diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 38c7b0d361..f068a786da 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -7,7 +7,7 @@ on:
     types: [run-all-tool-tests-command]
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_25.1
+  GALAXY_BRANCH: release_26.0
   MAX_CHUNKS: 40
 jobs:
   setup:
@@ -105,7 +105,7 @@ jobs:
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
         additional-planemo-options: --biocontainers --skip version_bumped
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       if: ${{ failure() }}
       with:
         name: 'Tool linting output'
@@ -145,7 +145,7 @@ jobs:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Get number of CPU cores
-      uses: SimenB/github-actions-cpu-cores@v2
+      uses: SimenB/github-actions-cpu-cores@v3
       id: cpu-cores
     - name: Clean dotnet folder for space
       run: rm -Rf /usr/share/dotnet
@@ -162,7 +162,7 @@ jobs:
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
         # Limit each test to 15 minutes
         test_timeout: 900
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -181,7 +181,7 @@ jobs:
     # This job runs on Linux
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v7
+    - uses: actions/download-artifact@v8
       with:
         path: artifacts
     - uses: actions/setup-python@v6
@@ -200,7 +200,7 @@ jobs:
         mode: combine
         html-report: true
         markdown-report: true
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       with:
         name: 'All tool test results'
         path: upload
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index c323c233ff..1ac7fb0397 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -17,7 +17,7 @@ on:
       - '*'
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_25.1
+  GALAXY_BRANCH: release_26.0
   MAX_CHUNKS: 4
   MAX_FILE_SIZE: 1M
 concurrency:
@@ -167,7 +167,7 @@ jobs:
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
         additional-planemo-options: ${{ env.EXTRA_SKIP }}
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       if: ${{ failure() }}
       with:
         name: 'Tool linting output'
@@ -200,7 +200,7 @@ jobs:
       run: pip install flake8 flake8-import-order
     - name: Flake8
       run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --output-file pylint_report.txt --tee
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       if: ${{ failure() }}
       with:
         name: 'Python linting output'
@@ -239,7 +239,7 @@ jobs:
         echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' -n 1 ./.github/styler.R --dry off
         git status
         git diff --exit-code | tee rlint_report.txt
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       if: ${{ failure() }}
       with:
         name: 'R linting output'
@@ -267,7 +267,7 @@ jobs:
           cat file_size_report.txt
           exit 1
         fi
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       if: ${{ failure() }}
       with:
         name: 'File size report'
@@ -314,7 +314,7 @@ jobs:
         path: ~/.planemo
         key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Get number of CPU cores
-      uses: SimenB/github-actions-cpu-cores@v2
+      uses: SimenB/github-actions-cpu-cores@v3
       id: cpu-cores
     - name: Clean dotnet folder for space
       run: rm -Rf /usr/share/dotnet
@@ -330,8 +330,8 @@ jobs:
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
         # Limit each test to 15 minutes
-        test_timeout: 1800
-    - uses: actions/upload-artifact@v6
+        test_timeout: 900
+    - uses: actions/upload-artifact@v7
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -350,7 +350,7 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/download-artifact@v7
+    - uses: actions/download-artifact@v8
       with:
         path: artifacts
     - uses: actions/setup-python@v6
@@ -369,7 +369,7 @@ jobs:
         mode: combine
         html-report: true
         markdown-report: true
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       with:
         name: 'All tool test results'
         path: upload
@@ -393,7 +393,6 @@ jobs:
     needs: [setup, lint, combine_outputs]
     if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'bgruening' }}
     runs-on: ubuntu-latest
-    environment: toolshed-deployment
     strategy:
       matrix:
         python-version: ['3.11']
@@ -429,9 +428,8 @@ jobs:
   deploy-report:
     name: Report deploy status
     needs: [deploy]
-    if: ${{ always() && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) }}
+    if: ${{ always() && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'bgruening' }}
     runs-on: ubuntu-latest
-    environment: toolshed-deployment
     steps:
     # report to the PR if deployment failed
     - name: Get PR object
diff --git a/.github/workflows/pr_without_tool_change.yaml b/.github/workflows/pr_without_tool_change.yaml
index edff41005f..b2e2a5b2bb 100644
--- a/.github/workflows/pr_without_tool_change.yaml
+++ b/.github/workflows/pr_without_tool_change.yaml
@@ -4,9 +4,13 @@ name: Fallback
 # see https://docs.github.com/en/repositories/configuring-branches-and-merges-in-your-repository/defining-the-mergeability-of-pull-requests/troubleshooting-required-status-checks#handling-skipped-but-required-checks
 on:
   pull_request:
+    paths:
+    - 'deprecated/**'
+    - 'docs/**'
+    - '.github/**'
+    - '*'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
 jobs:
   determine-success:
     name: Check workflow success
diff --git a/tools/3dtrees_forestmamba/.shed.yml b/tools/3dtrees_forestmamba/.shed.yml
new file mode 100644
index 0000000000..285c3baab7
--- /dev/null
+++ b/tools/3dtrees_forestmamba/.shed.yml
@@ -0,0 +1,11 @@
+name: 3dtrees_forestmamba
+owner: bgruening
+description: Forest instance segmentation with ForestMamba.
+homepage_url: https://github.com/3dTrees-earth/3Dtrees_ForestMamba
+long_description: |
+  Performs forest instance and semantic segmentation on LAZ/LAS point clouds using the
+  ForestMamba model.
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/3dtrees_forestmamba
+type: unrestricted
+categories:
+- "Geo Science"
diff --git a/tools/3dtrees_forestmamba/forestmamba.xml b/tools/3dtrees_forestmamba/forestmamba.xml
new file mode 100644
index 0000000000..7acf570a9c
--- /dev/null
+++ b/tools/3dtrees_forestmamba/forestmamba.xml
@@ -0,0 +1,101 @@
+<tool id="3dtrees_forestmamba" name="3Dtrees: ForestMamba" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
+    <description>
+        Forest instance and semantic segmentation of point clouds using the ForestMamba model.
