+  write.table(summary_output,
+              file.path(opt$outdir, "combined_annotations.tsv"),
+              sep = "\t", row.names = FALSE)
 }
 
-
-write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)
-
+write.table(summary_output,
+            file.path(opt$outdir, "combined_annotations.tsv"),
+            sep = "\t", row.names = FALSE)
 
 closeAllConnections()
-
diff --git a/tools/msPurity/createDatabase.R b/tools/msPurity/createDatabase.R
index 0c2879b..c7ab9c5 100644
--- a/tools/msPurity/createDatabase.R
+++ b/tools/msPurity/createDatabase.R
@@ -3,19 +3,18 @@ library(optparse)
 library(xcms)
 library(CAMERA)
 print(sessionInfo())
-print('CREATING DATABASE')
+print("CREATING DATABASE")
 
-xset_pa_filename_fix <- function(opt, pa, xset){
+xset_pa_filename_fix <- function(opt, pa, xset) {
 
-  if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
+  if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)) {
     # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
     # needs to be done due to Galaxy moving the files around and screwing up any links to files
 
-    filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
+    filepaths <- trimws(strsplit(opt$mzML_files, ",")[[1]])
     filepaths <- filepaths[filepaths != ""]
-    new_names <- basename(filepaths)
 
-    galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
+    galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]])
     galaxy_names <- galaxy_names[galaxy_names != ""]
 
     nsave <- names(pa@fileList)
@@ -28,10 +27,10 @@ xset_pa_filename_fix <- function(opt, pa, xset){
   }
 
 
- if(!all(basename(pa@fileList)==basename(xset@filepaths))){
-    if(!all(names(pa@fileList)==basename(xset@filepaths))){
-       print('FILELISTS DO NOT MATCH')
-       message('FILELISTS DO NOT MATCH')
+ if (!all(basename(pa@fileList) == basename(xset@filepaths))) {
+    if (!all(names(pa@fileList) == basename(xset@filepaths))) {
+       print("FILELISTS DO NOT MATCH")
+       message("FILELISTS DO NOT MATCH")
        quit(status = 1)
     }else{
       xset@filepaths <- unname(pa@fileList)
@@ -48,23 +47,23 @@ xset_pa_filename_fix <- function(opt, pa, xset){
 
 
 option_list <- list(
-  make_option(c("-o", "--outDir"), type="character"),
-  make_option("--pa", type="character"),
-  make_option("--xset_xa", type="character"),
-  make_option("--xcms_camera_option", type="character"),
-  make_option("--eic", action="store_true"),
-  make_option("--cores", default=4),
-  make_option("--mzML_files", type="character"),
-  make_option("--galaxy_names", type="character"),
-  make_option("--grpPeaklist", type="character")
+  make_option(c("-o", "--outDir"), type = "character"),
+  make_option("--pa", type = "character"),
+  make_option("--xset_xa", type = "character"),
+  make_option("--xcms_camera_option", type = "character"),
+  make_option("--eic", action = "store_true"),
+  make_option("--cores", default = 4),
+  make_option("--mzML_files", type = "character"),
+  make_option("--galaxy_names", type = "character"),
+  make_option("--grpPeaklist", type = "character")
 )
 
 
 # store options
-opt<- parse_args(OptionParser(option_list=option_list))
+opt <- parse_args(OptionParser(option_list = option_list))
 print(opt)
 
-loadRData <- function(rdata_path, name){
+loadRData <- function(rdata_path, name) {
 #loads an RData file, and returns the named xset object if it is there
     load(rdata_path)
     return(get(ls()[ls() %in% name]))
@@ -73,36 +72,36 @@ loadRData <- function(rdata_path, name){
 getxcmsSetObject <- function(xobject) {
     # XCMS 1.x
     if (class(xobject) == "xcmsSet")
-        return (xobject)
+        return(xobject)
     # XCMS 3.x
     if (class(xobject) == "XCMSnExp") {
         # Get the legacy xcmsSet object
-        suppressWarnings(xset <- as(xobject, 'xcmsSet'))
-        sampclass(xset) <- xset@phenoData$sample_group
-        return (xset)
+        suppressWarnings(xset <- as(xobject, "xcmsSet"))
+        xcms::sampclass(xset) <- xset@phenoData$sample_group
+        return(xset)
     }
 }
 
 
-print(paste('pa', opt$pa))
+print(paste("pa", opt$pa))
 print(opt$xset)
 
 print(opt$xcms_camera_option)
 # Requires
-pa <- loadRData(opt$pa, 'pa')
+pa <- loadRData(opt$pa, "pa")
 
 
 print(pa@fileList)
 
 # Missing list element causes failures (should be updated
 # in msPurity R package for future releases)
-if (!exists('allfrag', where=pa@filter_frag_params)){
+if (!exists("allfrag", where = pa@filter_frag_params)) {
     pa@filter_frag_params$allfrag <- FALSE
 }
 
-if (opt$xcms_camera_option=='xcms'){
+if (opt$xcms_camera_option == "xcms") {
 
-  xset <- loadRData(opt$xset, c('xset','xdata'))
+  xset <- loadRData(opt$xset, c("xset", "xdata"))
   xset <- getxcmsSetObject(xset)
   fix <- xset_pa_filename_fix(opt, pa, xset)
   pa <- fix[[1]]
@@ -110,7 +109,7 @@ if (opt$xcms_camera_option=='xcms'){
   xa <- NULL
 }else{
 
-  xa <- loadRData(opt$xset, 'xa')
+  xa <- loadRData(opt$xset, "xa")
   fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet)
   pa <- fix[[1]]
   xa@xcmsSet <- fix[[2]]
@@ -118,36 +117,33 @@ if (opt$xcms_camera_option=='xcms'){
 }
 
 
-
-if(is.null(opt$grpPeaklist)){
-  grpPeaklist = NA
+if (is.null(opt$grpPeaklist)) {
+  grpPeaklist <- NA
 }else{
-  grpPeaklist = opt$grpPeaklist
+  grpPeaklist <- opt$grpPeaklist
 }
 
-
-
 dbPth <- msPurity::createDatabase(pa,
-                                   xset=xset,
-                                   xsa=xa,
-                                   outDir=opt$outDir,
-                                   grpPeaklist=grpPeaklist,
-                                   dbName='createDatabase_output.sqlite'
+                                   xset = xset,
+                                   xsa = xa,
+                                   outDir = opt$outDir,
+                                   grpPeaklist = grpPeaklist,
+                                   dbName = "createDatabase_output.sqlite"
 )
 
 
 
 
 
-if (!is.null(opt$eic)){
+if (!is.null(opt$eic)) {
 
-  if (is.null(xset)){
+  if (is.null(xset)) {
       xset <- xa@xcmsSet
   }
   # previous check should have matched filelists together
   xset@filepaths <- unname(pa@fileList)
 
-  convert2Raw <- function(x, xset){
+  convert2Raw <- function(x, xset) {
     sid <- unique(x$sample)
     # for each file get list of peaks
     x$rt_raw <- xset@rt$raw[[sid]][match(x$rt, xset@rt$corrected[[sid]])]
@@ -157,13 +153,14 @@ if (!is.null(opt$eic)){
 
   }
 
-  xset@peaks <- as.matrix(plyr::ddply(data.frame(xset@peaks), ~ sample, convert2Raw, xset=xset))
+  xset@peaks <- as.matrix(
+    plyr::ddply(data.frame(xset@peaks), ~ sample, convert2Raw, xset = xset))
 
   # Saves the EICS into the previously created database
   px <- msPurity::purityX(xset,
                           saveEIC = TRUE,
-                          cores=1,
-                          sqlitePth=dbPth,
+                          cores = 1,
+                          sqlitePth = dbPth,
                           rtrawColumns = TRUE)
 
 }
diff --git a/tools/msPurity/createDatabase.xml b/tools/msPurity/createDatabase.xml
index 6974a40..851b0e0 100644
--- a/tools/msPurity/createDatabase.xml
+++ b/tools/msPurity/createDatabase.xml
@@ -101,7 +101,7 @@ Create SQLite database for LC-MS(/MS) dataset
 
 Create and SQLite database of an LC-MS(/MS) experiment (replaces the create_database function).
 
-Schema details can be found [here](https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-datatabase-schema.html).
+Schema details can be found [here](https://www.bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html).
 
 **Example LC-MS/MS processing workflow**
 
diff --git a/tools/msPurity/createMSP.R b/tools/msPurity/createMSP.R
index 985cff2..180fff6 100644
--- a/tools/msPurity/createMSP.R
+++ b/tools/msPurity/createMSP.R
@@ -4,39 +4,40 @@ print(sessionInfo())
 
 # Get the parameter
 option_list <- list(
-  make_option("--rdata_input",type="character"),
-  make_option("--method",type="character"),
-  make_option("--metadata",type="character"),
-  make_option("--metadata_cols",type="character"),
-  make_option("--metadata_cols_filter",type="character"),
-  make_option("--adduct_split", action="store_true"),
-  make_option("--xcms_groupids",type="character"),
-  make_option("--filter",action="store_true"),
-  make_option("--intensity_ra",type="character"),
-  make_option("--include_adducts",type="character"),
-  make_option("--msp_schema",type="character"),
-  make_option("--include_adducts_custom",type="character", default=""),
-  make_option("--out_dir",type="character", default=".")
+  make_option("--rdata_input", type = "character"),
+  make_option("--method", type = "character"),
+  make_option("--metadata", type = "character"),
+  make_option("--metadata_cols", type = "character"),
+  make_option("--metadata_cols_filter", type = "character"),
+  make_option("--adduct_split", action = "store_true"),
+  make_option("--xcms_groupids", type = "character"),
+  make_option("--filter", action = "store_true"),
+  make_option("--intensity_ra", type = "character"),
+  make_option("--include_adducts", type = "character"),
+  make_option("--msp_schema", type = "character"),
+  make_option("--include_adducts_custom", type = "character", default = ""),
+  make_option("--out_dir", type = "character", default = ".")
 )
-opt <- parse_args(OptionParser(option_list=option_list))
+opt <- parse_args(OptionParser(option_list = option_list))
 
 print(opt)
 
 load(opt$rdata_input)
 
-if (is.null(opt$metadata)){
+if (is.null(opt$metadata)) {
   metadata <- NULL
 }else{
-  metadata <- read.table(opt$metadata,  header = TRUE, sep='\t', stringsAsFactors = FALSE, check.names = FALSE)
+  metadata <- read.table(opt$metadata,  header = TRUE, sep = "\t",
+                         stringsAsFactors = FALSE, check.names = FALSE)
 
-  if(!opt$metadata_cols_filter==''){
-     metadata_cols_filter <- strsplit(opt$metadata_cols_filter, ',')[[1]]
+  if (!opt$metadata_cols_filter == "") {
+     metadata_cols_filter <- strsplit(opt$metadata_cols_filter, ",")[[1]]
 
-     metadata <- metadata[,metadata_cols_filter, drop=FALSE]
+     metadata <- metadata[, metadata_cols_filter, drop = FALSE]
      print(metadata)
 
-     if (!"grpid" %in% colnames(metadata)){
-       metadata$grpid <- 1:nrow(metadata)
+     if (!"grpid" %in% colnames(metadata)) {
+       metadata$grpid <- seq_len(nrow(metadata))
      }
 
      print(metadata)
@@ -47,7 +48,7 @@ if (is.null(opt$metadata)){
 
 
 
-if (is.null(opt$metadata_cols) || opt$metadata_cols==''){
+if (is.null(opt$metadata_cols) || opt$metadata_cols == "") {
     metadata_cols <- NULL
 }else{
     metadata_cols <- opt$metadata_cols
@@ -55,36 +56,33 @@ if (is.null(opt$metadata_cols) || opt$metadata_cols==''){
 }
 
 
-if(is.null(opt$adduct_split)){
+if (is.null(opt$adduct_split)) {
   adduct_split <- FALSE
 }else{
   adduct_split <- TRUE
 }
 
-if (is.null(opt$xcms_groupids)){
+if (is.null(opt$xcms_groupids)) {
   xcms_groupids <- NULL
 }else{
-  xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ',')[[1]])
+  xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ",")[[1]])
 }
 
 
-
-
-
-if (is.null(opt$include_adducts_custom)){
-  include_adducts_custom <- ''
+if (is.null(opt$include_adducts_custom)) {
+  include_adducts_custom <- ""
 }else{
   include_adducts_custom <- opt$include_adducts_custom
 }
 
 
-if (opt$include_adducts=='None'){
-  include_adducts <- ''
+if (opt$include_adducts == "None") {
+  include_adducts <- ""
 }else{
   include_adducts <- opt$include_adducts
 }
 
-include_adducts_all <- paste(include_adducts_custom, ',', include_adducts, sep="")
+include_adducts_all <- paste(include_adducts_custom, ",", include_adducts, sep = "")
 
 include_adducts_all <- gsub("^,", "", include_adducts_all)
 include_adducts_all <- gsub(",$", "", include_adducts_all)
@@ -96,7 +94,7 @@ include_adducts_all <- gsub(",", " ", include_adducts_all)
 
 
 
-if(is.null(opt$filter)){
+if (is.null(opt$filter)) {
   filter <- FALSE
 }else{
   filter <- TRUE
@@ -105,15 +103,15 @@ if(is.null(opt$filter)){
 
 
 msPurity::createMSP(pa,
-                    msp_file_pth = file.path(opt$out_dir, 'lcmsms_spectra.msp'),
+                    msp_file_pth = file.path(opt$out_dir, "lcmsms_spectra.msp"),
                     metadata = metadata,
                     metadata_cols = metadata_cols,
                     method = opt$method,
                     adduct_split = adduct_split,
                     xcms_groupids = xcms_groupids,
                     filter = filter,
-                    intensity_ra=opt$intensity_ra,
-                    include_adducts=include_adducts_all,
-                    msp_schema=opt$msp_schema)
+                    intensity_ra = opt$intensity_ra,
+                    include_adducts = include_adducts_all,
+                    msp_schema = opt$msp_schema)
 
