diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
index 71a57b0719..42fc17a097 100644
--- a/.github/workflows/pypi.yml
+++ b/.github/workflows/pypi.yml
@@ -1,33 +1,33 @@
 name: pypi upload
 
 on:
-  create:
-    tags:
-    - '*'
+    create:
+        tags:
+            - "*"
 
 defaults:
-  run:
-    shell: bash -l {0}
+    run:
+        shell: bash -l {0}
 
 jobs:
-  pypi:
-    if: ${{ startsWith(github.ref, 'refs/tags/') }}
-    name: upload to pypi
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with:
-        python-version: '3.12'
-        cache: 'pip'
-    - name: build
-      run: |
-        pip install .[actions]
-        rm -f dist/*
-        python -m build
-    - name: upload
-      env:
-        TWINE_USERNAME: "__token__"
-        TWINE_PASSWORD: ${{ secrets.pypi_password }}
-      run: |
-        twine upload dist/*
+    pypi:
+        if: ${{ startsWith(github.ref, 'refs/tags/') }}
+        name: upload to pypi
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v7
+            - uses: actions/setup-python@v6
+              with:
+                  python-version: "3.12"
+                  cache: "pip"
+            - name: build
+              run: |
+                  pip install .[actions]
+                  rm -f dist/*
+                  python -m build
+            - name: upload
+              env:
+                  TWINE_USERNAME: "__token__"
+                  TWINE_PASSWORD: ${{ secrets.pypi_password }}
+              run: |
+                  twine upload dist/*
diff --git a/.github/workflows/test_planemo.yml b/.github/workflows/test_planemo.yml
index dd5d0a413b..063ffb4046 100644
--- a/.github/workflows/test_planemo.yml
+++ b/.github/workflows/test_planemo.yml
@@ -2,59 +2,59 @@ name: tests_planemo
 on: [push, pull_request, workflow_dispatch]
 
 env:
-  GALAXY_BRANCH: release_24.1
+    GALAXY_BRANCH: release_26.0
 
 defaults:
-  run:
-    shell: bash -l {0}
+    run:
+        shell: bash -l {0}
 
 jobs:
-  planemo_test:
-    name: Planemo test
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        chunk: [1, 2, 3]
-    steps:
-    - uses: actions/checkout@v4
-    - uses: conda-incubator/setup-miniconda@v3
-      with:
-        miniconda-version: "latest"
-        auto-activate-base: true
-        python-version: "3.12"
-    - name: get samtools
-      run: |
-        conda install -c conda-forge -c bioconda samtools
-    - name: pip install
-      run: |
-        pip install .[actions]
-    - name: planemo
-      run: |
-        ./.planemo.sh ${{ matrix.chunk }} ${{ env.GALAXY_BRANCH }}
-    - uses: actions/upload-artifact@v4
-      with:
-        name: 'Tool test output ${{ matrix.chunk }}'
-        path: upload
-  planemo_combine_outputs:
-    name: Combine chunked test results
-    needs: planemo_test
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/download-artifact@v4
-      with:
-        path: artifacts
-    - name: Combine outputs
-      uses: galaxyproject/planemo-ci-action@v1
-      id: combine
-      with:
-        mode: combine
-        html-report: true
-    - uses: actions/upload-artifact@v4
-      with:
-        name: 'All tool test results'
-        path: upload
-    - name: Check outputs
-      uses: galaxyproject/planemo-ci-action@v1
-      id: check
-      with:
-        mode: check
\ No newline at end of file
+    planemo_test:
+        name: Planemo test
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                chunk: [1, 2, 3]
+        steps:
+            - uses: actions/checkout@v7
+            - uses: conda-incubator/setup-miniconda@v4
+              with:
+                  miniconda-version: "latest"
+                  auto-activate-base: true
+                  python-version: "3.12"
+            - name: get samtools
+              run: |
+                  conda install -c conda-forge -c bioconda samtools
+            - name: pip install
+              run: |
+                  pip install .[actions]
+            - name: planemo
+              run: |
+                  ./.planemo.sh ${{ matrix.chunk }} ${{ env.GALAXY_BRANCH }}
+            - uses: actions/upload-artifact@v7
+              with:
+                  name: "Tool test output ${{ matrix.chunk }}"
+                  path: upload
+    planemo_combine_outputs:
+        name: Combine chunked test results
+        needs: planemo_test
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/download-artifact@v8
+              with:
+                  path: artifacts
+            - name: Combine outputs
+              uses: galaxyproject/planemo-ci-action@v1
+              id: combine
+              with:
+                  mode: combine
+                  html-report: true
+            - uses: actions/upload-artifact@v7
+              with:
+                  name: "All tool test results"
+                  path: upload
+            - name: Check outputs
+              uses: galaxyproject/planemo-ci-action@v1
+              id: check
+              with:
+                  mode: check
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
index 76c439767b..2a8dd339bc 100644
--- a/.github/workflows/wheels.yml
+++ b/.github/workflows/wheels.yml
@@ -3,200 +3,199 @@ name: build wheels
 # Also, see: https://github.com/jackh726/bigtools/blob/master/.github/workflows/release-python.yml
 