+    </description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <container type="docker">ghcr.io/3dtrees-earth/3dtrees_forestmamba:@TOOL_VERSION@</container>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p output_dir work_dir &&
+        ln -s '$input' 'input.${input.ext}' &&
+        python -u /workspace/src/run.py
+            --dataset-path 'input.${input.ext}'
+            --output-dir output_dir
+            --work-dir work_dir
+            --repo-dir /workspace
+            --checkpoint /workspace/work_dirs/forestmamba_chm_radius16_qp300_2many_v6/v6_epoch_1500_fix.pth
+            --config-base /workspace/configs/ForAINetv2/forestmamba_chm_radius16_qp300_2many_v6.py
+            --preprocess-workers \${GALAXY_SLOTS:-1}
+            --chunk-size '$chunk_size'
+            --semantic-dim '$semantic_dim'
+            --instance-dim '$instance_dim'
+            --score-dim '$score_dim'
+            --bluepoint-iterations '$bluepoint_iterations'
+            #if $bluepoint_score_threshold:
+                --bluepoint-score-threshold '$bluepoint_score_threshold'
+            #end if
+            --bluepoint-second-pass-threshold '$bluepoint_second_pass_threshold'
+            --spatial-match-tolerance '$spatial_match_tolerance'
+    ]]></command>
+    <environment_variables>
+        <environment_variable name="NUMBA_CACHE_DIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
+        <environment_variable name="WANDB_MODE">disabled</environment_variable>
+    </environment_variables>
+    <inputs>
+        <param name="input" type="data" format="laz,las" label="Input LAZ/LAS point cloud" help="Point cloud to segment with ForestMamba."/>
+        <param argument="--bluepoint-iterations" type="integer" min="0" max="5" value="0" label="Bluepoint iterations" help="0 keeps standard one-pass inference. 2 enables the dense-forest first/second bluepoint pass."/>
+        <param argument="--bluepoint-score-threshold" type="float" min="0" max="1" value="" optional="true" label="Bluepoint score threshold" help="Optional model score_th override for bluepoint rounds."/>
+        <param argument="--bluepoint-second-pass-threshold" type="float" min="0" max="1" value="0.01" label="Second pass threshold" help="Run the second bluepoint pass only when more than this fraction of first-pass points are non-ground with raw instance_pred == -1. Default 0.01 = 1%."/>
+        <param argument="--spatial-match-tolerance" type="float" min="0" value="0.01" label="Spatial match tolerance" help="Maximum coordinate distance used when matching bluepoint predictions back to the input points."/>
+        <param argument="--chunk-size" type="integer" min="1" value="1000000" label="LAZ write chunk size" help="Number of points processed per streamed LAZ read/write chunk."/>
+        <param argument="--semantic-dim" type="text" value="PredSemantic_FM" label="Semantic prediction dimension" help="Output extra dimension name for ForestMamba semantic predictions.">
+            <validator type="regex" message="Only letters, numbers, and underscores are allowed">^[A-Za-z0-9_]+$</validator>
+        </param>
+        <param argument="--instance-dim" type="text" value="PredInstance_FM" label="Instance prediction dimension" help="Output extra dimension name for ForestMamba instance predictions.">
+            <validator type="regex" message="Only letters, numbers, and underscores are allowed">^[A-Za-z0-9_]+$</validator>
+        </param>
+        <param argument="--score-dim" type="text" value="PredScore_FM" label="Score prediction dimension" help="Output extra dimension name for ForestMamba confidence scores.">
+            <validator type="regex" message="Only letters, numbers, and underscores are allowed">^[A-Za-z0-9_]+$</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="laz" from_work_dir="output_dir/input_forestmamba.laz" label="${tool.name} on ${on_string}: Segmented point cloud"/>
+        <data name="summary" format="json" from_work_dir="output_dir/summary.json" label="${tool.name}: summary"/>
+    </outputs>
+    <tests>
+        <!-- GitHub CI has no GPU, so this test is expected to fail there. -->
+        <test expect_failure="true">
+            <param name="input" value="mikro" ftype="laz"/>
+            <assert_stderr>
+                <has_text text="RuntimeError: No CUDA GPUs are available"/>
+            </assert_stderr>
+        </test>
+    </tests>
+    <help format="markdown">
+## What it does
+
+This tool runs ForestMamba on one LAS/LAZ point cloud and writes a segmented
+LAZ output with ForestMamba prediction dimensions.
+
+## Parameters
+
+- **Input LAZ/LAS point cloud**: the point cloud to segment.
+- **Bluepoint iterations**: `0` runs the normal one-pass prediction. `2` enables
+  the dense-forest bluepoint flow: first pass, then an optional second pass on
+  points that remained unassigned.
+- **Bluepoint score threshold**: optional model confidence threshold override
+  for bluepoint runs. Leave empty to use the model/config default.
+- **Second pass threshold**: fraction of first-pass non-ground points with raw
+  `instance_pred == -1` required before the second bluepoint pass runs. The
+  default `0.01` means more than 1%.
+
+## Outputs
+
+- Segmented LAZ with `PredSemantic_FM`, `PredInstance_FM`, and `PredScore_FM`
+  by default.
+- JSON summary of the wrapper run.
+
+Valid ForestMamba instance IDs are preserved. Raw negative instance IDs are
+written as `0` in the final LAZ.