-print('msp created')
+print("msp created")
diff --git a/tools/msPurity/dbconfig.R b/tools/msPurity/dbconfig.R
index dd000ad..f411256 100644
--- a/tools/msPurity/dbconfig.R
+++ b/tools/msPurity/dbconfig.R
@@ -1,9 +1,9 @@
-compoundDbType <- 'mysql'
+compoundDbType <- "mysql"
 compoundDbPth <- NA
-compoundDbName <- 'metab_compound'
-compoundDbPort <- '3306'
-compoundDbUser <- 'metab_compound'
-compoundDbPass <- 'metab_compound'
+compoundDbName <- "metab_compound"
+compoundDbPort <- "3306"
+compoundDbUser <- "metab_compound"
+compoundDbPass <- "metab_compound"
 
 q_dbPth <- NA
 q_dbType <- NA
diff --git a/tools/msPurity/dimsPredictPuritySingle.R b/tools/msPurity/dimsPredictPuritySingle.R
index ad3f894..8079c5c 100644
--- a/tools/msPurity/dimsPredictPuritySingle.R
+++ b/tools/msPurity/dimsPredictPuritySingle.R
@@ -3,27 +3,27 @@ library(optparse)
 print(sessionInfo())
 
 option_list <- list(
-  make_option(c("--mzML_file"), type="character"),
-  make_option(c("--mzML_files"), type="character"),
-  make_option(c("--mzML_filename"), type="character", default=''),
-  make_option(c("--mzML_galaxy_names"), type="character", default=''),
-  make_option(c("--peaks_file"), type="character"),
-  make_option(c("-o", "--out_dir"), type="character"),
-  make_option("--minoffset", default=0.5),
-  make_option("--maxoffset", default=0.5),
-  make_option("--ilim", default=0.05),
-  make_option("--ppm", default=4),
-  make_option("--dimspy", action="store_true"),
-  make_option("--sim", action="store_true"),
-  make_option("--remove_nas", action="store_true"),
-  make_option("--iwNorm", default="none", type="character"),
-  make_option("--file_num_dimspy", default=1),
-  make_option("--exclude_isotopes", action="store_true"),
-  make_option("--isotope_matrix", type="character")
+  make_option(c("--mzML_file"), type = "character"),
+  make_option(c("--mzML_files"), type = "character"),
+  make_option(c("--mzML_filename"), type = "character", default = ""),
+  make_option(c("--mzML_galaxy_names"), type = "character", default = ""),
+  make_option(c("--peaks_file"), type = "character"),
+  make_option(c("-o", "--out_dir"), type = "character"),
+  make_option("--minoffset", default = 0.5),
+  make_option("--maxoffset", default = 0.5),
+  make_option("--ilim", default = 0.05),
+  make_option("--ppm", default = 4),
+  make_option("--dimspy", action = "store_true"),
+  make_option("--sim", action = "store_true"),
+  make_option("--remove_nas", action = "store_true"),
+  make_option("--iwNorm", default = "none", type = "character"),
+  make_option("--file_num_dimspy", default = 1),
+  make_option("--exclude_isotopes", action = "store_true"),
+  make_option("--isotope_matrix", type = "character")
 )
 
 # store options
-opt<- parse_args(OptionParser(option_list=option_list))
+opt <- parse_args(OptionParser(option_list = option_list))
 
 print(sessionInfo())
 print(opt)
@@ -31,119 +31,118 @@ print(opt)
 print(opt$mzML_files)
 print(opt$mzML_galaxy_names)
 
-str_to_vec <- function(x){
+str_to_vec <- function(x) {
     print(x)
-    x <- trimws(strsplit(x, ',')[[1]])
+    x <- trimws(strsplit(x, ",")[[1]])
     return(x[x != ""])
 }
 
-find_mzml_file <- function(mzML_files, galaxy_names, mzML_filename){
+find_mzml_file <- function(mzML_files, galaxy_names, mzML_filename) {
     mzML_filename <- trimws(mzML_filename)
     mzML_files <- str_to_vec(mzML_files)
     galaxy_names <- str_to_vec(galaxy_names)
-    if (mzML_filename %in% galaxy_names){
-        return(mzML_files[galaxy_names==mzML_filename])
+    if (mzML_filename %in% galaxy_names) {
+        return(mzML_files[galaxy_names == mzML_filename])
     }else{
         stop(paste("mzML file not found - ", mzML_filename))
     }
 }
 
 
-if (is.null(opt$dimspy)){
-    df <- read.table(opt$peaks_file, header = TRUE, sep='\t')
-    if (file.exists(opt$mzML_file)){
+if (is.null(opt$dimspy)) {
+    df <- read.table(opt$peaks_file, header = TRUE, sep = "\t")
+    if (file.exists(opt$mzML_file)) {
         mzML_file <- opt$mzML_file
-    }else if (!is.null(opt$mzML_files)){
-        mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names, 
+    }else if (!is.null(opt$mzML_files)) {
+        mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names,
                                     opt$mzML_filename)
     }else{
-        mzML_file <- file.path(opt$mzML_file, filename)    
-    }	
+        mzML_file <- file.path(opt$mzML_file, filename)
+    }
 }else{
     indf <- read.table(opt$peaks_file,
-                       header = TRUE, sep='\t', stringsAsFactors = FALSE)
-    
+                       header = TRUE, sep = "\t", stringsAsFactors = FALSE)
+
     filename <- colnames(indf)[8:ncol(indf)][opt$file_num_dimspy]
     print(filename)
     # check if the data file is mzML or RAW (can only use mzML currently) so
     # we expect an mzML file of the same name in the same folder
-    indf$i <- indf[,colnames(indf)==filename]
-    indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename])
-    
-    filename = sub("raw", "mzML", filename, ignore.case = TRUE)
+    indf$i <- indf[, colnames(indf) == filename]
+    indf[, colnames(indf) == filename] <- as.numeric(indf[, colnames(indf) == filename])
+
+    filename <- sub("raw", "mzML", filename, ignore.case = TRUE)
     print(filename)
-    
-    
-    if (file.exists(opt$mzML_file)){
+
+    if (file.exists(opt$mzML_file)) {
         mzML_file <- opt$mzML_file
-    }else if (!is.null(opt$mzML_files)){
+    }else if (!is.null(opt$mzML_files)) {
         mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names, filename)
     }else{
-        mzML_file <- file.path(opt$mzML_file, filename)    
-    }	
-    
-    # Update the dimspy output with the correct information 
-    df <- indf[4:nrow(indf),]
-    if ('blank_flag' %in% colnames(df)){
-        df <- df[df$blank_flag==1,]
+        mzML_file <- file.path(opt$mzML_file, filename)
     }
-    colnames(df)[colnames(df)=='m.z'] <- 'mz'
-    
-    if ('nan' %in% df$mz){
-        df[df$mz=='nan',]$mz <- NA
+
+    # Update the dimspy output with the correct information
+    df <- indf[4:nrow(indf), ]
+    if ("blank_flag" %in% colnames(df)) {
+        df <- df[df$blank_flag == 1, ]
+    }
+    colnames(df)[colnames(df) == "m.z"] <- "mz"
+
+    if ("nan" %in% df$mz) {
+        df[df$mz == "nan", ]$mz <- NA
     }
     df$mz <- as.numeric(df$mz)
 }
 
-if (!is.null(opt$remove_nas)){
-  df <- df[!is.na(df$mz),]
+if (!is.null(opt$remove_nas)) {
+  df <- df[!is.na(df$mz), ]
 }
 
-if (is.null(opt$isotope_matrix)){
+if (is.null(opt$isotope_matrix)) {
     im <- NULL
 }else{
     im <- read.table(opt$isotope_matrix,
-                     header = TRUE, sep='\t', stringsAsFactors = FALSE)
+                     header = TRUE, sep = "\t", stringsAsFactors = FALSE)
 }
 
-if (is.null(opt$exclude_isotopes)){
+if (is.null(opt$exclude_isotopes)) {
     isotopes <- FALSE
 }else{
     isotopes <- TRUE
 }
 
-if (is.null(opt$sim)){
-    sim=FALSE
+if (is.null(opt$sim)) {
+    sim <- FALSE
 }else{
-    sim=TRUE
+    sim <- TRUE
 }
 
-minOffset = as.numeric(opt$minoffset)
-maxOffset = as.numeric(opt$maxoffset)
-
-if (opt$iwNorm=='none'){
-    iwNorm = FALSE
-    iwNormFun = NULL
-}else if (opt$iwNorm=='gauss'){
-    iwNorm = TRUE
-    iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset)
-}else if (opt$iwNorm=='rcosine'){
-    iwNorm = TRUE
-    iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset)
-}else if (opt$iwNorm=='QE5'){
-    iwNorm = TRUE
-    iwNormFun = msPurity::iwNormQE.5()
+minOffset <- as.numeric(opt$minoffset)
+maxOffset <- as.numeric(opt$maxoffset)
+
+if (opt$iwNorm == "none") {
+    iwNorm <- FALSE
+    iwNormFun <- NULL
+}else if (opt$iwNorm == "gauss") {
+    iwNorm <- TRUE
+    iwNormFun <- msPurity::iwNormGauss(minOff = -minOffset, maxOff = maxOffset)
+}else if (opt$iwNorm == "rcosine") {
+    iwNorm <- TRUE
+    iwNormFun <- msPurity::iwNormRcosine(minOff = -minOffset, maxOff = maxOffset)
+}else if (opt$iwNorm == "QE5") {
+    iwNorm <- TRUE
+    iwNormFun <- msPurity::iwNormQE.5()
 }
 
-print('FIRST ROWS OF PEAK FILE')
+print("FIRST ROWS OF PEAK FILE")
 print(head(df))
 print(mzML_file)
 predicted <- msPurity::dimsPredictPuritySingle(df$mz,
-                                     filepth=mzML_file,
-                                     minOffset=minOffset,
-                                     maxOffset=maxOffset,
-                                     ppm=opt$ppm,
-                                     mzML=TRUE,
+                                     filepth = mzML_file,
+                                     minOffset = minOffset,
+                                     maxOffset = maxOffset,
+                                     ppm = opt$ppm,
+                                     mzML = TRUE,
                                      sim = sim,
                                      ilim = opt$ilim,
                                      isotopes = isotopes,
@@ -154,10 +153,8 @@ predicted <- msPurity::dimsPredictPuritySingle(df$mz,
 predicted <- cbind(df, predicted)
 
 print(head(predicted))
-print(file.path(opt$out_dir, 'dimsPredictPuritySingle_output.tsv'))
-
-write.table(predicted, 
-            file.path(opt$out_dir, 'dimsPredictPuritySingle_output.tsv'),
-            row.names=FALSE, sep='\t')
-
+print(file.path(opt$out_dir, "dimsPredictPuritySingle_output.tsv"))
 
+write.table(predicted,
+            file.path(opt$out_dir, "dimsPredictPuritySingle_output.tsv"),
+            row.names = FALSE, sep = "\t")
diff --git a/tools/msPurity/filterFragSpectra.R b/tools/msPurity/filterFragSpectra.R
index 010784f..9020bb4 100644
--- a/tools/msPurity/filterFragSpectra.R
+++ b/tools/msPurity/filterFragSpectra.R
@@ -5,96 +5,95 @@ print(sessionInfo())
 
 
 option_list <- list(
-  make_option("--out_rdata", type="character"),
-  make_option("--out_peaklist_prec", type="character"),
-  make_option("--out_peaklist_frag", type="character"),
-  make_option("--pa", type="character"),
+  make_option("--out_rdata", type = "character"),
+  make_option("--out_peaklist_prec", type = "character"),
+  make_option("--out_peaklist_frag", type = "character"),
+  make_option("--pa", type = "character"),
 
-  make_option("--ilim", default=0.0),
-  make_option("--plim", default=0.0),
+  make_option("--ilim", default = 0.0),
+  make_option("--plim", default = 0.0),
 
-  make_option("--ra", default=0.0),  
-  make_option("--snr", default=0.0),
+  make_option("--ra", default = 0.0),
+  make_option("--snr", default = 0.0),
 
-  make_option("--rmp", action="store_true"),
-  make_option("--snmeth", default="median", type="character")
+  make_option("--rmp", action = "store_true"),
+  make_option("--snmeth", default = "median", type = "character")
 )
 
-opt <- parse_args(OptionParser(option_list=option_list))
+opt <- parse_args(OptionParser(option_list = option_list))
 print(opt)
 
 
-loadRData <- function(rdata_path, name){
+loadRData <- function(rdata_path, name) {
     #loads an RData file, and returns the named xset object if it is there
     load(rdata_path)
     return(get(ls()[ls() %in% name]))
 }
 
 # Requires
-pa <- loadRData(opt$pa, 'pa')
+pa <- loadRData(opt$pa, "pa")
 
-if(is.null(opt$rmp)){
-  opt$rmp = FALSE
+if (is.null(opt$rmp)) {
+  opt$rmp <- FALSE
 }else{
-  opt$rmp = TRUE
+  opt$rmp <- TRUE
 }
 
-pa <- filterFragSpectra(pa, 
-                        ilim=opt$ilim, 
-                        plim=opt$plim,
-                        ra=opt$ra,
-                        snr=opt$snr,
-                        rmp=opt$rmp,
-                        snmeth=opt$snmeth)
+pa <- filterFragSpectra(pa,
+                        ilim = opt$ilim,
+                        plim = opt$plim,
+                        ra = opt$ra,
+                        snr = opt$snr,
+                        rmp = opt$rmp,
+                        snmeth = opt$snmeth)
 
 print(pa)
-save(pa, file=opt$out_rdata)
+save(pa, file = opt$out_rdata)
 