 on:
-  push:
-  pull_request:
+    push:
+    pull_request:
 
 permissions:
-  contents: read
+    contents: read
 
 jobs:
+    linux:
+        runs-on: ${{ matrix.platform.runner }}
+        strategy:
+            matrix:
+                platform:
+                    - runner: ubuntu-22.04
+                      target: x86_64
+                    - runner: ubuntu-22.04
+                      target: aarch64
+        steps:
+            - uses: actions/checkout@v7
+            - uses: actions/setup-python@v5
+              with:
+                  python-version: 3.x
+            - name: Build wheels
+              uses: PyO3/maturin-action@v1
+              with:
+                  target: ${{ matrix.platform.target }}
+                  args: --release --out dist --find-interpreter
+                  # sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+                  manylinux: 2_28
+                  before-script-linux: |
+                      set -ex
+                      cat /etc/*release*
+                      if [ "${{ matrix.platform.target }}" = "x86_64" ]; then
+                        # maturin-action's manylinux switches to AlmaLinux 8
+                        dnf install -y epel-release && dnf update -y
+                        dnf install -y gcc gcc-c++ make perl curl clang xz-devel pkgconfig
+                        ## we've vendored openssl via Cargo.toml anyway, so this part is no longer used...
+                        # dnf install -y openssl-devel
+                        # export OPENSSL_INCLUDE_DIR=$(pkg-config --variable=includedir openssl)
+                        # export OPENSSL_LIB_DIR=$(pkg-config --variable=libdir openssl)
+                        # export OPENSSL_DIR="$OPENSSL_LIB_DIR/ssl"
+                      elif [ "${{ matrix.platform.target }}" = "aarch64" ]; then
+                        # cross-compiling on Ubuntu 22.04
+                        ## We're vendoring openssl because libssl-dev:aarch64 is not available!
+                        apt-get update
+                        apt-get install -y build-essential perl curl clang liblzma-dev pkg-config \
+                          gcc-aarch64-linux-gnu g++-aarch64-linux-gnu libc6-dev-arm64-cross crossbuild-essential-arm64
+                        # export OPENSSL_LIB_DIR=/usr/lib/aarch64-linux-gnu
+                        # export OPENSSL_INCLUDE_DIR=/usr/include/aarch64-linux-gnu
+                        # export OPENSSL_DIR=/usr/lib/aarch64-linux-gnu
+                        # export OPENSSL_NO_VENDOR=1
+                      fi
+                      # export OPENSSL_NO_VENDOR=1
+                      # if [ -z "$OPENSSL_LIB_DIR" ] || [ -z "$OPENSSL_INCLUDE_DIR" ]; then
+                      #     echo "OpenSSL development files are not installed or pkg-config is not configured correctly."
+                      #     exit 1
+                      # fi
+                      # env | grep SSL  # for debugging when rust crate fails to find headers
+            - name: Upload wheels
+              uses: actions/upload-artifact@v4
+              with:
+                  name: wheels-linux-${{ matrix.platform.target }}
+                  path: dist
 