+    </help>
+    <creator>
+        <organization name="3Dtrees-Team, University of Freiburg" url="https://github.com/3dTrees-earth"/>
+    </creator>
+    <citations>
+        <citation type="doi">10.48550/arXiv.2606.01549</citation>
+    </citations>
+</tool>
diff --git a/tools/3dtrees_forestmamba/test-data/mikro b/tools/3dtrees_forestmamba/test-data/mikro
new file mode 100644
index 0000000000..37743aacaf
Binary files /dev/null and b/tools/3dtrees_forestmamba/test-data/mikro differ
diff --git a/tools/3dtrees_potree/3dtrees_potree.xml b/tools/3dtrees_potree/3dtrees_potree.xml
index b86d835d83..baf1c4ab7a 100644
--- a/tools/3dtrees_potree/3dtrees_potree.xml
+++ b/tools/3dtrees_potree/3dtrees_potree.xml
@@ -1,7 +1,7 @@
 <tool id="3dtrees_potree" name="3Dtrees: Potree Converter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
     <description>Convert LAS/LAZ point clouds to Potree octree format for web visualization</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.1.0</token>
+        <token name="@TOOL_VERSION@">1.2.0</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
@@ -33,7 +33,7 @@
             --special-coloring-palette '$special_coloring.palette'
             --special-coloring-n-colors '$special_coloring.n_colors'
             --special-coloring-n-neighbors '$special_coloring.n_neighbors'
-            --special-coloring-instance-attribute '$special_coloring.instance_attribute'
+            --special-coloring-instance-attributes '$special_coloring.instance_attributes'
             --special-coloring-ground-id '$special_coloring.ground_id'
             --special-coloring-ground-color '$special_coloring.ground_color'
             $special_coloring.sidecar_json
@@ -78,7 +78,7 @@
         <param argument="--no-chunking" type="boolean" truevalue="--no-chunking" falsevalue="" checked="false" label="No Chunking" help="Disable chunking phase" />
         <param argument="--no-indexing" type="boolean" truevalue="--no-indexing" falsevalue="" checked="false" label="No Indexing" help="Disable indexing phase" />
         <conditional name="special_coloring">
-            <param name="enabled" argument="--special-coloring" type="select" label="Special Coloring" help="Add a coloring_id extra dimension using neighbor-aware instance colors.">
+            <param name="enabled" argument="--special-coloring" type="select" label="Special Coloring" help="Add neighbor-aware coloring dimensions for one or more instance attributes.">
                 <option value="false" selected="true">Disabled</option>
                 <option value="true">Enabled</option>
             </param>
@@ -88,8 +88,8 @@
                 </param>
                 <param name="n_colors" argument="--special-coloring-n-colors" type="integer" value="10" min="1" label="Special Coloring Color Count" help="Number of non-ground coloring IDs to generate" />
                 <param name="n_neighbors" argument="--special-coloring-n-neighbors" type="integer" value="10" min="1" label="Special Coloring Neighbors" help="Nearest instance centroids considered when avoiding nearby color collisions" />
-                <param name="instance_attribute" argument="--special-coloring-instance-attribute" type="text" value="PredInstance" label="Special Coloring Instance Attribute" help="Point attribute containing instance IDs">
-                    <validator type="regex" message="Only letters, numbers, and underscores are allowed">^[A-Za-z0-9_]+$</validator>
+                <param name="instance_attributes" argument="--special-coloring-instance-attributes" type="text" value="PredInstance_SAT,PredInstance_FoMa" label="Special Coloring Instance Attributes" help="Comma-separated point attributes containing instance IDs. PredInstance_FoMa also accepts inputs named PredInstance_FM.">
+                    <validator type="regex" message="Only letters, numbers, underscores, and commas are allowed">^[A-Za-z0-9_,]+$</validator>
                 </param>
                 <param name="ground_id" argument="--special-coloring-ground-id" type="integer" value="0" label="Special Coloring Ground Instance ID" help="Instance ID treated as ground/background" />
                 <param name="ground_color" argument="--special-coloring-ground-color" type="text" value="#808080" label="Special Coloring Ground Color" help="Ground/background color as #RRGGBB">
@@ -112,7 +112,7 @@
         <!-- Collection output - discovers files in output directory -->
         <collection name="potree_output" type="list" label="Potree Output">
             <discover_datasets pattern="(?P&lt;designation&gt;metadata)\.json$" directory="output" format="json" recurse="true"/>
-            <discover_datasets pattern="(?P&lt;designation&gt;special_coloring_mapping)\.json$" directory="output" format="json"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;special_coloring_mapping[^/]*?)\.json$" directory="output" format="json"/>
             <discover_datasets pattern="(?P&lt;designation&gt;hierarchy)\.bin$" directory="output" format="binary" recurse="true"/>
             <discover_datasets pattern="(?P&lt;designation&gt;octree)\.bin$" directory="output" format="binary" recurse="true"/>
             <discover_datasets pattern="(?P&lt;designation&gt;log)\.txt$" directory="output" format="txt" recurse="true"/>
@@ -153,21 +153,40 @@
             </output_collection>
         </test>
         <test expect_num_outputs="1">
-            <param name="input" value="mikro_segmented.laz" ftype="laz"/>
+            <param name="input" value="mikro_multi_segmented.laz" ftype="laz"/>
             <param name="special_coloring|enabled" value="true"/>
             <param name="special_coloring|palette" value="#ff0000,#00ff00"/>
             <param name="special_coloring|sidecar_json" value="true"/>
-            <output_collection name="potree_output" type="list" count="5">
+            <output_collection name="potree_output" type="list" count="6">
                 <element name="metadata" ftype="json">
                     <assert_contents>
                         <has_json_property_with_value property="points" value="12917" />
+                        <has_text text="PredInstance_SAT" />
+                        <has_text text="PredInstance_FM" />
+                        <has_text text="species_id_sat" />
+                        <has_text text="species_id_foma" />
+                        <has_text text="coloring_id_sat" />
+                        <has_text text="coloring_foma" />
                     </assert_contents>
                 </element>
-                <element name="special_coloring_mapping" ftype="json">
+                <element name="special_coloring_mapping_coloring_foma" ftype="json">
                     <assert_contents>
                         <has_json_property_with_value property="version" value="1" />
-                        <has_json_property_with_value property="color_attribute" value='"coloring_id"' />
-                        <has_json_property_with_value property="instance_attribute" value='"PredInstance"' />
+                        <has_json_property_with_value property="color_attribute" value='"coloring_foma"' />
+                        <has_json_property_with_value property="instance_attribute" value='"PredInstance_FM"' />
+                        <has_json_property_with_value property="ground_instance_id" value="0" />
+                        <has_json_property_with_value property="ground_coloring_id" value="0" />
+                        <has_json_property_with_value property="ground_color" value='"#808080"' />
+                        <has_json_property_with_value property="palette" value='"#ff0000,#00ff00"' />
+                        <has_json_property_with_value property="n_colors" value="10" />
+                        <has_json_property_with_value property="n_neighbors" value="10" />
+                    </assert_contents>
+                </element>
+                <element name="special_coloring_mapping_coloring_id_sat" ftype="json">
+                    <assert_contents>
+                        <has_json_property_with_value property="version" value="1" />
+                        <has_json_property_with_value property="color_attribute" value='"coloring_id_sat"' />
+                        <has_json_property_with_value property="instance_attribute" value='"PredInstance_SAT"' />
                         <has_json_property_with_value property="ground_instance_id" value="0" />
                         <has_json_property_with_value property="ground_coloring_id" value="0" />
                         <has_json_property_with_value property="ground_color" value='"#808080"' />
@@ -196,7 +215,7 @@ This tool converts LAS/LAZ point cloud files to the Potree octree format for eff
 3. **Flexible sampling methods**: Choose between Poisson, Poisson Average, or Random sampling
 4. **Web-ready output**: Generates files that can be directly served for Potree viewer visualization
 5. **Optional web page generation**: Can generate a ready-to-use HTML viewer page
-6. **Special instance coloring**: Optionally adds a display-only ``coloring_id`` attribute from ``PredInstance`` while preserving original RGB
+6. **Special instance coloring**: Optionally adds display-only coloring attributes from one or more instance attributes while preserving original RGB
 
 -----
 
@@ -211,14 +230,14 @@ This tool converts LAS/LAZ point cloud files to the Potree octree format for eff
 - **Keep Chunks**: Preserve temporary chunk files after conversion
 - **No Chunking**: Disable the chunking phase
 - **No Indexing**: Disable the indexing phase
-- **Special Coloring**: Add a ``coloring_id`` point attribute for neighbor-aware instance colors.