 # get the msms data for grpid from the purityA object
-msmsgrp <- function(grpid, pa){
+msmsgrp <- function(grpid, pa) {
   msms <- pa@grped_ms2[grpid]
-  
-  grpinfo <- pa@grped_df[pa@grped_df$grpid==grpid,]
-  
-  grpinfo$subsetid <- 1:nrow(grpinfo)
-  result <- plyr::ddply(grpinfo, ~subsetid, setid, msms=msms)
+
+  grpinfo <- pa@grped_df[pa@grped_df$grpid == grpid, ]
+
+  grpinfo$subsetid <- seq_len(nrow(grpinfo))
+  result <- plyr::ddply(grpinfo, ~subsetid, setid, msms = msms)
   return(result)
 }
 
-# Set the relevant details 
-setid <- function(grpinfo_i, msms){
+# Set the relevant details
+setid <- function(grpinfo_i, msms) {
   msms_i <- msms[[1]][[grpinfo_i$subsetid]]
   n <- nrow(msms_i)
   msms_i <- data.frame(msms_i)
-  colnames(msms_i)[1:2] <- c('mz', 'i')
-  m <- cbind('grpid'=rep(grpinfo_i$grpid,n), 'pid'=rep(grpinfo_i$pid,n), 'fileid'=rep(grpinfo_i$fileid,n), msms_i)
+  colnames(msms_i)[1:2] <- c("mz", "i")
+  m <- cbind("grpid" = rep(grpinfo_i$grpid, n), "pid" = rep(grpinfo_i$pid, n), "fileid" = rep(grpinfo_i$fileid, n), msms_i)
   return(m)
 }
 
 
 
-if (length(pa)>0){
+if (length(pa) > 0) {
 
-  if (length(pa@grped_ms2)==0){
-    message('No spectra available')
-  } else{
+  if (length(pa@grped_ms2) == 0) {
+    message("No spectra available")
+  } else {
 
     # get group ids
     grpids <- unique(as.character(pa@grped_df$grpid))
 
     # loop through all the group ids
-    df_fragments = plyr::adply(grpids, 1, msmsgrp, pa=pa)
-    df_fragments = merge(df_fragments, pa@puritydf[,c("pid", "acquisitionNum", "precursorScanNum")], by="pid")
-    df_fragments = df_fragments[order(df_fragments$grpid, df_fragments$pid, df_fragments$mz),]
+    df_fragments <- plyr::adply(grpids, 1, msmsgrp, pa = pa)
+    df_fragments <- merge(df_fragments, pa@puritydf[, c("pid", "acquisitionNum", "precursorScanNum")], by = "pid")
+    df_fragments <- df_fragments[order(df_fragments$grpid, df_fragments$pid, df_fragments$mz), ]
     #select and reorder columns
-    df_fragments = df_fragments[,c("grpid", "pid", "precursorScanNum", "acquisitionNum", "fileid", "mz", "i", "snr", "ra", "purity_pass_flag", "intensity_pass_flag", "ra_pass_flag", "snr_pass_flag", "pass_flag")]
+    df_fragments <- df_fragments[, c("grpid", "pid", "precursorScanNum", "acquisitionNum", "fileid", "mz", "i", "snr", "ra", "purity_pass_flag", "intensity_pass_flag", "ra_pass_flag", "snr_pass_flag", "pass_flag")]
 
-    pa@grped_df$filename = sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)])
+    pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)])
 
-    print(head(pa@grped_df))    
-    write.table(pa@grped_df, opt$out_peaklist_prec, row.names=FALSE, sep='\t')
+    print(head(pa@grped_df))
+    write.table(pa@grped_df, opt$out_peaklist_prec, row.names = FALSE, sep = "\t")
     print(head(df_fragments))
-    write.table(df_fragments, opt$out_peaklist_frag, row.names=FALSE, sep='\t')
+    write.table(df_fragments, opt$out_peaklist_frag, row.names = FALSE, sep = "\t")
   }
 }
-
diff --git a/tools/msPurity/flagRemove.R b/tools/msPurity/flagRemove.R
index 13eec03..8ba8bde 100644
--- a/tools/msPurity/flagRemove.R
+++ b/tools/msPurity/flagRemove.R
@@ -2,105 +2,100 @@ library(msPurity)
 library(optparse)
 print(sessionInfo())
 option_list <- list(
-  make_option(c("-o", "--out_dir"), type="character", default=getwd(),
-              help="Output folder for resulting files [default = %default]"
+  make_option(c("-o", "--out_dir"), type = "character", default = getwd(),
+              help = "Output folder for resulting files [default = %default]"
   ),
-  make_option(c("-x", "--xset_path"), type="character", default=file.path(getwd(),"xset.rds"),
-              help="The path to the xcmsSet object [default = %default]"
+  make_option(c("-x", "--xset_path"), type = "character", default = file.path(getwd(), "xset.rds"),
+              help = "The path to the xcmsSet object [default = %default]"
   ),
-  make_option("--polarity", default=NA,
-              help="polarity (just used for naming purpose for files being saved) [positive, negative, NA] [default %default]"
+  make_option("--polarity", default = NA,
+              help = "polarity (just used for naming purpose for files being saved) [positive, negative, NA] [default %default]"
   ),
-  make_option("--rsd_i_blank", default=100,
-              help="RSD threshold for the blank [default = %default]"
+  make_option("--rsd_i_blank", default = 100,
+              help = "RSD threshold for the blank [default = %default]"
   ),
-  make_option("--minfrac_blank", default=0.5,
-              help="minimum fraction of files for features needed for the blank [default = %default]"
+  make_option("--minfrac_blank", default = 0.5,
+              help = "minimum fraction of files for features needed for the blank [default = %default]"
   ),
-  make_option("--rsd_rt_blank", default=100,
-              help="RSD threshold for the RT of the blank [default = %default]"
+  make_option("--rsd_rt_blank", default = 100,
+              help = "RSD threshold for the RT of the blank [default = %default]"
   ),
 
-  make_option("--ithres_blank", default=0,
-              help="Intensity threshold for the blank [default = %default]"
+  make_option("--ithres_blank", default = 0,
+              help = "Intensity threshold for the blank [default = %default]"
   ),
-  make_option("--s2b", default=10,
-              help="fold change (sample/blank) needed for sample peak to be allowed. e.g.
+  make_option("--s2b", default = 10,
+              help = "fold change (sample/blank) needed for sample peak to be allowed. e.g.
                     if s2b set to 10 and the recorded sample 'intensity' value was 100 and blank was 10.
                     1000/10 = 100, so sample has fold change higher than the threshold and the peak
                     is not considered a blank [default = %default]"
   ),
-  make_option("--blank_class", default='blank', type="character",
-              help="A string representing the class that will be used for the blank.[default = %default]"
+  make_option("--blank_class", default = "blank", type = "character",
+              help = "A string representing the class that will be used for the blank.[default = %default]"
   ),
-  make_option("--egauss_thr", default=NA,
-              help="Threshold for filtering out non gaussian shaped peaks. Note this only works
+  make_option("--egauss_thr", default = NA,
+              help = "Threshold for filtering out non gaussian shaped peaks. Note this only works
                             if the 'verbose columns' and 'fit gauss' was used with xcms
                             [default = %default]"
   ),
-  make_option("--rsd_i_sample", default=100,
-              help="RSD threshold for the samples [default = %default]"
+  make_option("--rsd_i_sample", default = 100,
+              help = "RSD threshold for the samples [default = %default]"
   ),
-  make_option("--minfrac_sample", default=0.8,
-              help="minimum fraction of files for features needed for the samples [default = %default]"
+  make_option("--minfrac_sample", default = 0.8,
+              help = "minimum fraction of files for features needed for the samples [default = %default]"
   ),
-  make_option("--rsd_rt_sample", default=100,
-              help="RSD threshold for the RT of the samples [default = %default]"
+  make_option("--rsd_rt_sample", default = 100,
+              help = "RSD threshold for the RT of the samples [default = %default]"
   ),
-  make_option("--ithres_sample", default=5000,
-              help="Intensity threshold for the sample [default = %default]"
+  make_option("--ithres_sample", default = 5000,
+              help = "Intensity threshold for the sample [default = %default]"
   ),
-  make_option("--grp_rm_ids", default=NA,
-              help="vector of grouped_xcms peaks to remove (corresponds to the row from xcms::group output)
+  make_option("--grp_rm_ids", default = NA,
+              help = "vector of grouped_xcms peaks to remove (corresponds to the row from xcms::group output)
               [default = %default]"
   ),
-  make_option("--remove_spectra",  action="store_true",
-              help=" TRUE if flagged spectra is to be removed [default = %default]"
+  make_option("--remove_spectra",  action = "store_true",
+              help = "TRUE if flagged spectra is to be removed [default = %default]"
   ),
-  make_option("--minfrac_xcms", default=0.5,
-              help="minfrac for xcms  grouping [default = %default]"
+  make_option("--minfrac_xcms", default = 0.5,
+              help = "minfrac for xcms  grouping [default = %default]"
   ),
-  make_option("--mzwid", default=0.001,
-              help="mzwid for xcms  grouping [default = %default]"
+  make_option("--mzwid", default = 0.001,
+              help = "mzwid for xcms  grouping [default = %default]"
   ),
-  make_option("--bw", default=5,
-              help="bw for xcms  grouping [default = %default]"
+  make_option("--bw", default = 5,
+              help = "bw for xcms  grouping [default = %default]"
   ),
 
-  make_option("--temp_save",  action="store_true",
-              help="Assign True if files for each step saved (for testing purposes) [default = %default]"
+  make_option("--temp_save",  action = "store_true",
+              help = "Assign True if files for each step saved (for testing purposes) [default = %default]"
   ),
 
-  make_option("--samplelist",  type="character", help="Sample list to determine the blank class")
-
-
-
-
+  make_option("--samplelist",  type = "character", help = "Sample list to determine the blank class")
 
 )
 
-  #make_option("--multilist", action="store_true"
-  #            help="NOT CURRENTLY IMPLEMENTED: If paired blank removal is to be performed a - multilist -  sample list file has to be provided"
-  #),
+# nolint start
+#  make_option("--multilist", action="store_true"
+#            help="NOT CURRENTLY IMPLEMENTED: If paired blank removal is to be performed a - multilist -  sample list file has to be provided"
+# ),
+# nolint end
 
 # store options
-opt<- parse_args(OptionParser(option_list=option_list))
+opt <- parse_args(OptionParser(option_list = option_list))
 
 opt <- replace(opt, opt == "NA", NA)
 
-
-
-
-if (is.null(opt$temp_save)){
-    temp_save<-FALSE
+if (is.null(opt$temp_save)) {
+    temp_save <- FALSE
 }else{
-    temp_save<-TRUE
+    temp_save <- TRUE
 }
 
-if (is.null(opt$remove_spectra)){
-    remove_spectra<-FALSE
+if (is.null(opt$remove_spectra)) {
+    remove_spectra <- FALSE
 }else{
-    remove_spectra<-TRUE
+    remove_spectra <- TRUE
 }
 
 
@@ -109,35 +104,35 @@ print(opt)
 getxcmsSetObject <- function(xobject) {
     # XCMS 1.x
     if (class(xobject) == "xcmsSet")
-        return (xobject)
+        return(xobject)
     # XCMS 3.x
     if (class(xobject) == "XCMSnExp") {
         # Get the legacy xcmsSet object
-        suppressWarnings(xset <- as(xobject, 'xcmsSet'))
-        sampclass(xset) <- xset@phenoData$sample_group
-        return (xset)
+        suppressWarnings(xset <- as(xobject, "xcmsSet"))
+        xcms::sampclass(xset) <- xset@phenoData$sample_group
+        return(xset)
     }
 }
 
 
-loadRData <- function(rdata_path, name){
+loadRData <- function(rdata_path, name) {
 #loads an RData file, and returns the named xset object if it is there
     load(rdata_path)
     return(get(ls()[ls() %in% name]))
 }
 
-xset <- getxcmsSetObject(loadRData(opt$xset_path, c('xset','xdata')))
+xset <- getxcmsSetObject(loadRData(opt$xset_path, c("xset", "xdata")))
 
 print(xset)
-if (is.null(opt$samplelist)){
+if (is.null(opt$samplelist)) {
     blank_class <- opt$blank_class
 }else{
-    samplelist <- read.table(opt$samplelist, sep='\t', header=TRUE)
-    samplelist_blank <- unique(samplelist$sample_class[samplelist$blank=='yes'])
+    samplelist <- read.table(opt$samplelist, sep = "\t", header = TRUE)
+    samplelist_blank <- unique(samplelist$sample_class[samplelist$blank == "yes"])
 
     chosen_blank <- samplelist_blank[samplelist_blank %in% xset@phenoData$class]
-    if (length(chosen_blank)>1){
-        print('ERROR: only 1 blank is currently allowed to be used with this tool')
+    if (length(chosen_blank) > 1) {
+        print("ERROR: only 1 blank is currently allowed to be used with this tool")
         quit()
     }
     blank_class <- as.character(chosen_blank)
@@ -145,47 +140,47 @@ if (is.null(opt$samplelist)){
 }
 