-  linux:
-    runs-on: ${{ matrix.platform.runner }}
-    strategy:
-      matrix:
-        platform:
-          - runner: ubuntu-22.04
-            target: x86_64
-          - runner: ubuntu-22.04 
-            target: aarch64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.x
-      - name: Build wheels
-        uses: PyO3/maturin-action@v1
-        with:
-          target: ${{ matrix.platform.target }}
-          args: --release --out dist --find-interpreter
-          # sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
-          manylinux: 2_28
-          before-script-linux: |
-            set -ex
-            cat /etc/*release*
-            if [ "${{ matrix.platform.target }}" = "x86_64" ]; then
-              # maturin-action's manylinux switches to AlmaLinux 8
-              dnf install -y epel-release && dnf update -y
-              dnf install -y gcc gcc-c++ make perl curl clang xz-devel pkgconfig
-              ## we've vendored openssl via Cargo.toml anyway, so this part is no longer used...
-              # dnf install -y openssl-devel
-              # export OPENSSL_INCLUDE_DIR=$(pkg-config --variable=includedir openssl)
-              # export OPENSSL_LIB_DIR=$(pkg-config --variable=libdir openssl)
-              # export OPENSSL_DIR="$OPENSSL_LIB_DIR/ssl"
-            elif [ "${{ matrix.platform.target }}" = "aarch64" ]; then
-              # cross-compiling on Ubuntu 22.04
-              ## We're vendoring openssl because libssl-dev:aarch64 is not available!
-              apt-get update
-              apt-get install -y build-essential perl curl clang liblzma-dev pkg-config \
-                gcc-aarch64-linux-gnu g++-aarch64-linux-gnu libc6-dev-arm64-cross crossbuild-essential-arm64
-              # export OPENSSL_LIB_DIR=/usr/lib/aarch64-linux-gnu
-              # export OPENSSL_INCLUDE_DIR=/usr/include/aarch64-linux-gnu
-              # export OPENSSL_DIR=/usr/lib/aarch64-linux-gnu
-              # export OPENSSL_NO_VENDOR=1
-            fi
-            # export OPENSSL_NO_VENDOR=1
-            # if [ -z "$OPENSSL_LIB_DIR" ] || [ -z "$OPENSSL_INCLUDE_DIR" ]; then
-            #     echo "OpenSSL development files are not installed or pkg-config is not configured correctly."
-            #     exit 1
-            # fi
-            # env | grep SSL  # for debugging when rust crate fails to find headers
-      - name: Upload wheels
-        uses: actions/upload-artifact@v4
-        with:
-          name: wheels-linux-${{ matrix.platform.target }}
-          path: dist
+    musllinux:
+        runs-on: ${{ matrix.platform.runner }}
+        strategy:
+            matrix:
+                platform:
+                    - runner: ubuntu-22.04
+                      target: x86_64
+                    - runner: ubuntu-22.04
+                      target: aarch64
+        steps:
+            - uses: actions/checkout@v7
+            - uses: actions/setup-python@v5
+              with:
+                  python-version: 3.x
+            - name: Build wheels
+              uses: PyO3/maturin-action@v1
+              with:
+                  target: ${{ matrix.platform.target }}
+                  args: --release --out dist --find-interpreter
+                  # sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+                  manylinux: musllinux_1_2
+                  before-script-linux: |
+                      apt-get update
+                      apt-get install -y musl-tools musl-dev
+                      if [ "${{ matrix.platform.target }}" = "aarch64" ]; then
+                        apt-get install -y gcc-aarch64-linux-gnu g++-aarch64-linux-gnu
+                      fi
+            - name: Upload wheels
+              uses: actions/upload-artifact@v4
+              with:
+                  name: wheels-musllinux-${{ matrix.platform.target }}
+                  path: dist
 