+- **Special Coloring**: Add point attributes for neighbor-aware instance colors.
 - **Special Coloring Palette**: Built-in palette name (sky, sea, cozy, fairy, winter, rainbow, pastel, candy, boring) or custom comma-separated ``#RRGGBB`` colors
 - **Special Coloring Color Count**: Number of non-ground coloring IDs
 - **Special Coloring Neighbors**: Number of nearest instance centroids considered when avoiding nearby color reuse
-- **Special Coloring Instance Attribute**: Point attribute containing instance IDs, default ``PredInstance``
+- **Special Coloring Instance Attributes**: Comma-separated point attributes containing instance IDs, default ``PredInstance_SAT,PredInstance_FoMa``
 - **Special Coloring Ground Instance ID**: Instance ID treated as ground/background, default ``0``. Negative instance IDs are also treated as background.
 - **Special Coloring Ground Color**: Ground/background color as ``#RRGGBB``
-- **Write Special Coloring JSON**: Write ``special_coloring_mapping.json`` and patch generated Potree HTML viewers to use the sidecar colors.
+- **Write Special Coloring JSON**: Write ``special_coloring_mapping*.json`` files and patch generated Potree HTML viewers to use the first sidecar color mapping.
 - **Generate Page**: Create a web viewer page with the specified name
 - **Viewer Title**: Optional title shown in the generated viewer page
 
@@ -232,7 +251,7 @@ The tool produces a collection containing:
 - **hierarchy** (binary): Binary file containing the octree hierarchy
 - **octree** (binary): Binary file containing the point data
 - **log** (text): Conversion log file
-- **special_coloring_mapping** (JSON, optional): Mapping from ``coloring_id`` to colors and from ``PredInstance`` to ``coloring_id`` when Write Special Coloring JSON is enabled
+- **special_coloring_mapping*** (JSON, optional): Mapping from coloring IDs to colors and from each instance attribute to coloring IDs when Write Special Coloring JSON is enabled
 
 When **Generate Page** is specified (e.g., "viewer"):
 
diff --git a/tools/3dtrees_potree/test-data/mikro_multi_segmented.laz b/tools/3dtrees_potree/test-data/mikro_multi_segmented.laz
new file mode 100644
index 0000000000..712043643b
Binary files /dev/null and b/tools/3dtrees_potree/test-data/mikro_multi_segmented.laz differ
diff --git a/tools/instagraal/instagraal.xml b/tools/instagraal/instagraal.xml
index 7d37b3dcce..bf474fcaf9 100644
--- a/tools/instagraal/instagraal.xml
+++ b/tools/instagraal/instagraal.xml
@@ -1,15 +1,16 @@
-<tool id="instagraal" name="instaGRAAL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
+<tool id="instagraal" name="instaGRAAL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Large genome reassembly based on Hi-C data</description>
-    <xrefs>
-        <xref type="bio.tools">instagraal</xref>
-    </xrefs>
     <macros>
-        <token name="@TOOL_VERSION@">0.1.6</token>
+        <token name="@TOOL_VERSION@">0.2.0</token>
         <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">25.0</token>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">instagraal</xref>
+    </xrefs>
     <requirements>
         <!-- use a versioned copy of the upstream container at koszullab/instagraal -->
-        <container type="docker">quay.io/galaxy/instagraal:0.1.6</container>
+        <container type="docker">quay.io/galaxy/instagraal:v@TOOL_VERSION@</container>
         <resource type="cuda_version_min">10.0</resource>
         <resource type="cuda_compute_capability">3.0</resource>
         <resource type="cuda_device_count_min">1</resource>
@@ -42,90 +43,105 @@ ln -s '$info_contigs' hic_folder/info_contigs.txt &&
 instagraal
     ./hic_folder
     $ref_genome
-    ./outputs/
-
+    -o ./outputs/
     --level $level
     --cycles $cycles
     --coverage-std $coverage_std
     --neighborhood $neighborhood
-
-$circular
-$bomb
-$pyramid_only
-$simple
+    $circular
+    $bomb
+    $pyramid_only
+    $simple
+    $save_matrix
 &&
 
 mv ./outputs/*/test_*/genome.fasta ./outputs/genome.fasta &&
-mv ./outputs/*/test_*/info_frags.txt ./outputs/info_frags.txt
+mv ./outputs/*/test_*/info_frags.txt ./outputs/info_frags.txt &&
+
+mkdir -p matrix_previews &&
+( mv ./outputs/*/test_*/matrix_cycle_*.png matrix_previews/ 2>/dev/null || true )
 
 &&
 instagraal-polish
   -m polishing
   -i ./outputs/info_frags.txt
   -f $ref_genome
-  -o ./outputs/curated.fasta
+  -o ./polish_out
   -j $gap_string
-
     ]]>
     </command>
     <inputs>
- 
         <param name="abs_fragments_contacts_weighted" type="data" format="tabular" label="Abs fragments contacts weighted"/>
         <param name="fragments_list" type="data" format="tabular" label="Fragments list"/>
         <param name="info_contigs" type="data" format="tabular" label="info_contigs"/>
-
         <conditional name="ref_source">
             <param type="select" name="source" label="Reference genome source">
                 <option value="history" selected="true">History</option>
                 <option value="builtin">Built-in</option>
             </param>
             <when value="history">
-                <param type="data" format="fasta" name="ref_fasta" label="Reference genome" />
+                <param type="data" format="fasta" name="ref_fasta" label="Reference genome"/>
             </when>
             <when value="builtin">
                 <param type="select" name="ref_fasta_builtin" label="Reference genome">
-                    <options from_data_table="all_fasta" />
+                    <options from_data_table="all_fasta"/>
                 </param>
             </when>
         </conditional>
-
-        <param argument="--level" type="integer" value="4" min="3" max="6" label="Level (resolution) of the contact map"
-            help="Increasing level by one means a threefold smaller resolution but also a threefold faster computation time."/>
-
-        <param argument="--cycles" type="integer" value="30" min="20" max="100" label="Number of iterations to perform for each bin (row/column of the contact map)"
-            help="A high number of cycles has diminishing returns but there is a necessary minimum for assembly convergence."/>
-
-        <param argument="--coverage-std" type="integer" value="1" min="0" max="1" label="Number of standard deviations below the mean"
-            help="Coverage below which fragments should be filtered out prior to binning." />