 
-if (is.null(opt$multilist)){
+if (is.null(opt$multilist)) {
     ffrm_out <- flag_remove(xset,
-                        pol=opt$polarity,
-                        rsd_i_blank=opt$rsd_i_blank,
-                        minfrac_blank=opt$minfrac_blank,
-                        rsd_rt_blank=opt$rsd_rt_blank,
-                        ithres_blank=opt$ithres_blank,
-                        s2b=opt$s2b,
-                        ref.class=blank_class,
-                        egauss_thr=opt$egauss_thr,
-                        rsd_i_sample=opt$rsd_i_sample,
-                        minfrac_sample=opt$minfrac_sample,
-                        rsd_rt_sample=opt$rsd_rt_sample,
-                        ithres_sample=opt$ithres_sample,
-                        minfrac_xcms=opt$minfrac_xcms,
-                        mzwid=opt$mzwid,
-                        bw=opt$bw,
-                        out_dir=opt$out_dir,
-                        temp_save=temp_save,
-                        remove_spectra=remove_spectra,
-                        grp_rm_ids=unlist(strsplit(as.character(opt$grp_rm_ids), split=", "))[[1]])
-    print('flag remove finished')
+                        pol = opt$polarity,
+                        rsd_i_blank = opt$rsd_i_blank,
+                        minfrac_blank = opt$minfrac_blank,
+                        rsd_rt_blank = opt$rsd_rt_blank,
+                        ithres_blank = opt$ithres_blank,
+                        s2b = opt$s2b,
+                        ref.class = blank_class,
+                        egauss_thr = opt$egauss_thr,
+                        rsd_i_sample = opt$rsd_i_sample,
+                        minfrac_sample = opt$minfrac_sample,
+                        rsd_rt_sample = opt$rsd_rt_sample,
+                        ithres_sample = opt$ithres_sample,
+                        minfrac_xcms = opt$minfrac_xcms,
+                        mzwid = opt$mzwid,
+                        bw = opt$bw,
+                        out_dir = opt$out_dir,
+                        temp_save = temp_save,
+                        remove_spectra = remove_spectra,
+                        grp_rm_ids = unlist(strsplit(as.character(opt$grp_rm_ids), split = ", "))[[1]])
+    print("flag remove finished")
     xset <- ffrm_out[[1]]
     grp_peaklist <- ffrm_out[[2]]
     removed_peaks <- ffrm_out[[3]]
 
-    save.image(file=file.path(opt$out_dir, 'xset_filtered.RData'), version=2)
+    save.image(file = file.path(opt$out_dir, "xset_filtered.RData"), version = 2)
 
     # grpid needed for mspurity ID needed for deconrank... (will clean up at some up)
-    peak_pth <- file.path(opt$out_dir, 'peaklist_filtered.tsv')
+    peak_pth <- file.path(opt$out_dir, "peaklist_filtered.tsv")
     print(peak_pth)
-    write.table(data.frame('grpid'=rownames(grp_peaklist), 'ID'=rownames(grp_peaklist), grp_peaklist),
-                peak_pth, row.names=FALSE, sep='\t')
+    write.table(data.frame("grpid" = rownames(grp_peaklist), "ID" = rownames(grp_peaklist), grp_peaklist),
+                peak_pth, row.names = FALSE, sep = "\t")
 
     removed_peaks <- data.frame(removed_peaks)
-    write.table(data.frame('ID'=rownames(removed_peaks),removed_peaks),
-        file.path(opt$out_dir, 'removed_peaks.tsv'), row.names=FALSE, sep='\t')
+    write.table(data.frame("ID" = rownames(removed_peaks), removed_peaks),
+        file.path(opt$out_dir, "removed_peaks.tsv"), row.names = FALSE, sep = "\t")
 
 }else{
 
-   
+   # nolint start
    # TODO
    #xsets <- split(xset, multilist_df$multlist)
    #
@@ -193,12 +188,10 @@ if (is.null(opt$multilist)){
    #
    #for (mgrp in mult_grps){
    #   xset_i <- xsets[mgrp]
-   #   xcms::group(xset_i, 
+   #   xcms::group(xset_i,
    #
    # }
-
+   # nolint end
 
 
 }
-
-
diff --git a/tools/msPurity/frag4feature.R b/tools/msPurity/frag4feature.R
index 88f9d8f..92eb54a 100644
--- a/tools/msPurity/frag4feature.R
+++ b/tools/msPurity/frag4feature.R
@@ -3,18 +3,18 @@ library(msPurity)
 library(xcms)
 print(sessionInfo())
 
-xset_pa_filename_fix <- function(opt, pa, xset=NULL){
+xset_pa_filename_fix <- function(opt, pa, xset=NULL) {
 
 
-  if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
+  if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)) {
     # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
     # needs to be done due to Galaxy moving the files around and screwing up any links to files
 
-    filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
+    filepaths <- trimws(strsplit(opt$mzML_files, ",")[[1]]) # nolint
+
     filepaths <- filepaths[filepaths != ""]
-    new_names <- basename(filepaths)
 
-    galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
+    galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]])
     galaxy_names <- galaxy_names[galaxy_names != ""]
 
     nsave <- names(pa@fileList)
@@ -28,14 +28,14 @@ xset_pa_filename_fix <- function(opt, pa, xset=NULL){
   }
   print(pa@fileList)
 
-  if(!is.null(xset)){
+  if (!is.null(xset)) {
 
     print(xset@filepaths)
 
-    if(!all(basename(pa@fileList)==basename(xset@filepaths))){
-       if(!all(names(pa@fileList)==basename(xset@filepaths))){
-          print('FILELISTS DO NOT MATCH')
-          message('FILELISTS DO NOT MATCH')
+    if (!all(basename(pa@fileList) == basename(xset@filepaths))) {
+       if (!all(names(pa@fileList) == basename(xset@filepaths))) {
+          print("FILELISTS DO NOT MATCH")
+          message("FILELISTS DO NOT MATCH")
           quit(status = 1)
        }else{
           xset@filepaths <- unname(pa@fileList)
@@ -48,26 +48,26 @@ xset_pa_filename_fix <- function(opt, pa, xset=NULL){
 
 
 option_list <- list(
-  make_option(c("-o", "--out_dir"), type="character"),
-  make_option("--pa", type="character"),
-  make_option("--xset", type="character"),
-  make_option("--ppm", default=10),
-  make_option("--plim", default=0.0),
-  make_option("--convert2RawRT", action="store_true"),
-  make_option("--intense", action="store_true"),
-  make_option("--createDB", action="store_true"),
-  make_option("--cores", default=4),
-  make_option("--mzML_files", type="character"),
-  make_option("--galaxy_names", type="character"),
-  make_option("--grp_peaklist", type="character"),
-  make_option("--useGroup", action="store_true")
+  make_option(c("-o", "--out_dir"), type = "character"),
+  make_option("--pa", type = "character"),
+  make_option("--xset", type = "character"),
+  make_option("--ppm", default = 10),
+  make_option("--plim", default = 0.0),
+  make_option("--convert2RawRT", action = "store_true"),
+  make_option("--intense", action = "store_true"),
+  make_option("--createDB", action = "store_true"),
+  make_option("--cores", default = 4),
+  make_option("--mzML_files", type = "character"),
+  make_option("--galaxy_names", type = "character"),
+  make_option("--grp_peaklist", type = "character"),
+  make_option("--useGroup", action = "store_true")
 )
 
 # store options
-opt<- parse_args(OptionParser(option_list=option_list))
+opt <- parse_args(OptionParser(option_list = option_list))
 print(opt)
 
-loadRData <- function(rdata_path, name){
+loadRData <- function(rdata_path, name) {
 #loads an RData file, and returns the named xset object if it is there
     load(rdata_path)
     return(get(ls()[ls() %in% name]))
@@ -78,19 +78,19 @@ loadRData <- function(rdata_path, name){
 getxcmsSetObject <- function(xobject) {
     # XCMS 1.x
     if (class(xobject) == "xcmsSet")
-        return (xobject)
+        return(xobject)
     # XCMS 3.x
     if (class(xobject) == "XCMSnExp") {
         # Get the legacy xcmsSet object
-        suppressWarnings(xset <- as(xobject, 'xcmsSet'))
+        suppressWarnings(xset <- as(xobject, "xcmsSet"))
         sampclass(xset) <- xset@phenoData$sample_group
-        return (xset)
+        return(xset)
     }
 }
 
 # Requires
-pa <- loadRData(opt$pa, 'pa')
-xset <- loadRData(opt$xset, c('xset','xdata'))
+pa <- loadRData(opt$pa, "pa")
+xset <- loadRData(opt$xset, c("xset", "xdata"))
 xset <- getxcmsSetObject(xset)
 
 pa@cores <- opt$cores
@@ -98,63 +98,60 @@ pa@cores <- opt$cores
 print(pa@fileList)
 print(xset@filepaths)
 
-if(is.null(opt$intense)){
-  intense = FALSE
+if (is.null(opt$intense)) {
+  intense <- FALSE
 }else{
-  intense = TRUE
+  intense <- TRUE
 }
 
-if(is.null(opt$convert2RawRT)){
-    convert2RawRT = FALSE
+if (is.null(opt$convert2RawRT)) {
+    convert2RawRT <- FALSE
 }else{
-    convert2RawRT= TRUE
+    convert2RawRT <- TRUE
 }
 
-if(is.null(opt$createDB)){
-    createDB = FALSE
+if (is.null(opt$createDB)) {
+    createDB <- FALSE
 }else{
-    createDB = TRUE
+    createDB <- TRUE
 }
 
-if(is.null(opt$useGroup)){
+if (is.null(opt$useGroup)) {
     fix <- xset_pa_filename_fix(opt, pa, xset)
     pa <- fix[[1]]
     xset <- fix[[2]]
-    useGroup=FALSE
+    useGroup <- FALSE
 }else{
     # if are only aligning to the group not eah file we do not need to align the files between the xset and pa object
-    print('useGroup')
+    print("useGroup")
     fix <- xset_pa_filename_fix(opt, pa)
     pa <- fix[[1]]
-    useGroup=TRUE
+    useGroup <- TRUE
 }
 
 
-if(is.null(opt$grp_peaklist)){
-    grp_peaklist = NA
+if (is.null(opt$grp_peaklist)) {
+    grp_peaklist <- NA
 }else{
-    grp_peaklist = opt$grp_peaklist
+    grp_peaklist <- opt$grp_peaklist
 }
 print(useGroup)
 
-
-
-pa <- msPurity::frag4feature(pa=pa,
-                             xset=xset,
-                             ppm=opt$ppm,
-                             plim=opt$plim,
-                             intense=intense,
-                             convert2RawRT=convert2RawRT,
-                             db_name='alldata.sqlite',
-                             out_dir=opt$out_dir,
-                             grp_peaklist=grp_peaklist,
-                             create_db=createDB,
-                             use_group=useGroup)
-
+pa <- msPurity::frag4feature(pa = pa,
+                             xset = xset,
+                             ppm = opt$ppm,
+                             plim = opt$plim,
+                             intense = intense,
+                             convert2RawRT = convert2RawRT,
+                             db_name = "alldata.sqlite",
+                             out_dir = opt$out_dir,
+                             grp_peaklist = grp_peaklist,
+                             create_db = createDB,
+                             use_group = useGroup)
 print(pa)
-save(pa, file=file.path(opt$out_dir, 'frag4feature_output.RData'))
+save(pa, file = file.path(opt$out_dir, "frag4feature_output.RData"))
 
 pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)])
 
 print(head(pa@grped_df))
-write.table(pa@grped_df, file.path(opt$out_dir, 'frag4feature_output.tsv'), row.names=FALSE, sep='\t')
+write.table(pa@grped_df, file.path(opt$out_dir, "frag4feature_output.tsv"), row.names = FALSE, sep = "\t")
diff --git a/tools/msPurity/macros.xml b/tools/msPurity/macros.xml
index 7359644..6e0ce14 100644
--- a/tools/msPurity/macros.xml
+++ b/tools/msPurity/macros.xml
@@ -1,17 +1,17 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.12.2</token>
-    <token name="@GALAXY_TOOL_VERSION@">3</token>
+    <token name="@TOOL_VERSION@">1.16.2</token>
+    <token name="@GALAXY_TOOL_VERSION@">0</token>
 
     <xml name="requirements">
         <requirements>
            <requirement type="package" version="@TOOL_VERSION@" >bioconductor-mspurity</requirement>
-           <requirement type="package" version="1.42.0" >bioconductor-camera</requirement>
-           <requirement type="package" version="3.8.0" >bioconductor-xcms</requirement>
-           <requirement type="package" version="1.14.0" >bioconductor-mspuritydata</requirement>
-           <requirement type="package" version="1.6.4">r-optparse</requirement>
-           <requirement type="package" version="1.1.1">r-rpostgres</requirement>
-           <requirement type="package" version="0.10.17">r-rmysql</requirement>
+           <requirement type="package" version="1.46.0" >bioconductor-camera</requirement>
+           <requirement type="package" version="3.12.0" >bioconductor-xcms</requirement>
+           <requirement type="package" version="1.16.0" >bioconductor-mspuritydata</requirement>
+           <requirement type="package" version="1.6.6">r-optparse</requirement>
+           <requirement type="package" version="1.3.1">r-rpostgres</requirement>
+           <requirement type="package" version="0.10.21">r-rmysql</requirement>
             <yield />
         </requirements>
     </xml>
@@ -29,7 +29,7 @@
                100.0 then the range would be from 100.0 to 100.5"/>
     </xml>
     <xml name="general_params">
-        <param argument="--ilim" type="float" value="0.05" 
+        <param argument="--ilim" type="float" value="0.05"
                label="Threshold to remove peaks below x % of the relative intensity of
                precursor of interest"
                help="All peaks less than this percentage of the precursor ion of interest will be
@@ -337,8 +337,8 @@
                 <when value="true">
                     <param argument="--@QL_SHRT@_spectraTypes" type="select" multiple="true"  label="Spectra type" >
                         <option value="av_all" selected="true">Averaged all spectra ignoring inter-intra relationships </option>
-                        <option value="av_inter">Averaged inter spectra</option>
-                        <option value="av_intra">Averaged intra spectra </option>
+                        <option value="inter">Averaged inter spectra</option>
+                        <option value="intra">Averaged intra spectra </option>
                         <option value="scans">All individual scans</option>
                         <option value="NA">Not applicable/defined</option>
                     </param>
diff --git a/tools/msPurity/purityA.R b/tools/msPurity/purityA.R
index 6cfe19e..8b628eb 100644
--- a/tools/msPurity/purityA.R
+++ b/tools/msPurity/purityA.R
@@ -3,91 +3,90 @@ library(optparse)
 print(sessionInfo())
 
 option_list <- list(
-  make_option(c("-o", "--out_dir"), type="character"),
-  make_option("--mzML_files", type="character"),
-  make_option("--galaxy_names", type="character"),
-  make_option("--minOffset", type="numeric"),
-  make_option("--maxOffset", type="numeric"),
-  make_option("--ilim", type="numeric"),
-  make_option("--iwNorm", default="none", type="character"),
-  make_option("--exclude_isotopes", action="store_true"),
-  make_option("--isotope_matrix", type="character"),
-  make_option("--mostIntense", action="store_true"),
-  make_option("--plotP", action="store_true"),
-  make_option("--nearest", action="store_true"),
-  make_option("--cores", default=4),
-  make_option("--ppmInterp", default=7)
+  make_option(c("-o", "--out_dir"), type = "character"),
+  make_option("--mzML_files", type = "character"),
+  make_option("--galaxy_names", type = "character"),
+  make_option("--minOffset", type = "numeric"),
+  make_option("--maxOffset", type = "numeric"),
+  make_option("--ilim", type = "numeric"),
+  make_option("--iwNorm", default = "none", type = "character"),
+  make_option("--exclude_isotopes", action = "store_true"),
+  make_option("--isotope_matrix", type = "character"),
+  make_option("--mostIntense", action = "store_true"),
+  make_option("--plotP", action = "store_true"),
+  make_option("--nearest", action = "store_true"),
+  make_option("--cores", default = 4),
+  make_option("--ppmInterp", default = 7)
 )
 