-  musllinux:
-    runs-on: ${{ matrix.platform.runner }}
-    strategy:
-      matrix:
-        platform:
-          - runner: ubuntu-22.04
-            target: x86_64
-          - runner: ubuntu-22.04
-            target: aarch64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.x
-      - name: Build wheels
-        uses: PyO3/maturin-action@v1
-        with:
-          target: ${{ matrix.platform.target }}
-          args: --release --out dist --find-interpreter
-          # sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
-          manylinux: musllinux_1_2
-          before-script-linux: |
-            apt-get update
-            apt-get install -y musl-tools musl-dev
-            if [ "${{ matrix.platform.target }}" = "aarch64" ]; then
-              apt-get install -y gcc-aarch64-linux-gnu g++-aarch64-linux-gnu
-            fi
-      - name: Upload wheels
-        uses: actions/upload-artifact@v4
-        with:
-          name: wheels-musllinux-${{ matrix.platform.target }}
-          path: dist
+    # windows:
+    #   runs-on: ${{ matrix.platform.runner }}
+    #   strategy:
+    #     matrix:
+    #       platform:
+    #         - runner: windows-latest
+    #           target: x64
+    #         - runner: windows-latest
+    #           target: x86
+    #   steps:
+    #     - uses: actions/checkout@v4
+    #     - uses: actions/setup-python@v5
+    #       with:
+    #         python-version: 3.x
+    #         architecture: ${{ matrix.platform.target }}
+    #     - name: Install And Configure Dependencies
+    #       env:
+    #         VCPKG_DEFAULT_TRIPLET: ${{ matrix.platform.target }}-windows
+    #         OPENSSL_DIR: ${{ github.workspace }}/vcpkg/installed/${{ matrix.platform.target }}-windows
+    #         OPENSSL_ROOT: ${{ github.workspace }}/vcpkg/installed/${{ matrix.platform.target }}-windows
+    #         LZMA_ROOT: ${{ github.workspace }}/vcpkg/installed/${{ matrix.platform.target }}-windows
+    #       run: |
+    #         vcpkg install openssl liblzma
+    #     - name: Build wheels
+    #       uses: PyO3/maturin-action@v1
+    #       with:
+    #         target: ${{ matrix.platform.target }}
+    #         args: --release --out dist --find-interpreter
+    #         # sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+    #     - name: Upload wheels
+    #       uses: actions/upload-artifact@v4
+    #       with:
+    #         name: wheels-windows-${{ matrix.platform.target }}
+    #         path: dist
 
-  # windows:
-  #   runs-on: ${{ matrix.platform.runner }}
-  #   strategy:
-  #     matrix:
-  #       platform:
-  #         - runner: windows-latest
-  #           target: x64
-  #         - runner: windows-latest
-  #           target: x86
-  #   steps:
-  #     - uses: actions/checkout@v4
-  #     - uses: actions/setup-python@v5
-  #       with:
-  #         python-version: 3.x
-  #         architecture: ${{ matrix.platform.target }}
-  #     - name: Install And Configure Dependencies
-  #       env:
-  #         VCPKG_DEFAULT_TRIPLET: ${{ matrix.platform.target }}-windows
-  #         OPENSSL_DIR: ${{ github.workspace }}/vcpkg/installed/${{ matrix.platform.target }}-windows
-  #         OPENSSL_ROOT: ${{ github.workspace }}/vcpkg/installed/${{ matrix.platform.target }}-windows
-  #         LZMA_ROOT: ${{ github.workspace }}/vcpkg/installed/${{ matrix.platform.target }}-windows
-  #       run: |
-  #         vcpkg install openssl liblzma
-  #     - name: Build wheels
-  #       uses: PyO3/maturin-action@v1
-  #       with:
-  #         target: ${{ matrix.platform.target }}
-  #         args: --release --out dist --find-interpreter
-  #         # sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
-  #     - name: Upload wheels
-  #       uses: actions/upload-artifact@v4
-  #       with:
-  #         name: wheels-windows-${{ matrix.platform.target }}
-  #         path: dist
+    macos:
+        runs-on: ${{ matrix.platform.runner }}
+        strategy:
+            matrix:
+                platform:
+                    - runner: macos-latest
+                      target: x86_64
+                    - runner: macos-latest
+                      target: aarch64
+        steps:
+            - uses: actions/checkout@v7
+            - uses: actions/setup-python@v5
+              with:
+                  python-version: 3.x
+            - name: Build wheels
+              uses: PyO3/maturin-action@v1
+              with:
+                  target: ${{ matrix.platform.target }}
+                  args: --release --out dist --find-interpreter
+                  # sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+            - name: Upload wheels
+              uses: actions/upload-artifact@v4
+              with:
+                  name: wheels-macos-${{ matrix.platform.target }}
+                  path: dist
 
-  macos:
-    runs-on: ${{ matrix.platform.runner }}
-    strategy:
-      matrix:
-        platform:
-          - runner: macos-13
-            target: x86_64
-          - runner: macos-14
-            target: aarch64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.x
-      - name: Build wheels
-        uses: PyO3/maturin-action@v1
-        with:
-          target: ${{ matrix.platform.target }}
-          args: --release --out dist --find-interpreter
-          # sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
-      - name: Upload wheels
-        uses: actions/upload-artifact@v4
-        with:
-          name: wheels-macos-${{ matrix.platform.target }}
-          path: dist
+    sdist:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v7
+            - name: Build sdist
+              uses: PyO3/maturin-action@v1
+              with:
+                  command: sdist
+                  args: --out dist
+                  # sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+            - name: Upload sdist
+              uses: actions/upload-artifact@v4
+              with:
+                  name: wheels-sdist
+                  path: dist
 