-
-        <param argument="--neighborhood" type="integer" value="5" min="0" max="100" label="Number of neighbors to sample for potential mutations for each bin" />
-        <param argument="--circular" type="boolean" truevalue="--circular" falsevalue="" label="Indicates genome is circular" />
-        <param argument="--bomb" type="boolean" truevalue="--bomb" falsevalue="" label="Explode the genome prior to scaffolding" />
-        <param argument="--pyramid-only" type="boolean" truevalue="--pyramid-only" falsevalue="" label="Only build multi-resolution contact maps (pyramids) and don't do any scaffolding" />
-        <param argument="--simple" type="boolean" truevalue="--simple" falsevalue="" label="Only perform operations at the edge of the contigs" />
-        <param name="number_of_n" type="integer" value="10" min="1" label="Number of Ns that you want to include during the polishing step" />
-
+        <param argument="--level" type="integer" value="4" min="3" max="6" label="Level (resolution) of the contact map" help="Increasing level by one means a threefold smaller resolution but also a threefold faster computation time."/>
+        <param argument="--cycles" type="integer" value="30" min="20" max="100" label="Number of iterations to perform for each bin (row/column of the contact map)" help="A high number of cycles has diminishing returns but there is a necessary minimum for assembly convergence."/>
+        <param argument="--coverage-std" type="float" value="1.0" min="0" label="Number of standard deviations below the mean" help="Coverage below which fragments should be filtered out prior to binning."/>
+        <param argument="--neighborhood" type="integer" value="5" min="0" max="100" label="Number of neighbors to sample for potential mutations for each bin"/>
+        <param argument="--circular" type="boolean" truevalue="--circular" falsevalue="" label="Indicates genome is circular"/>
+        <param argument="--bomb" type="boolean" truevalue="--bomb" falsevalue="" label="Explode the genome prior to scaffolding"/>
+        <param argument="--pyramid-only" type="boolean" truevalue="--pyramid-only" falsevalue="" label="Only build multi-resolution contact maps (pyramids) and don't do any scaffolding"/>
+        <param argument="--simple" type="boolean" truevalue="--simple" falsevalue="" label="Only perform operations at the edge of the contigs"/>
+        <param argument="--save-matrix" type="boolean" truevalue="--save-matrix" falsevalue="" checked="false" label="Save a contact-map preview (PNG) after each cycle"/>
+        <param name="number_of_n" type="integer" value="10" min="1" label="Number of Ns that you want to include during the polishing step"/>
     </inputs>
     <outputs>
         <data name="genome" format="fasta" from_work_dir="./outputs/genome.fasta" label="${tool.name} on ${on_string}: Genome sequence"/>
         <data name="frags" format="tabular" from_work_dir="./outputs/info_frags.txt" label="${tool.name} on ${on_string}: Fragment information"/>
-        <data name="curated" format="fasta" from_work_dir="./outputs/curated.fasta" label="${tool.name} on ${on_string}: Curated sequences"/>
+        <data name="curated" format="fasta" from_work_dir="./polish_out/polished_genome.fa" label="${tool.name} on ${on_string}: Curated sequences"/>
+        <collection name="matrix_previews" type="list" format="png" label="${tool.name} on ${on_string}: Contact map previews">
+            <discover_datasets pattern="__name_and_ext__" directory="matrix_previews"/>
+            <filter>save_matrix is True</filter>
+        </collection>
     </outputs>
     <tests>
-        <test>
-            <param name="abs_fragments_contacts_weighted" value="abs_fragments_contacts_weighted.tabular" />
-            <param name="fragments_list" value="fragments_list.tabular" />
-            <param name="info_contigs" value="info_contigs.tabular" />
+        <test expect_num_outputs="3">
+            <param name="abs_fragments_contacts_weighted" value="abs_fragments_contacts_weighted.tabular"/>
+            <param name="fragments_list" value="fragments_list.tabular"/>
+            <param name="info_contigs" value="info_contigs.tabular"/>
             <conditional name="ref_source">
                 <param name="source" value="history"/>
-                <param name="ref_fasta" value="fake.fasta" />
+                <param name="ref_fasta" value="fake.fasta"/>
             </conditional>
             <assert_command>
-                <has_text text="NNNNNNNNNN"/> <!--  10 long, the default -->
-                <not_has_text text="NNNNNNNNNNN"/> <!-- too long -->
-                <has_text text="--cycles 30" />
-                <has_text text="instagraal" />
-                <has_text text="instagraal-polish" />
+                <has_text text="NNNNNNNNNN"/>
+                <!--  10 long, the default -->
+                <not_has_text text="NNNNNNNNNNN"/>
+                <!-- too long -->
+                <has_text text="--cycles 30"/>
+                <has_text text="-o ./outputs/"/>
+                <has_text text="instagraal"/>
+                <has_text text="instagraal-polish"/>
+                <has_text text="-o ./polish_out"/>
+                <not_has_text text="--save-matrix"/>
+                <!-- off by default -->
+            </assert_command>
+        </test>
+        <test expect_num_outputs="4">
+            <param name="abs_fragments_contacts_weighted" value="abs_fragments_contacts_weighted.tabular"/>
+            <param name="fragments_list" value="fragments_list.tabular"/>
+            <param name="info_contigs" value="info_contigs.tabular"/>
+            <conditional name="ref_source">
+                <param name="source" value="history"/>
+                <param name="ref_fasta" value="fake.fasta"/>
+            </conditional>
+            <param name="save_matrix" value="true"/>
+            <assert_command>
+                <has_text text="--save-matrix"/>
             </assert_command>
         </test>
     </tests>
@@ -155,6 +171,8 @@ After the scaffolder is done running, whatever path you specified as output will
 * genome.fasta: the scaffolded genome. Scaffolds will be ordered by increasing size in fragments, which roughly (but not always) translates into increasing size in bp.