-opt <- parse_args(OptionParser(option_list=option_list))
+opt <- parse_args(OptionParser(option_list = option_list))
 print(opt)
 
-
-if (opt$iwNorm=='none'){
-    iwNorm = FALSE
-    iwNormFun = NULL
-}else if (opt$iwNorm=='gauss'){
-    iwNorm = TRUE
-    if (is.null(opt$minOffset) || is.null(opt$maxOffset)){
-      print('User has to define offsets if using Gaussian normalisation')
+if (opt$iwNorm == "none") {
+    iwNorm <- FALSE
+    iwNormFun <- NULL
+}else if (opt$iwNorm == "gauss") {
+    iwNorm <- TRUE
+    if (is.null(opt$minOffset) || is.null(opt$maxOffset)) {
+      print("User has to define offsets if using Gaussian normalisation")
     }else{
-      iwNormFun = msPurity::iwNormGauss(minOff=-as.numeric(opt$minOffset), 
-                                      maxOff=as.numeric(opt$maxOffset))
+      iwNormFun <- msPurity::iwNormGauss(minOff = -as.numeric(opt$minOffset),
+                                         maxOff = as.numeric(opt$maxOffset))
     }
-}else if (opt$iwNorm=='rcosine'){
-    iwNorm = TRUE
-    if (is.null(opt$minOffset) || is.null(opt$maxOffset)){
-      print('User has to define offsets if using R-cosine normalisation')
+}else if (opt$iwNorm == "rcosine") {
+    iwNorm <- TRUE
+    if (is.null(opt$minOffset) || is.null(opt$maxOffset)) {
+      print("User has to define offsets if using R-cosine normalisation")
     }else{
-      iwNormFun = msPurity::iwNormRcosine(minOff=-as.numeric(opt$minOffset), 
-                                          maxOff=as.numeric(opt$maxOffset))
+      iwNormFun <- msPurity::iwNormRcosine(minOff = -as.numeric(opt$minOffset),
+                                           maxOff = as.numeric(opt$maxOffset))
     }
-}else if (opt$iwNorm=='QE5'){
-    iwNorm = TRUE
-    iwNormFun = msPurity::iwNormQE.5()
+}else if (opt$iwNorm == "QE5") {
+    iwNorm <- TRUE
+    iwNormFun <- msPurity::iwNormQE.5()
 }
 
-filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
+filepaths <- trimws(strsplit(opt$mzML_files, ",")[[1]])
 filepaths <- filepaths[filepaths != ""]
 
 
 
-if(is.null(opt$minOffset) || is.null(opt$maxOffset)){
-    offsets = NA
+if (is.null(opt$minOffset) || is.null(opt$maxOffset)) {
+    offsets <- NA
 }else{
-    offsets = as.numeric(c(opt$minOffset, opt$maxOffset))
+    offsets <- as.numeric(c(opt$minOffset, opt$maxOffset))
 }
 
 
-if(is.null(opt$mostIntense)){
-    mostIntense = FALSE
+if (is.null(opt$mostIntense)) {
+    mostIntense <- FALSE
 }else{
-    mostIntense = TRUE
+    mostIntense <- TRUE
 }
 
-if(is.null(opt$nearest)){
-    nearest = FALSE
+if (is.null(opt$nearest)) {
+    nearest <- FALSE
 }else{
-    nearest = TRUE
+    nearest <- TRUE
 }
 
-if(is.null(opt$plotP)){
-    plotP = FALSE
-    plotdir = NULL
+if (is.null(opt$plotP)) {
+    plotP <- FALSE
+    plotdir <- NULL
 }else{
-    plotP = TRUE
-    plotdir = opt$out_dir
+    plotP <- TRUE
+    plotdir <- opt$out_dir
 }
 
 
-if (is.null(opt$isotope_matrix)){
+if (is.null(opt$isotope_matrix)) {
     im <- NULL
 }else{
     im <- read.table(opt$isotope_matrix,
-                     header = TRUE, sep='\t', stringsAsFactors = FALSE)
+                     header = TRUE, sep = "\t", stringsAsFactors = FALSE)
 }
 
-if (is.null(opt$exclude_isotopes)){
+if (is.null(opt$exclude_isotopes)) {
     isotopes <- FALSE
 }else{
     isotopes <- TRUE
@@ -110,20 +109,16 @@ pa <- msPurity::purityA(filepaths,
                         ppmInterp = opt$ppmInterp)
 
 
-if (!is.null(opt$galaxy_names)){
-    galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
+if (!is.null(opt$galaxy_names)) {
+    galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]])
     galaxy_names <- galaxy_names[galaxy_names != ""]
     names(pa@fileList) <- galaxy_names
 }
 
 print(pa)
-save(pa, file=file.path(opt$out_dir, 'purityA_output.RData'))
+save(pa, file = file.path(opt$out_dir, "purityA_output.RData"))
 
 pa@puritydf$filename <- sapply(pa@puritydf$fileid, function(x) names(pa@fileList)[as.integer(x)])
 
 print(head(pa@puritydf))
-write.table(pa@puritydf, file.path(opt$out_dir, 'purityA_output.tsv'), row.names=FALSE, sep='\t')
-
-# removed_peaks <- data.frame(removed_peaks)
-# write.table(data.frame('ID'=rownames(removed_peaks),removed_peaks),
-#         file.path(opt$out_dir, 'removed_peaks.txt'), row.names=FALSE, sep='\t')
+write.table(pa@puritydf, file.path(opt$out_dir, "purityA_output.tsv"), row.names = FALSE, sep = "\t")
diff --git a/tools/msPurity/purityX.R b/tools/msPurity/purityX.R
index 1a0df60..de9a986 100644
--- a/tools/msPurity/purityX.R
+++ b/tools/msPurity/purityX.R
@@ -3,67 +3,66 @@ library(optparse)
 print(sessionInfo())
 
 option_list <- list(
-  make_option(c("--xset_path"), type="character"),
-  make_option(c("-o", "--out_dir"), type="character"),
-  make_option(c("--mzML_path"), type="character"),
-  make_option("--minOffset", default=0.5),
-  make_option("--maxOffset", default=0.5),
-  make_option("--ilim", default=0.05),
-  make_option("--iwNorm", default="none", type="character"),
-  make_option("--exclude_isotopes", action="store_true"),
-  make_option("--isotope_matrix", type="character"),
-  make_option("--purityType", default="purityFWHMmedian"),
-  make_option("--singleFile", default=0),
-  make_option("--cores", default=4),
-  make_option("--xgroups", type="character"),
-  make_option("--rdata_name", default='xset'),
-  make_option("--camera_xcms", default='xset'),
-  make_option("--files", type="character"),
-  make_option("--galaxy_files", type="character"),
-  make_option("--choose_class", type="character"),
-  make_option("--ignore_files", type="character"),
-  make_option("--rtraw_columns",  action="store_true")
+  make_option(c("--xset_path"), type = "character"),
+  make_option(c("-o", "--out_dir"), type = "character"),
+  make_option(c("--mzML_path"), type = "character"),
+  make_option("--minOffset", default = 0.5),
+  make_option("--maxOffset", default = 0.5),
+  make_option("--ilim", default = 0.05),
+  make_option("--iwNorm", default = "none", type = "character"),
+  make_option("--exclude_isotopes", action = "store_true"),
+  make_option("--isotope_matrix", type = "character"),
+  make_option("--purityType", default = "purityFWHMmedian"),
+  make_option("--singleFile", default = 0),
+  make_option("--cores", default = 4),
+  make_option("--xgroups", type = "character"),
+  make_option("--rdata_name", default = "xset"),
+  make_option("--camera_xcms", default = "xset"),
+  make_option("--files", type = "character"),
+  make_option("--galaxy_files", type = "character"),
+  make_option("--choose_class", type = "character"),
+  make_option("--ignore_files", type = "character"),
+  make_option("--rtraw_columns",  action = "store_true")
 )
 
 
-opt<- parse_args(OptionParser(option_list=option_list))
+opt <- parse_args(OptionParser(option_list = option_list))
 print(opt)
 
 
-if (!is.null(opt$xgroups)){
-    xgroups = as.numeric(strsplit(opt$xgroups, ',')[[1]])
+if (!is.null(opt$xgroups)) {
+    xgroups <- as.numeric(strsplit(opt$xgroups, ",")[[1]])
 }else{
-    xgroups = NULL
+    xgroups <- NULL
 }
 
 
-
 print(xgroups)
 
-if (!is.null(opt$remove_nas)){
-  df <- df[!is.na(df$mz),]
+if (!is.null(opt$remove_nas)) {
+  df <- df[!is.na(df$mz), ]
 }
 
-if (is.null(opt$isotope_matrix)){
+if (is.null(opt$isotope_matrix)) {
     im <- NULL
 }else{
     im <- read.table(opt$isotope_matrix,
-                     header = TRUE, sep='\t', stringsAsFactors = FALSE)
+                     header = TRUE, sep = "\t", stringsAsFactors = FALSE)
 }
 
-if (is.null(opt$exclude_isotopes)){
+if (is.null(opt$exclude_isotopes)) {
     isotopes <- FALSE
 }else{
     isotopes <- TRUE
 }
 
-if (is.null(opt$rtraw_columns)){
+if (is.null(opt$rtraw_columns)) {
     rtraw_columns <- FALSE
 }else{
     rtraw_columns <- TRUE
 }
 
-loadRData <- function(rdata_path, xset_name){
+loadRData <- function(rdata_path, xset_name) {
 #loads an RData file, and returns the named xset object if it is there
     load(rdata_path)
     return(get(ls()[ls() == xset_name]))
@@ -71,7 +70,7 @@ loadRData <- function(rdata_path, xset_name){
 
 target_obj <- loadRData(opt$xset_path, opt$rdata_name)
 
-if (opt$camera_xcms=='camera'){
+if (opt$camera_xcms == "camera") {
     xset <- target_obj@xcmsSet
 }else{
     xset <- target_obj
@@ -79,36 +78,35 @@ if (opt$camera_xcms=='camera'){
 
 print(xset)
 
-minOffset = as.numeric(opt$minOffset)
-maxOffset = as.numeric(opt$maxOffset)
-
-
-if (opt$iwNorm=='none'){
-    iwNorm = FALSE
-    iwNormFun = NULL
-}else if (opt$iwNorm=='gauss'){
-    iwNorm = TRUE
-    iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset)
-}else if (opt$iwNorm=='rcosine'){
-    iwNorm = TRUE
-    iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset)
-}else if (opt$iwNorm=='QE5'){
-    iwNorm = TRUE
-    iwNormFun = msPurity::iwNormQE.5()
+minOffset <- as.numeric(opt$minOffset)
+maxOffset <- as.numeric(opt$maxOffset)
+
+if (opt$iwNorm == "none") {
+    iwNorm <- FALSE
+    iwNormFun <- NULL
+}else if (opt$iwNorm == "gauss") {
+    iwNorm <- TRUE
+    iwNormFun <- msPurity::iwNormGauss(minOff = -minOffset, maxOff = maxOffset)
+}else if (opt$iwNorm == "rcosine") {
+    iwNorm <- TRUE
+    iwNormFun <- msPurity::iwNormRcosine(minOff = -minOffset, maxOff = maxOffset)
+}else if (opt$iwNorm == "QE5") {
+    iwNorm <- TRUE
+    iwNormFun <- msPurity::iwNormQE.5()
 }
 
 print(xset@filepaths)
 
-if (!is.null(opt$files)){
-  updated_filepaths <- trimws(strsplit(opt$files, ',')[[1]])
+if (!is.null(opt$files)) {
+  updated_filepaths <- trimws(strsplit(opt$files, ",")[[1]])
   updated_filepaths <- updated_filepaths[updated_filepaths != ""]
   print(updated_filepaths)
-  updated_filenames = basename(updated_filepaths)
-  original_filenames = basename(xset@filepaths)
-  update_idx = match(updated_filenames, original_filenames)
+  updated_filenames <- basename(updated_filepaths)
+  original_filenames <- basename(xset@filepaths)
+  update_idx <- match(updated_filenames, original_filenames)
 