-  sdist:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Build sdist
-        uses: PyO3/maturin-action@v1
-        with:
-          command: sdist
-          args: --out dist
-          # sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
-      - name: Upload sdist
-        uses: actions/upload-artifact@v4
-        with:
-          name: wheels-sdist
-          path: dist
-
-  release:
-    name: Release
-    runs-on: ubuntu-latest
-    if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
-    needs: [linux, macos, sdist]
-    permissions:
-      id-token: write
-      contents: write
-      attestations: write
-    steps:
-      - uses: actions/download-artifact@v4
-      - name: Generate artifact attestation
-        uses: actions/attest-build-provenance@v1
-        with:
-          subject-path: 'wheels-*/*'
-      - name: Publish to PyPI
-        if: ${{ startsWith(github.ref, 'refs/tags/') }}
-        uses: PyO3/maturin-action@v1
-        env:
-          MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
-        with:
-          command: upload
-          args: --non-interactive --skip-existing wheels-*/*
+    release:
+        name: Release
+        runs-on: ubuntu-latest
+        if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
+        needs: [linux, macos, sdist]
+        permissions:
+            id-token: write
+            contents: write
+            attestations: write
+        steps:
+            - uses: actions/download-artifact@v4
+            - name: Generate artifact attestation
+              uses: actions/attest-build-provenance@v1
+              with:
+                  subject-path: "wheels-*/*"
+            - name: Publish to PyPI
+              if: ${{ startsWith(github.ref, 'refs/tags/') }}
+              uses: PyO3/maturin-action@v1
+              env:
+                  MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
+              with:
+                  command: upload
+                  args: --non-interactive --skip-existing wheels-*/*
diff --git a/galaxy/wrapper/test-data/bamCompare_result2.bw b/galaxy/wrapper/test-data/bamCompare_result2.bw
index 75b87e5000..a25d50888e 100644
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diff --git a/galaxy/wrapper/test-data/bamCoverage_result1.bw b/galaxy/wrapper/test-data/bamCoverage_result1.bw
index 695105d378..11273f5076 100644
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diff --git a/galaxy/wrapper/test-data/bamCoverage_result2.bw b/galaxy/wrapper/test-data/bamCoverage_result2.bw
index 846ed84a57..a0e7e9f7ce 100644
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diff --git a/galaxy/wrapper/test-data/bamCoverage_result6.bw b/galaxy/wrapper/test-data/bamCoverage_result6.bw
index 969d8052a5..e539b01669 100644
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diff --git a/galaxy/wrapper/test-data/bamPEFragmentSize_histogram_result1.png b/galaxy/wrapper/test-data/bamPEFragmentSize_histogram_result1.png
index 25ae59a929..af9abe4216 100644
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diff --git a/galaxy/wrapper/test-data/plotCorrelation_result1.png b/galaxy/wrapper/test-data/plotCorrelation_result1.png
index c2373582bb..535715ea09 100644
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diff --git a/galaxy/wrapper/test-data/plotCoverage_result1.png b/galaxy/wrapper/test-data/plotCoverage_result1.png
index e22727ca52..6669cb87ae 100644
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diff --git a/galaxy/wrapper/test-data/plotEnrichment_output.png b/galaxy/wrapper/test-data/plotEnrichment_output.png
index 6302d95453..94d402bc3c 100644
Binary files a/galaxy/wrapper/test-data/plotEnrichment_output.png and b/galaxy/wrapper/test-data/plotEnrichment_output.png differ
diff --git a/galaxy/wrapper/test-data/profiler_result2.png b/galaxy/wrapper/test-data/profiler_result2.png
index 2e67acf103..445da93b84 100644
Binary files a/galaxy/wrapper/test-data/profiler_result2.png and b/galaxy/wrapper/test-data/profiler_result2.png differ
diff --git a/pydeeptools/deeptools/bamPEFragmentSize.py b/pydeeptools/deeptools/bamPEFragmentSize.py
index 9569abbe66..362b118555 100755
--- a/pydeeptools/deeptools/bamPEFragmentSize.py
+++ b/pydeeptools/deeptools/bamPEFragmentSize.py
@@ -391,7 +391,6 @@ def main(args=None):
             parser.print_help()
             return
     args = parser.parse_args(args)
-    print(args)
     fraglengths = {}
     readlengths = {}
     of = None