 * info_frags.txt: a file that contains, for each newly formed scaffold, the original coordinates of every single bin in that scaffold, in the format chromosome, id, orientation, start, end. Each bin has a unique ID that provides a convenient way of tracking consecutive stretches. Orientations are relative to one another, and when "-1" is supplied, it is understood that the reverse complement should be taken.
 
+If *Save a contact-map preview (PNG) after each cycle* is enabled, a collection of per-cycle contact-map preview images (matrix_cycle_N.png) is also produced.
+
 
     ]]>
     </help>
diff --git a/tools/kat/.shed.yml b/tools/kat/.shed.yml
index 05a46ede9d..6a23a97d46 100644
--- a/tools/kat/.shed.yml
+++ b/tools/kat/.shed.yml
@@ -6,7 +6,7 @@ long_description: |
   using k-mer frequency analysis. It includes tools for generating k-mer histicity plots, comparing
   k-mer spectra between datasets, filtering sequences by k-mer content, and analysing GC/coverage
   distributions.
-homepage_url: https://github.com/TGAC/KAT
+homepage_url: https://github.com/EarlhamInst/KAT
 remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/kat
 type: unrestricted
 categories:
diff --git a/tools/kat/kat_comp.xml b/tools/kat/kat_comp.xml
new file mode 100644
index 0000000000..bfd210b4fa
--- /dev/null
+++ b/tools/kat/kat_comp.xml
@@ -0,0 +1,506 @@
+<tool id="kat_comp" name="KAT Comp" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>compares k-mer count hashes</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <stdio>
+        <regex match="corrupted double-linked list" source="stderr" level="warning" description="KAT C++ heap corruption — output files were still produced correctly"/>
+        <exit_code range="2:133" level="fatal" description="Error occurred"/>
+        <exit_code range="135:" level="fatal" description="Error occurred"/>
+        <exit_code range=":-1" level="fatal" description="Error occurred"/>
+    </stdio>
+    <version_command>echo @TOOL_VERSION@</version_command>
+    <command><![CDATA[
+        ## Link dataset 1 files with appropriate extensions
+        #for $i, $f in enumerate($input1.files):
+            @SET_EXT@
+            cp '$f' 'input1_${i}${ext}' &&
+        #end for
+
+        ## Link dataset 2 files with appropriate extensions
+        #for $i, $f in enumerate($input2.files):
+            @SET_EXT@
+            cp '$f' 'input2_${i}${ext}' &&
+        #end for
+
+        ## Link optional dataset 3 files with appropriate extensions
+        #if $input3.use_input3 == 'yes':
+            #for $i, $f in enumerate($input3.files):
+                @SET_EXT@
+                cp '$f' 'input3_${i}${ext}' &&
+            #end for
+        #end if
+
+        kat comp
+            -o kat-comp
+            -t "\${GALAXY_SLOTS:-1}"
+            -x '$dataset_options.d1_scale'
+            -y '$dataset_options.d2_scale'
+            -i '$dataset_options.d1_bins'
+            -j '$dataset_options.d2_bins'
+            #if str($dataset_options.d1_5ptrim).strip():
+                --d1_5ptrim '$dataset_options.d1_5ptrim'
+            #end if
+            #if str($dataset_options.d2_5ptrim).strip():
+                --d2_5ptrim '$dataset_options.d2_5ptrim'
+            #end if
+            $input1.non_canonical_1
+            $input2.non_canonical_2
+            $kmer_options.disable_hash_grow
+            -m '$kmer_options.mer_len'
+            -H '$kmer_options.hash_size_1'
+            -I '$kmer_options.hash_size_2'
+            $output_options.density_plot
+            -p '$output_options.output_type'
+            $output_options.output_hists
+            #if $input3.use_input3 == 'yes':
+                $input3.non_canonical_3
+                -J '$input3.hash_size_3'
+                #if str($input3.d3_5ptrim).strip():
+                    --d3_5ptrim '$input3.d3_5ptrim'
+                #end if
+            #end if
+            #for $i, $f in enumerate($input1.files):
+                @SET_EXT@
+                'input1_${i}${ext}'
+            #end for
+            #for $i, $f in enumerate($input2.files):
+                @SET_EXT@
+                'input2_${i}${ext}'
+            #end for
+            #if $input3.use_input3 == 'yes':
+                #for $i, $f in enumerate($input3.files):
+                    @SET_EXT@
+                    'input3_${i}${ext}'
+                #end for
+            #end if
+    ]]></command>
+    <inputs>
+        <!-- Dataset 1 -->
+        <section name="input1" title="Dataset 1" expanded="true">
+            <param name="files" type="data" format="fasta,fastqsanger,fasta.gz,fastqsanger.gz,jellyfish" multiple="true" label="Dataset 1 files" help="First set of FASTA/FASTQ files (gzip accepted) or a pre-counted Jellyfish hash. For the reads-vs-assembly use case, provide reads here."/>
+            <param argument="--non_canonical_1" type="boolean" truevalue="--non_canonical_1" falsevalue="" checked="false" label="Non-canonical k-mers (dataset 1)" help="Store explicit k-mer as found. By default, canonical k-mers are stored, counting both strands."/>
+        </section>
+
+        <!-- Dataset 2 -->
+        <section name="input2" title="Dataset 2" expanded="true">
+            <param name="files" type="data" format="fasta,fastqsanger,fasta.gz,fastqsanger.gz,jellyfish" multiple="true" label="Dataset 2 files" help="Second set of FASTA/FASTQ files (gzip accepted) or a pre-counted Jellyfish hash. For the reads-vs-assembly use case, provide the assembly here."/>
+            <param argument="--non_canonical_2" type="boolean" truevalue="--non_canonical_2" falsevalue="" checked="false" label="Non-canonical k-mers (dataset 2)" help="Store explicit k-mer as found. By default, canonical k-mers are stored, counting both strands."/>
+        </section>
+
+        <!-- Optional Dataset 3 -->
+        <conditional name="input3">
+            <param name="use_input3" type="select" label="Use a third dataset as a k-mer filter">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <param name="files" type="data" format="fasta,fastqsanger,fasta.gz,fastqsanger.gz,jellyfish" multiple="true" label="Dataset 3 files" help="Optional third dataset used as a k-mer filter, restricting analysis to k-mers present in this set."/>
+                <param argument="--non_canonical_3" type="boolean" truevalue="--non_canonical_3" falsevalue="" checked="false" label="Non-canonical k-mers (dataset 3)" help="Store explicit k-mer as found. By default, canonical k-mers are stored, counting both strands."/>