-    if (!is.null(opt$galaxy_files)){
-        galaxy_files <- trimws(strsplit(opt$galaxy_files, ',')[[1]])
+    if (!is.null(opt$galaxy_files)) {
+        galaxy_files <- trimws(strsplit(opt$galaxy_files, ",")[[1]])
         galaxy_files <- galaxy_files[galaxy_files != ""]
         xset@filepaths <- galaxy_files[update_idx]
     }else{
@@ -116,27 +114,26 @@ if (!is.null(opt$files)){
     }
 }
 
-if (!is.null(opt$choose_class)){
-  classes <- trimws(strsplit(opt$choose_class, ',')[[1]])
-
+if (!is.null(opt$choose_class)) {
+  classes <- trimws(strsplit(opt$choose_class, ",")[[1]])
 
   ignore_files_class <- which(!as.character(xset@phenoData$class) %in% classes)
 
-  print('choose class')
+  print("choose class")
   print(ignore_files_class)
 }else{
   ignore_files_class <- NA
 }
 
-if (!is.null(opt$ignore_files)){
-  ignore_files_string <- trimws(strsplit(opt$ignore_files, ',')[[1]])
+if (!is.null(opt$ignore_files)) {
+  ignore_files_string <- trimws(strsplit(opt$ignore_files, ",")[[1]])
   filenames <- rownames(xset@phenoData)
   ignore_files <- which(filenames %in% ignore_files_string)
 
   ignore_files <- unique(c(ignore_files, ignore_files_class))
   ignore_files <- ignore_files[ignore_files != ""]
 }else{
-  if (anyNA(ignore_files_class)){
+  if (anyNA(ignore_files_class)) {
     ignore_files <- NULL
   }else{
     ignore_files <- ignore_files_class
@@ -144,41 +141,40 @@ if (!is.null(opt$ignore_files)){
 
 }
 
-print('ignore_files')
+print("ignore_files")
 print(ignore_files)
 
 
-ppLCMS <- msPurity::purityX(xset=xset,
-                                offsets=c(minOffset, maxOffset),
-                                cores=opt$cores,
-                                xgroups=xgroups,
-                                purityType=opt$purityType,
-                                ilim = opt$ilim,
-                                isotopes = isotopes,
-                                im = im,
-                                iwNorm = iwNorm,
-                                iwNormFun = iwNormFun,
-                                singleFile = opt$singleFile,
-                                fileignore = ignore_files,
-                                rtrawColumns=rtraw_columns)
-
+ppLCMS <- msPurity::purityX(xset = xset,
+                            offsets = c(minOffset, maxOffset),
+                            cores = opt$cores,
+                            xgroups = xgroups,
+                            purityType = opt$purityType,
+                            ilim = opt$ilim,
+                            isotopes = isotopes,
+                            im = im,
+                            iwNorm = iwNorm,
+                            iwNormFun = iwNormFun,
+                            singleFile = opt$singleFile,
+                            fileignore = ignore_files,
+                            rtrawColumns = rtraw_columns)
 
 dfp <- ppLCMS@predictions
 
 # to make compatable with deconrank
-colnames(dfp)[colnames(dfp)=='grpid'] = 'peakID'
-colnames(dfp)[colnames(dfp)=='median'] = 'medianPurity'
-colnames(dfp)[colnames(dfp)=='mean'] = 'meanPurity'
-colnames(dfp)[colnames(dfp)=='sd'] = 'sdPurity'
-colnames(dfp)[colnames(dfp)=='stde'] = 'sdePurity'
-colnames(dfp)[colnames(dfp)=='RSD'] = 'cvPurity'
-colnames(dfp)[colnames(dfp)=='pknm'] = 'pknmPurity'
-if(sum(is.na(dfp$medianPurity))>0){
-    dfp[is.na(dfp$medianPurity),]$medianPurity = 0
+colnames(dfp)[colnames(dfp) == "grpid"] <- "peakID"
+colnames(dfp)[colnames(dfp) == "median"] <- "medianPurity"
+colnames(dfp)[colnames(dfp) == "mean"] <- "meanPurity"
+colnames(dfp)[colnames(dfp) == "sd"] <- "sdPurity"
+colnames(dfp)[colnames(dfp) == "stde"] <- "sdePurity"
+colnames(dfp)[colnames(dfp) == "RSD"] <- "cvPurity"
+colnames(dfp)[colnames(dfp) == "pknm"] <- "pknmPurity"
+
+if (sum(is.na(dfp$medianPurity)) > 0) {
+  dfp[is.na(dfp$medianPurity), ]$medianPurity <- 0
 }
 
-
 print(head(dfp))
-write.table(dfp, file.path(opt$out_dir, 'purityX_output.tsv'), row.names=FALSE, sep='\t')
+write.table(dfp, file.path(opt$out_dir, "purityX_output.tsv"), row.names = FALSE, sep = "\t")
 
-save.image(file.path(opt$out_dir, 'purityX_output.RData'))
+save.image(file.path(opt$out_dir, "purityX_output.RData"))
diff --git a/tools/msPurity/spectralMatching.R b/tools/msPurity/spectralMatching.R
index d7cd2a7..26c8a65 100644
--- a/tools/msPurity/spectralMatching.R
+++ b/tools/msPurity/spectralMatching.R
@@ -3,107 +3,111 @@ library(msPurityData)
 library(optparse)
 print(sessionInfo())
 # load in library spectra config
-source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
+source_local <- function(fname) {
+  argv <- commandArgs(trailingOnly = FALSE)
+  base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+  source(paste(base_dir, fname, sep = "/"))
+}
 source_local("dbconfig.R")
 
 option_list <- list(
-  make_option(c("-o", "--outDir"), type="character"),
-  make_option("--q_dbPth", type="character"),
-  make_option("--l_dbPth", type="character"),
+  make_option(c("-o", "--outDir"), type = "character"),
+  make_option("--q_dbPth", type = "character"),
+  make_option("--l_dbPth", type = "character"),
 
-  make_option("--q_dbType", type="character", default=NA),
-  make_option("--l_dbType", type="character", default=NA),
+  make_option("--q_dbType", type = "character", default = NA),
+  make_option("--l_dbType", type = "character", default = NA),
 
-  make_option("--q_msp", type="character", default=NA),
-  make_option("--l_msp", type="character", default=NA),
+  make_option("--q_msp", type = "character", default = NA),
+  make_option("--l_msp", type = "character", default = NA),
 
-  make_option("--q_defaultDb", action="store_true"),
-  make_option("--l_defaultDb", action="store_true"),
+  make_option("--q_defaultDb", action = "store_true"),
+  make_option("--l_defaultDb", action = "store_true"),
 
-  make_option("--q_ppmPrec", type="double"),
-  make_option("--l_ppmPrec", type="double"),
+  make_option("--q_ppmPrec", type = "double"),
+  make_option("--l_ppmPrec", type = "double"),
 
-  make_option("--q_ppmProd", type="double"),
-  make_option("--l_ppmProd", type="double"),
+  make_option("--q_ppmProd", type = "double"),
+  make_option("--l_ppmProd", type = "double"),
 
-  make_option("--q_raThres", type="double", default=NA),
-  make_option("--l_raThres", type="double", default=NA),
+  make_option("--q_raThres", type = "double", default = NA),
+  make_option("--l_raThres", type = "double", default = NA),
 
-  make_option("--q_polarity", type="character", default=NA),
-  make_option("--l_polarity", type="character", default=NA),
+  make_option("--q_polarity", type = "character", default = NA),
+  make_option("--l_polarity", type = "character", default = NA),
 
-  make_option("--q_purity", type="double", default=NA),
-  make_option("--l_purity", type="double", default=NA),
+  make_option("--q_purity", type = "double", default = NA),
+  make_option("--l_purity", type = "double", default = NA),
 
-  make_option("--q_xcmsGroups", type="character", default=NA),
-  make_option("--l_xcmsGroups", type="character", default=NA),
+  make_option("--q_xcmsGroups", type = "character", default = NA),
+  make_option("--l_xcmsGroups", type = "character", default = NA),
 
-  make_option("--q_pids", type="character", default=NA),
-  make_option("--l_pids", type="character", default=NA),
+  make_option("--q_pids", type = "character", default = NA),
+  make_option("--l_pids", type = "character", default = NA),
 
-  make_option("--q_rtrangeMin", type="double", default=NA),
-  make_option("--l_rtrangeMin", type="double", default=NA),
+  make_option("--q_rtrangeMin", type = "double", default = NA),
+  make_option("--l_rtrangeMin", type = "double", default = NA),
 
-  make_option("--q_rtrangeMax", type="double", default=NA),
-  make_option("--l_rtrangeMax", type="double", default=NA),
+  make_option("--q_rtrangeMax", type = "double", default = NA),
+  make_option("--l_rtrangeMax", type = "double", default = NA),
 
-  make_option("--q_accessions", type="character", default=NA),
-  make_option("--l_accessions", type="character", default=NA),
+  make_option("--q_accessions", type = "character", default = NA),
+  make_option("--l_accessions", type = "character", default = NA),
 
-  make_option("--q_sources", type="character", default=NA),
-  make_option("--l_sources", type="character", default=NA),
+  make_option("--q_sources", type = "character", default = NA),
+  make_option("--l_sources", type = "character", default = NA),
 
-  make_option("--q_sourcesUser", type="character", default=NA),
-  make_option("--l_sourcesUser", type="character", default=NA),
+  make_option("--q_sourcesUser", type = "character", default = NA),
+  make_option("--l_sourcesUser", type = "character", default = NA),
 
-  make_option("--q_instrumentTypes", type="character", default=NA),
-  make_option("--l_instrumentTypes", type="character", default=NA),
+  make_option("--q_instrumentTypes", type = "character", default = NA),
+  make_option("--l_instrumentTypes", type = "character", default = NA),
 
-  make_option("--q_instrumentTypesUser", type="character", default=NA),
-  make_option("--l_instrumentTypesUser", type="character", default=NA),
+  make_option("--q_instrumentTypesUser", type = "character", default = NA),
+  make_option("--l_instrumentTypesUser", type = "character", default = NA),
 
-  make_option("--q_instruments", type="character", default=NA),
-  make_option("--l_instruments", type="character", default=NA),
+  make_option("--q_instruments", type = "character", default = NA),
+  make_option("--l_instruments", type = "character", default = NA),
 
-  make_option("--q_spectraTypes", type="character", default=NA),
-  make_option("--l_spectraTypes", type="character", default=NA),
+  make_option("--q_spectraTypes", type = "character", default = NA),
+  make_option("--l_spectraTypes", type = "character", default = NA),
 
-  make_option("--q_spectraFilter", action="store_true"),
-  make_option("--l_spectraFilter", action="store_true"),
+  make_option("--q_spectraFilter", action = "store_true"),
+  make_option("--l_spectraFilter", action = "store_true"),
 
-  make_option("--usePrecursors", action="store_true"),
+  make_option("--usePrecursors", action = "store_true"),
 
-  make_option("--mzW", type="double"),
-  make_option("--raW", type="double"),
+  make_option("--mzW", type = "double"),
+  make_option("--raW", type = "double"),
 
-  make_option("--rttol", type="double", default=NA),
+  make_option("--rttol", type = "double", default = NA),
 
-  make_option("--updateDb", action="store_true"),
-  make_option("--copyDb", action="store_true"),
-  make_option("--cores", default=1)
+  make_option("--updateDb", action = "store_true"),
+  make_option("--copyDb", action = "store_true"),
+  make_option("--cores", default = 1)
 
 
 )
 
 # store options
-opt<- parse_args(OptionParser(option_list=option_list))
+opt <- parse_args(OptionParser(option_list = option_list))
 
 print(opt)
 
 # check if the sqlite databases have any spectra
-checkSPeakMeta <- function(dbPth, nme){
-    if(is.null(dbPth)){
+checkSPeakMeta <- function(dbPth, nme) {
+    if (is.null(dbPth)) {
         return(TRUE)
-    }else if ((file.exists(dbPth)) & (file.info(dbPth)$size>0)){
+    }else if ((file.exists(dbPth)) & (file.info(dbPth)$size > 0)) {
         con <- DBI::dbConnect(RSQLite::SQLite(), dbPth)
-        if (DBI::dbExistsTable(con, "s_peak_meta")){
-            spm <- DBI::dbGetQuery(con, 'SELECT  * FROM s_peak_meta ORDER BY ROWID ASC LIMIT 1')
+        if (DBI::dbExistsTable(con, "s_peak_meta")) {
+            spm <- DBI::dbGetQuery(con, "SELECT  * FROM s_peak_meta ORDER BY ROWID ASC LIMIT 1")
             return(TRUE)
-        }else if(DBI::dbExistsTable(con, "library_spectra_meta")){
-            spm <- DBI::dbGetQuery(con, 'SELECT  * FROM library_spectra_meta ORDER BY ROWID ASC LIMIT 1')
+        }else if (DBI::dbExistsTable(con, "library_spectra_meta")) {
+            spm <- DBI::dbGetQuery(con, "SELECT  * FROM library_spectra_meta ORDER BY ROWID ASC LIMIT 1")
             return(TRUE)
         }else{
-            print(paste("No spectra available for ",nme))
+            print(paste("No spectra available for ", nme))
             return(FALSE)
         }
     }else{
@@ -111,110 +115,111 @@ checkSPeakMeta <- function(dbPth, nme){
         return(FALSE)
     }
 
-        
+
 }
 
 
-addQueryNameColumn <- function(sm){
-    if (is.null(sm$matchedResults) || length(sm$matchedResults)==1 || nrow(sm$matchedResults)==0){
+addQueryNameColumn <- function(sm) {
+    if (is.null(sm$matchedResults) || length(sm$matchedResults) == 1 || nrow(sm$matchedResults) == 0) {
         return(sm)
     }
 
-    con <- DBI::dbConnect(RSQLite::SQLite(),sm$q_dbPth)
-    if (DBI::dbExistsTable(con, "s_peak_meta")){
-        spm <- DBI::dbGetQuery(con, 'SELECT  pid, name AS query_entry_name FROM s_peak_meta')
-    }else if(DBI::dbExistsTable(con, "library_spectra_meta")){
-        spm <- DBI::dbGetQuery(con, 'SELECT  id AS pid, name  AS query_entry_name FROM library_spectra_meta')
+    con <- DBI::dbConnect(RSQLite::SQLite(), sm$q_dbPth)
+    if (DBI::dbExistsTable(con, "s_peak_meta")) {
+        spm <- DBI::dbGetQuery(con, "SELECT  pid, name AS query_entry_name FROM s_peak_meta")
+    }else if (DBI::dbExistsTable(con, "library_spectra_meta")) {
+        spm <- DBI::dbGetQuery(con, "SELECT  id AS pid, name  AS query_entry_name FROM library_spectra_meta")
     }
     print(sm$matchedResults)
-    if ('pid' %in% colnames(sm$matchedResults)){
-        sm$matchedResults <- merge(sm$matchedResults, spm, by.x='pid', by.y='pid')    
+    if ("pid" %in% colnames(sm$matchedResults)) {
+        sm$matchedResults <- merge(sm$matchedResults, spm, by.x = "pid", by.y = "pid")
     }else{
-        sm$matchedResults <- merge(sm$matchedResults, spm, by.x='qpid', by.y='pid')
+        sm$matchedResults <- merge(sm$matchedResults, spm, by.x = "qpid", by.y = "pid")
     }
-    
+
     print(sm$xcmsMatchedResults)
-    if (is.null(sm$xcmsMatchedResults) || length(sm$xcmsMatchedResults)==1 || nrow(sm$xcmsMatchedResults)==0){
+    if (is.null(sm$xcmsMatchedResults) || length(sm$xcmsMatchedResults) == 1 || nrow(sm$xcmsMatchedResults) == 0) {
         return(sm)
     }else{
-        if ('pid' %in% colnames(sm$xcmsMatchedResults)){
-            sm$xcmsMatchedResults<- merge(sm$xcmsMatchedResults, spm, by.x='pid', by.y='pid')    
+        if ("pid" %in% colnames(sm$xcmsMatchedResults)) {
+            sm$xcmsMatchedResults <- merge(sm$xcmsMatchedResults, spm, by.x = "pid", by.y = "pid")
         }else{
-            sm$xcmsMatchedResults <- merge(sm$xcmsMatchedResults, spm, by.x='qpid', by.y='pid')
+            sm$xcmsMatchedResults <- merge(sm$xcmsMatchedResults, spm, by.x = "qpid", by.y = "pid")
         }
     }
-    
+
     return(sm)
-    
+
 }
 
 
-updateDbF <- function(q_con, l_con){
-    message('Adding extra details to database')
-    q_con <- DBI::dbConnect(RSQLite::SQLite(),sm$q_dbPth)
-    if (DBI::dbExistsTable(q_con, "l_s_peak_meta")){
-        l_s_peak_meta <- DBI::dbGetQuery(q_con, 'SELECT  * FROM l_s_peak_meta')
-        colnames(l_s_peak_meta)[1] <- 'pid'
+updateDbF <- function(q_con, l_con) {
+    message("Adding extra details to database")
+    q_con <- DBI::dbConnect(RSQLite::SQLite(), sm$q_dbPth)
+    if (DBI::dbExistsTable(q_con, "l_s_peak_meta")) {
+        l_s_peak_meta <- DBI::dbGetQuery(q_con, "SELECT  * FROM l_s_peak_meta")
+        colnames(l_s_peak_meta)[1] <- "pid"
     }
-    
-    l_con <- DBI::dbConnect(RSQLite::SQLite(),l_dbPth)
-    if (DBI::dbExistsTable(l_con, "s_peaks")){
-        l_s_peaks <- DBI::dbGetQuery(q_con, sprintf("SELECT  * FROM s_peaks WHERE pid in (%s)", paste(unique(l_s_peak_meta$pid), collapse=',')))
-        
-    }else if(DBI::dbExistsTable(l_con, "library_spectra")){
+
+    l_con <- DBI::dbConnect(RSQLite::SQLite(), l_dbPth)
+    if (DBI::dbExistsTable(l_con, "s_peaks")) {
+        l_s_peaks <- DBI::dbGetQuery(q_con, sprintf("SELECT  * FROM s_peaks WHERE pid in (%s)", paste(unique(l_s_peak_meta$pid), collapse = ",")))
+
+    }else if (DBI::dbExistsTable(l_con, "library_spectra")) {
         l_s_peaks <- DBI::dbGetQuery(l_con, sprintf("SELECT  * FROM library_spectra
-                                                WHERE library_spectra_meta_id in (%s)", paste(unique(l_s_peak_meta$pid), collapse=',')))
+                                                WHERE library_spectra_meta_id in (%s)", paste(unique(l_s_peak_meta$pid), collapse = ",")))
     }else{
-        l_s_peaks = NULL
+        l_s_peaks <- NULL
     }
-    
-    if (DBI::dbExistsTable(l_con, "source")){
-        l_source <- DBI::dbGetQuery(l_con, 'SELECT  * FROM source')
+
+    if (DBI::dbExistsTable(l_con, "source")) {
+        l_source <- DBI::dbGetQuery(l_con, "SELECT  * FROM source")
     }else if (DBI::dbExistsTable(l_con, "library_spectra_source")) {
-        l_source <- DBI::dbGetQuery(l_con, 'SELECT  * FROM library_spectra_source')
+        l_source <- DBI::dbGetQuery(l_con, "SELECT  * FROM library_spectra_source")
     }else{
-        l_source = NULL
+        l_source <- NULL
     }
-    
-    if (!is.null(l_s_peaks)){
-        DBI::dbWriteTable(q_con, name='l_s_peaks', value=l_s_peaks, row.names=FALSE, append=TRUE)
+
+    if (!is.null(l_s_peaks)) {
+        DBI::dbWriteTable(q_con, name = "l_s_peaks", value = l_s_peaks, row.names = FALSE, append = TRUE)
     }
-    
-    if (!is.null(l_source)){
-        DBI::dbWriteTable(q_con, name='l_source', value=l_source, row.names=FALSE, append=TRUE)
+
+    if (!is.null(l_source)) {
+        DBI::dbWriteTable(q_con, name = "l_source", value = l_source, row.names = FALSE, append = TRUE)
     }
-    
-    
+
 }
 
 
-extractMultiple <- function(optParam){
-  if (!is.na(optParam)){
-     param <- trimws(strsplit(optParam, ',')[[1]])
+extractMultiple <- function(optParam) {
+  if (!is.na(optParam)) {
+     param <- trimws(strsplit(optParam, ",")[[1]])
      param <- param[param != ""]
-  }else{
+  }else {
      param <- NA
   }
   return(param)
 
 }
 
-if(!is.null(opt$q_defaultDb)){
-  q_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData")
-  q_dbType <- 'sqlite'
-}else if (!opt$q_dbType=='local_config'){
+if (!is.null(opt$q_defaultDb)) {
+  q_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package = "msPurityData")
+  q_dbType <- "sqlite"
+}else if (!opt$q_dbType == "local_config") {
   q_dbType <- opt$q_dbType
   q_dbPth <- opt$q_dbPth
 }
 
-if(!is.null(opt$l_defaultDb)){
-  l_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData")
-  l_dbType <- 'sqlite'
-}else if (!opt$l_dbType=='local_config'){
+if (!is.null(opt$l_defaultDb)) {
+  l_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package = "msPurityData")
+  l_dbType <- "sqlite"
+}else if (!opt$l_dbType == "local_config") {
   l_dbType <- opt$l_dbType
   l_dbPth <- opt$l_dbPth
 }
 
+q_spectraTypes <- extractMultiple(opt$q_spectraTypes)
+l_spectraTypes <- extractMultiple(opt$l_spectraTypes)
 
 q_polarity <- extractMultiple(opt$q_polarity)
 l_polarity <- extractMultiple(opt$l_polarity)
@@ -231,115 +236,118 @@ l_sources <- extractMultiple(opt$l_sources)
 q_sourcesUser <- extractMultiple(opt$q_sourcesUser)
 l_sourcesUser <- extractMultiple(opt$l_sourcesUser)
 
-q_sources <-c(q_sources, q_sourcesUser)
-l_sources <-c(l_sources, l_sourcesUser)
+q_sources <- c(q_sources, q_sourcesUser)
+l_sources <- c(l_sources, l_sourcesUser)
 
 q_instrumentTypes <- extractMultiple(opt$q_instrumentTypes)
 l_instrumentTypes <- extractMultiple(opt$l_instrumentTypes)
 
-q_instrumentTypes <-c(q_instrumentTypes, q_instrumentTypes)
-l_instrumentTypes <-c(l_instrumentTypes, l_instrumentTypes)
+q_instrumentTypes <- c(q_instrumentTypes, q_instrumentTypes)
+l_instrumentTypes <- c(l_instrumentTypes, l_instrumentTypes)
 
 
-if(!is.null(opt$l_spectraFilter)){
+if (!is.null(opt$l_spectraFilter)) {
   l_spectraFilter <- TRUE
 }else{
   l_spectraFilter <- FALSE
 }
 
-if(!is.null(opt$q_spectraFilter)){
+if (!is.null(opt$q_spectraFilter)) {
   q_spectraFilter <- TRUE
 }else{
   q_spectraFilter <- FALSE
 }
 
-if(!is.null(opt$updateDb)){
+if (!is.null(opt$updateDb)) {
   updateDb <- TRUE
 }else{
   updateDb <- FALSE
 }
 
-if(!is.null(opt$copyDb)){
+if (!is.null(opt$copyDb)) {
   copyDb <- TRUE
 }else{
   copyDb <- FALSE
 }
 
-if(!is.null(opt$l_rtrangeMax)){
+if (!is.null(opt$l_rtrangeMax)) {
   l_rtrangeMax <- opt$l_rtrangeMax
 }else{
   l_rtrangeMax <- NA
 }
 
-if(!is.null(opt$q_rtrangeMax)){
+if (!is.null(opt$q_rtrangeMax)) {
   q_rtrangeMax <- opt$q_rtrangeMax
 }else{
   q_rtrangeMax <- NA
 }
 
-if(!is.null(opt$l_rtrangeMin)){
+if (!is.null(opt$l_rtrangeMin)) {
   l_rtrangeMin <- opt$l_rtrangeMin
 }else{
   l_rtrangeMin <- NA
 }
 
-if(!is.null(opt$q_rtrangeMin)){
+if (!is.null(opt$q_rtrangeMin)) {
   q_rtrangeMin <- opt$q_rtrangeMin
 }else{
   q_rtrangeMin <- NA
 }
 
-q_check <- checkSPeakMeta(opt$q_dbPth, 'query')
-l_check <- checkSPeakMeta(opt$l_dbPth, 'library')
+q_check <- checkSPeakMeta(opt$q_dbPth, "query")
+l_check <- checkSPeakMeta(opt$l_dbPth, "library")
 
 
-if (q_check && l_check){
+if (q_check && l_check) {
     sm <- msPurity::spectralMatching(
         q_purity =  opt$q_purity,
         l_purity =  opt$l_purity,
-        
+
         q_ppmProd =  opt$q_ppmProd,
         l_ppmProd =  opt$l_ppmProd,
-        
+
         q_ppmPrec =  opt$q_ppmPrec,
         l_ppmPrec =  opt$l_ppmPrec,
-        
+
         q_raThres =  opt$q_raThres,
         l_raThres =  opt$l_raThres,
-        
+
         q_pol =  q_polarity,
         l_pol =  l_polarity,
-        
+
+        q_spectraFilter = q_spectraFilter,
+        l_spectraFilter = l_spectraFilter,
+
         q_xcmsGroups = q_xcmsGroups,
         l_xcmsGroups = l_xcmsGroups,
-        
+
         q_pids = q_pids,
         l_pids = l_pids,
-        
+
         q_sources = q_sources,
         l_sources = l_sources,
-        
+
         q_instrumentTypes = q_instrumentTypes,
         l_instrumentTypes = l_instrumentTypes,
-        
-        q_spectraFilter= q_spectraFilter,
-        l_spectraFilter= l_spectraFilter,
-        
-        l_rtrange=c(l_rtrangeMin, l_rtrangeMax),
-        q_rtrange=c(q_rtrangeMin, q_rtrangeMax),
-        
+
+        q_spectraTypes = q_spectraTypes,
+        l_spectraTypes = l_spectraTypes,
+
+        l_rtrange = c(l_rtrangeMin, l_rtrangeMax),
+        q_rtrange = c(q_rtrangeMin, q_rtrangeMax),
+
         q_accessions = opt$q_accessions,
-        l_accessions= opt$l_accessions,
-        
+        l_accessions = opt$l_accessions,
+
         raW = opt$raW,
         mzW = opt$mzW,
-        rttol=opt$rttol,
-        cores=opt$cores,
-        
-        copyDb=copyDb,
-        updateDb=updateDb,
+        rttol = opt$rttol,
+        cores = opt$cores,
+
+        copyDb = copyDb,
+        updateDb = updateDb,
         outPth = "db_with_spectral_matching.sqlite",
-        
+
         q_dbPth = q_dbPth,
         q_dbType = q_dbType,
         q_dbName = q_dbName,
@@ -347,7 +355,7 @@ if (q_check && l_check){
         q_dbUser = q_dbUser,
         q_dbPass = q_dbPass,
         q_dbPort = q_dbPort,
-        
+
         l_dbPth = l_dbPth,
         l_dbType = l_dbType,
         l_dbName = l_dbName,
@@ -355,15 +363,15 @@ if (q_check && l_check){
         l_dbUser = l_dbUser,
         l_dbPass = l_dbPass,
         l_dbPort = l_dbPort
-        
+
     )
-    
+
     sm <- addQueryNameColumn(sm)
     # Get name of the query results (and merged with the data frames)
-    write.table(sm$matchedResults, 'matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE)
-    write.table(sm$xcmsMatchedResults, 'xcms_matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE)
-    
-    if(updateDb){
+    write.table(sm$matchedResults, "matched_results.tsv", sep = "\t", row.names = FALSE, col.names = TRUE)
+    write.table(sm$xcmsMatchedResults, "xcms_matched_results.tsv", sep = "\t", row.names = FALSE, col.names = TRUE)
+
+    if (updateDb) {
         updateDbF(q_con, l_con)
     }
 }
diff --git a/tools/msPurity/spectralMatching.xml b/tools/msPurity/spectralMatching.xml
index cf394c8..b6ac784 100644
--- a/tools/msPurity/spectralMatching.xml
+++ b/tools/msPurity/spectralMatching.xml
@@ -221,6 +221,8 @@
     <tests>
         <test>
             <param name="q_dbPth" value="createDatabase_output.sqlite" />
+            <param name="q_spectraTypes_bool" value="true" />
+            <param name="q_spectraTypes" value="inter,av_all" />
 	        <param name="l_dbPth_select" value="userdb" />
             <param name="l_dbPth" value="PR100037.sqlite" />
             <param name="q_xcmsGroups_bool" value="true" />
@@ -234,6 +236,8 @@
         <test>
             <param name="l_instrumentTypes_bool" value="true" />
             <param name="q_dbPth" value="createDatabase_output.sqlite" />
+            <param name="q_spectraTypes_bool" value="true" />
+            <param name="q_spectraTypes" value="inter,av_all" />
 	    	<param name="l_dbPth_select" value="userdb" />
             <param name="l_dbPth" value="PR100037.sqlite" />
             <param name="q_xcmsGroups_bool" value="true" />
@@ -360,10 +364,10 @@ without the XCMS details. This table is useful to observe spectral matching resu
 for all MS/MS spectra irrespective of if they are linked to XCMS MS1 features.
 