+                <param argument="--hash_size_3" type="integer" value="100000000" min="1" label="Hash size (dataset 3)" help="Hash size for k-mer counting of dataset 3 if counting is required. (default: 100000000)"/>
+                <param name="d3_5ptrim" type="text" value="" label="5' trim length (dataset 3)" help="Ignore the first X bases from reads in dataset 3. For multiple files, provide comma-separated values (e.g. 5,10,0). Leave blank to disable.">
+                    <validator type="regex" message="Must be empty, a number, or comma-separated numbers">^[0-9]+(,[0-9]+)*$|^$</validator>
+                </param>
+            </when>
+        </conditional>
+
+        <!-- Dataset scaling and binning -->
+        <section name="dataset_options" title="Dataset Options" expanded="false">
+            <param argument="--d1_scale" type="float" value="1.0" min="0.0" label="Dataset 1 scaling factor" help="Float multiplier applied to k-mer counts from dataset 1 before comparison. (default: 1.0)"/>
+            <param argument="--d2_scale" type="float" value="1.0" min="0.0" label="Dataset 2 scaling factor" help="Float multiplier applied to k-mer counts from dataset 2 before comparison. (default: 1.0)"/>
+            <param argument="--d1_bins" type="integer" value="1001" min="1" label="Dataset 1 bins" help="Number of bins (rows in the matrix) for dataset 1. (default: 1001)"/>
+            <param argument="--d2_bins" type="integer" value="1001" min="1" label="Dataset 2 bins" help="Number of bins (columns in the matrix) for dataset 2. (default: 1001)"/>
+            <param argument="--d1_5ptrim" type="text" value="" label="5' trim length (dataset 1)" help="Ignore the first X bases from reads in dataset 1. For multiple files, provide comma-separated values (e.g. 5,10,0). Leave blank to disable.">
+                <validator type="regex" message="Must be empty, a number, or comma-separated numbers">^[0-9]+(,[0-9]+)*$|^$</validator>
+            </param>
+            <param argument="--d2_5ptrim" type="text" value="" label="5' trim length (dataset 2)" help="Ignore the first X bases from reads in dataset 2. For multiple files, provide comma-separated values (e.g. 5,10,0). Leave blank to disable.">
+                <validator type="regex" message="Must be empty, a number, or comma-separated numbers">^[0-9]+(,[0-9]+)*$|^$</validator>
+            </param>
+        </section>
+
+        <!-- K-mer options -->
+        <section name="kmer_options" title="K-mer Options" expanded="false">
+            <param argument="--mer_len" type="integer" value="27" min="1" label="K-mer length" help="Larger values provide more discriminating power between k-mers but require more memory and result in lower coverage. (default: 27)"/>
+            <param argument="--hash_size_1" type="integer" value="100000000" min="1" label="Hash size (dataset 1)" help="Hash size for k-mer counting of dataset 1 if counting is required. Doubled automatically if too small. (default: 100000000)"/>
+            <param argument="--hash_size_2" type="integer" value="100000000" min="1" label="Hash size (dataset 2)" help="Hash size for k-mer counting of dataset 2 if counting is required. Doubled automatically if too small. (default: 100000000)"/>
+            <param argument="--disable_hash_grow" type="boolean" truevalue="--disable_hash_grow" falsevalue="" checked="false" label="Disable automatic hash growing" help="By default, jellyfish doubles the hash size if filled and recounts. Enabling this disables that behaviour and throws an error instead. Useful for large genomes or strict memory limits."/>
+        </section>
+
+        <!-- Output options -->
+        <section name="output_options" title="Output Options" expanded="false">
+            <expand macro="output_type_param"/>
+            <param argument="--density_plot" type="boolean" truevalue="--density_plot" falsevalue="" checked="false" label="Create density plot" help="Makes a density plot. By default a spectra-cn plot is created."/>
+            <param argument="--output_hists" type="boolean" truevalue="--output_hists" falsevalue="" checked="false" label="Output histogram data and plots" help="Whether to output histogram data and plots for dataset 1 and dataset 2."/>
+        </section>
+    </inputs>
+
+    <outputs>
+        <!-- Comparison matrix -->
+        <data name="output_matrix" format="tabular" from_work_dir="kat-comp-main.mx" label="${tool.name} on ${on_string}: Comparison matrix"/>
+
+        <!-- Main plots -->
+        <data name="output_plot_png" format="png" from_work_dir="kat-comp-main.mx.spectra-cn.png" label="${tool.name} on ${on_string}: Spectra-CN Plot (PNG)">
+            <filter>output_options['output_type'] == 'png' and not output_options['density_plot']</filter>
+        </data>
+
+        <data name="output_plot_density_png" format="png" from_work_dir="kat-comp-main.mx.density.png" label="${tool.name} on ${on_string}: Density-CN Plot (PNG)">
+            <filter>output_options['output_type'] == 'png' and output_options['density_plot']</filter>
+        </data>
+
+        <data name="output_plot_pdf" format="pdf" from_work_dir="kat-comp-main.mx.spectra-cn.pdf" label="${tool.name} on ${on_string}: Spectra-CN Plot (PDF)">
+            <filter>output_options['output_type'] == 'pdf' and not output_options['density_plot']</filter>
+        </data>
+
+        <data name="output_plot_density_pdf" format="pdf" from_work_dir="kat-comp-main.mx.density.pdf" label="${tool.name} on ${on_string}: Density-CN Plot (PDF)">
+            <filter>output_options['output_type'] == 'pdf' and output_options['density_plot']</filter>
+        </data>
+
+        <!-- Stats -->
+        <data name="output_stats" format="tabular" from_work_dir="kat-comp.stats" label="${tool.name} on ${on_string}: Statistics"/>
+
+        <!-- Dataset 1 histogram (optional) -->
+        <data name="output_hist1" format="tabular" from_work_dir="kat-comp.1.hist" label="${tool.name} on ${on_string}: Dataset 1 histogram data">
+            <filter>output_options['output_hists']</filter>
+        </data>
+        <data name="output_hist1_plot_png" format="png" from_work_dir="kat-comp.1.hist.png" label="${tool.name} on ${on_string}: Dataset 1 histogram plot (PNG)">
+            <filter>output_options['output_hists'] and output_options['output_type'] == 'png'</filter>
+        </data>
+        <data name="output_hist1_plot_pdf" format="pdf" from_work_dir="kat-comp.1.hist.pdf" label="${tool.name} on ${on_string}: Dataset 1 histogram plot (PDF)">
+            <filter>output_options['output_hists'] and output_options['output_type'] == 'pdf'</filter>
+        </data>
+
+        <!-- Dataset 2 histogram (optional) -->