 
-.. _spectral_database_schema: https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-datatabase-schema.html
+.. _spectral_database_schema: https://www.bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html
 .. _larger_database: https://github.com/computational-metabolomics/msp2db/releases
 .. _msp2db: https://github.com/computational-metabolomics/msp2db/releases
-.. _msPurity_spectral_matching_vignette: https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html
+.. _msPurity_spectral_matching_vignette: https://www.bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html
 
     ]]></help>
 
diff --git a/tools/msPurity/test-data/createDatabase_output.sqlite b/tools/msPurity/test-data/createDatabase_output.sqlite
index a77dd85..74f7125 100644
Binary files a/tools/msPurity/test-data/createDatabase_output.sqlite and b/tools/msPurity/test-data/createDatabase_output.sqlite differ
diff --git a/tools/msPurity/test-data/createDatabase_output_eic.sqlite b/tools/msPurity/test-data/createDatabase_output_eic.sqlite
index 4b85f0a..62d2d99 100644
Binary files a/tools/msPurity/test-data/createDatabase_output_eic.sqlite and b/tools/msPurity/test-data/createDatabase_output_eic.sqlite differ
diff --git a/tools/msPurity/test-data/createMSP_output_av_all_metadata.msp b/tools/msPurity/test-data/createMSP_output_av_all_metadata.msp
index 7beaff8..9899202 100644
--- a/tools/msPurity/test-data/createMSP_output_av_all_metadata.msp
+++ b/tools/msPurity/test-data/createMSP_output_av_all_metadata.msp
@@ -10,7 +10,7 @@ CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
 CH$LINK: PUBCHEM CID:5328
 CH$NAME Unknown
 XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 
 PK$NUM_PEAK: 2
 PK$PEAK: m/z int. rel.int.
 112.050884246826	502873.46875	100
@@ -28,7 +28,7 @@ CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
 CH$LINK: PUBCHEM CID:5328
 CH$NAME Unknown
 XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 
 PK$NUM_PEAK: 2
 PK$PEAK: m/z int. rel.int.
 112.050884246826	502873.46875	100
diff --git a/tools/msPurity/test-data/createMSP_output_av_all_metadata_custom_adducts.msp b/tools/msPurity/test-data/createMSP_output_av_all_metadata_custom_adducts.msp
index 2f1fa88..5239b87 100644
--- a/tools/msPurity/test-data/createMSP_output_av_all_metadata_custom_adducts.msp
+++ b/tools/msPurity/test-data/createMSP_output_av_all_metadata_custom_adducts.msp
@@ -10,7 +10,7 @@ CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
 CH$LINK: PUBCHEM CID:5328
 CH$NAME Unknown
 XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 
 PK$NUM_PEAK: 2
 PK$PEAK: m/z int. rel.int.
 112.050884246826	502873.46875	100
@@ -28,7 +28,7 @@ CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
 CH$LINK: PUBCHEM CID:5328
 CH$NAME Unknown
 XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 
 PK$NUM_PEAK: 2
 PK$PEAK: m/z int. rel.int.
 112.050884246826	502873.46875	100
@@ -46,7 +46,7 @@ CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
 CH$LINK: PUBCHEM CID:5328
 CH$NAME Unknown
 XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 
 PK$NUM_PEAK: 2
 PK$PEAK: m/z int. rel.int.
 112.050884246826	502873.46875	100
@@ -64,7 +64,7 @@ CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
 CH$LINK: PUBCHEM CID:5328
 CH$NAME Unknown
 XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 
 PK$NUM_PEAK: 2
 PK$PEAK: m/z int. rel.int.
 112.050884246826	502873.46875	100
@@ -82,7 +82,7 @@ CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
 CH$LINK: PUBCHEM CID:5328
 CH$NAME Unknown
 XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 
 PK$NUM_PEAK: 2
 PK$PEAK: m/z int. rel.int.
 112.050884246826	502873.46875	100
@@ -100,7 +100,7 @@ CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
 CH$LINK: PUBCHEM CID:5328
 CH$NAME Unknown
 XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 
 PK$NUM_PEAK: 2
 PK$PEAK: m/z int. rel.int.
 112.050884246826	502873.46875	100
diff --git a/tools/msPurity/test-data/spectralMatching_db_with_spectral_matching.sqlite b/tools/msPurity/test-data/spectralMatching_db_with_spectral_matching.sqlite
index c674639..dae259c 100644
Binary files a/tools/msPurity/test-data/spectralMatching_db_with_spectral_matching.sqlite and b/tools/msPurity/test-data/spectralMatching_db_with_spectral_matching.sqlite differ
diff --git a/tools/msPurity/test-data/spectralMatching_db_with_spectral_matching_instrumentTypes.sqlite b/tools/msPurity/test-data/spectralMatching_db_with_spectral_matching_instrumentTypes.sqlite
index c674639..dae259c 100644
Binary files a/tools/msPurity/test-data/spectralMatching_db_with_spectral_matching_instrumentTypes.sqlite and b/tools/msPurity/test-data/spectralMatching_db_with_spectral_matching_instrumentTypes.sqlite differ
diff --git a/tools/msPurity/test-data/spectralMatching_matched_results.tsv b/tools/msPurity/test-data/spectralMatching_matched_results.tsv
index 4243d89..057687a 100644
--- a/tools/msPurity/test-data/spectralMatching_matched_results.tsv
+++ b/tools/msPurity/test-data/spectralMatching_matched_results.tsv
@@ -1,3 +1,3 @@
 "pid"	"grpid"	"mz"	"mzmin"	"mzmax"	"rt"	"rtmin"	"rtmax"	"npeaks"	"sample"	"LCMSMS_2"	"LCMSMS_1"	"LCMS_2"	"LCMS_1"	"grp_name"	"lpid"	"mid"	"dpc"	"rdpc"	"cdpc"	"mcount"	"allcount"	"mpercent"	"library_rt"	"query_rt"	"rtdiff"	"library_precursor_mz"	"query_precursor_mz"	"library_precursor_ion_purity"	"query_precursor_ion_purity"	"library_accession"	"library_precursor_type"	"library_entry_name"	"inchikey"	"library_source_name"	"library_compound_name"	"query_entry_name"
-1663	14	113.035283604395	113.035156497997	113.03541992282	80.50932	77.16429	83.64567	4	4	88462324.9597518	92812020.095242	77298864.2688328	77198465.9156761	"M113T81"	56653	1	0.942265461847349	0.996860823822942	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"	NA
-1664	14	113.035283604395	113.035156497997	113.03541992282	80.50932	77.16429	83.64567	4	4	88462324.9597518	92812020.095242	77298864.2688328	77198465.9156761	"M113T81"	56653	2	0.942265461847349	0.996860823822942	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"	NA
+1665	14	113.035283604395	113.035156497997	113.03541992282	80.50932	77.16429	83.64567	4	4	88462324.9597518	92812020.095242	77298864.2688328	77198465.9156761	"M113T81"	56653	1	0.942265461847349	0.945232713864488	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"	NA
+1666	14	113.035283604395	113.035156497997	113.03541992282	80.50932	77.16429	83.64567	4	4	88462324.9597518	92812020.095242	77298864.2688328	77198465.9156761	"M113T81"	56653	2	0.942265461847349	0.945232713864488	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"	NA
diff --git a/tools/msPurity/test-data/spectralMatching_matched_results_instrumentTypes.tsv b/tools/msPurity/test-data/spectralMatching_matched_results_instrumentTypes.tsv
index 4243d89..057687a 100644
--- a/tools/msPurity/test-data/spectralMatching_matched_results_instrumentTypes.tsv
+++ b/tools/msPurity/test-data/spectralMatching_matched_results_instrumentTypes.tsv
@@ -1,3 +1,3 @@
 "pid"	"grpid"	"mz"	"mzmin"	"mzmax"	"rt"	"rtmin"	"rtmax"	"npeaks"	"sample"	"LCMSMS_2"	"LCMSMS_1"	"LCMS_2"	"LCMS_1"	"grp_name"	"lpid"	"mid"	"dpc"	"rdpc"	"cdpc"	"mcount"	"allcount"	"mpercent"	"library_rt"	"query_rt"	"rtdiff"	"library_precursor_mz"	"query_precursor_mz"	"library_precursor_ion_purity"	"query_precursor_ion_purity"	"library_accession"	"library_precursor_type"	"library_entry_name"	"inchikey"	"library_source_name"	"library_compound_name"	"query_entry_name"
-1663	14	113.035283604395	113.035156497997	113.03541992282	80.50932	77.16429	83.64567	4	4	88462324.9597518	92812020.095242	77298864.2688328	77198465.9156761	"M113T81"	56653	1	0.942265461847349	0.996860823822942	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"	NA
-1664	14	113.035283604395	113.035156497997	113.03541992282	80.50932	77.16429	83.64567	4	4	88462324.9597518	92812020.095242	77298864.2688328	77198465.9156761	"M113T81"	56653	2	0.942265461847349	0.996860823822942	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"	NA
+1665	14	113.035283604395	113.035156497997	113.03541992282	80.50932	77.16429	83.64567	4	4	88462324.9597518	92812020.095242	77298864.2688328	77198465.9156761	"M113T81"	56653	1	0.942265461847349	0.945232713864488	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"	NA
+1666	14	113.035283604395	113.035156497997	113.03541992282	80.50932	77.16429	83.64567	4	4	88462324.9597518	92812020.095242	77298864.2688328	77198465.9156761	"M113T81"	56653	2	0.942265461847349	0.945232713864488	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"	NA
diff --git a/tools/msPurity/test-data/spectralMatching_xcms_matched_results.tsv b/tools/msPurity/test-data/spectralMatching_xcms_matched_results.tsv
index 7349920..658f8a8 100644
--- a/tools/msPurity/test-data/spectralMatching_xcms_matched_results.tsv
+++ b/tools/msPurity/test-data/spectralMatching_xcms_matched_results.tsv
@@ -1,3 +1,3 @@
 "qpid"	"lpid"	"mid"	"dpc"	"rdpc"	"cdpc"	"mcount"	"allcount"	"mpercent"	"library_rt"	"query_rt"	"rtdiff"	"library_precursor_mz"	"query_precursor_mz"	"library_precursor_ion_purity"	"query_precursor_ion_purity"	"library_accession"	"library_precursor_type"	"library_entry_name"	"inchikey"	"library_source_name"	"library_compound_name"	"query_entry_name"
-1663	56653	1	0.942265461847349	0.996860823822942	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"	NA
-1664	56653	2	0.942265461847349	0.996860823822942	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"	NA
+1665	56653	1	0.942265461847349	0.945232713864488	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"	NA
+1666	56653	2	0.942265461847349	0.945232713864488	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"	NA
diff --git a/tools/msPurity/test-data/spectralMatching_xcms_matched_results_instrumentTypes.tsv b/tools/msPurity/test-data/spectralMatching_xcms_matched_results_instrumentTypes.tsv
index 7349920..658f8a8 100644
--- a/tools/msPurity/test-data/spectralMatching_xcms_matched_results_instrumentTypes.tsv
+++ b/tools/msPurity/test-data/spectralMatching_xcms_matched_results_instrumentTypes.tsv
@@ -1,3 +1,3 @@
 "qpid"	"lpid"	"mid"	"dpc"	"rdpc"	"cdpc"	"mcount"	"allcount"	"mpercent"	"library_rt"	"query_rt"	"rtdiff"	"library_precursor_mz"	"query_precursor_mz"	"library_precursor_ion_purity"	"query_precursor_ion_purity"	"library_accession"	"library_precursor_type"	"library_entry_name"	"inchikey"	"library_source_name"	"library_compound_name"	"query_entry_name"
-1663	56653	1	0.942265461847349	0.996860823822942	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"	NA
-1664	56653	2	0.942265461847349	0.996860823822942	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"	NA
+1665	56653	1	0.942265461847349	0.945232713864488	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"	NA
+1666	56653	2	0.942265461847349	0.945232713864488	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"	NA