+        <data name="output_hist2" format="tabular" from_work_dir="kat-comp.2.hist" label="${tool.name} on ${on_string}: Dataset 2 histogram data">
+            <filter>output_options['output_hists']</filter>
+        </data>
+        <data name="output_hist2_plot_png" format="png" from_work_dir="kat-comp.2.hist.png" label="${tool.name} on ${on_string}: Dataset 2 histogram plot (PNG)">
+            <filter>output_options['output_hists'] and output_options['output_type'] == 'png'</filter>
+        </data>
+        <data name="output_hist2_plot_pdf" format="pdf" from_work_dir="kat-comp.2.hist.pdf" label="${tool.name} on ${on_string}: Dataset 2 histogram plot (PDF)">
+            <filter>output_options['output_hists'] and output_options['output_type'] == 'pdf'</filter>
+        </data>
+
+        <!-- Matrices generated if 3rd dataset is provided -->
+        <data name="kat_ends_matrix" format="tabular" from_work_dir="kat-comp-ends.mx" label="${tool.name} on ${on_string}: Ends Comparison matrix">
+            <filter>input3['use_input3'] == 'yes'</filter>
+        </data>
+
+        <data name="kat_middle_matrix" format="tabular" from_work_dir="kat-comp-middle.mx" label="${tool.name} on ${on_string}: Middle Comparison matrix">
+            <filter>input3['use_input3'] == 'yes'</filter>
+        </data>
+
+        <data name="kat_mixed_matrix" format="tabular" from_work_dir="kat-comp-mixed.mx" label="${tool.name} on ${on_string}: Mixed Comparison matrix">
+            <filter>input3['use_input3'] == 'yes'</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <!-- Test 01: Two FASTQ read sets (read-vs-read, density plot), PNG -->
+        <test expect_num_outputs="3">
+            <section name="input1">
+                <param name="files" value="ecoli_r1.1K.fastq" ftype="fastqsanger"/>
+            </section>
+            <section name="input2">
+                <param name="files" value="ecoli_r2.1K.fastq" ftype="fastqsanger"/>
+            </section>
+            <conditional name="input3">
+                <param name="use_input3" value="no"/>
+            </conditional>
+            <section name="kmer_options">
+                <param name="mer_len" value="27"/>
+            </section>
+            <section name="output_options">
+                <param name="output_type" value="png"/>
+                <param name="density_plot" value="true"/>
+            </section>
+            <output name="output_matrix" location="https://zenodo.org/records/20347489/files/kat_comp_matrix.mx">
+                <assert_contents>
+                    <has_n_columns n="1"/>
+                    <has_n_lines n="1013"/>
+                    <has_text text="# MaxVal:55758"/>
+                </assert_contents>
+            </output>
+            <output name="output_plot_density_png" file="kat_comp_density.png">
+                <assert_contents>
+                    <has_image_channels channels="4"/> 
+                    <has_image_height height="1800"/> 
+                    <has_image_width width="2400"/> 
+                </assert_contents>
+            </output>
+            <output name="output_stats" file="kat_comp_stats.tsv">
+                <assert_contents>
+                    <has_n_columns n="1"/>
+                    <has_n_lines n="39"/>
+                    <has_text text=" - Total shared found in hash 1: 14741"/>
+                    <has_text text=" - Total shared found in hash 2: 14213"/>
+                </assert_contents>
+            </output>
+        </test>
+
+        <!-- Test 02: Two FASTQ read sets (read-vs-read, density plot), PDF -->
+        <test expect_num_outputs="3">
+            <section name="input1">
+                <param name="files" value="ecoli_r1.1K.fastq" ftype="fastqsanger"/>
+            </section>
+            <section name="input2">
+                <param name="files" value="ecoli_r2.1K.fastq" ftype="fastqsanger"/>
+            </section>
+            <conditional name="input3">
+                <param name="use_input3" value="no"/>
+            </conditional>
+            <section name="kmer_options">
+                <param name="mer_len" value="27"/>
+            </section>
+            <section name="output_options">
+                <param name="output_type" value="pdf"/>
+                <param name="density_plot" value="true"/>
+            </section>
+            <output name="output_matrix">
+                <assert_contents>
+                    <has_n_columns n="1"/>
+                    <has_n_lines n="1013"/>
+                    <has_text text="# MaxVal:55758"/>
+                </assert_contents>
+            </output>
+            <output name="output_plot_density_pdf">
+                <assert_contents>
+                    <has_size value="21334"/>
+                </assert_contents>
+            </output>
+            <output name="output_stats">
+                <assert_contents>
+                    <has_n_columns n="1"/>
+                    <has_n_lines n="39"/>
+                    <has_text text=" - Total shared found in hash 1: 14741"/>
+                    <has_text text=" - Total shared found in hash 2: 14213"/>
+                </assert_contents>
+            </output>
+        </test>
+
+
+        <!-- Test 03: Reads vs assembly (spectra-cn), PNG -->
+        <test expect_num_outputs="3">
+            <section name="input1">
+                <param name="files" value="ecoli_r1.1K.fastq" ftype="fastqsanger"/>
+            </section>
+            <section name="input2">
+                <param name="files" location="https://zenodo.org/records/20347489/files/EcoliK12.fasta" ftype="fasta"/>
+            </section>
+            <conditional name="input3">
+                <param name="use_input3" value="no"/>
+            </conditional>
+            <section name="kmer_options">
+                <param name="mer_len" value="27"/>
+            </section>
+            <section name="output_options">
+                <param name="output_type" value="png"/>
+                <param name="density_plot" value="false"/>
+            </section>
+            <output name="output_matrix">
+                <assert_contents>
+                    <has_n_columns n="1"/>
+                    <has_n_lines n="1013"/>
+                    <has_text text="# MaxVal:4485405"/>
+                </assert_contents>
+            </output>
+            <output name="output_hist1_plot_png">
+                <assert_contents>
+                    <has_image_channels channels="4"/> 
+                    <has_image_height height="1800"/> 
+                    <has_image_width width="2400"/> 
+                </assert_contents>
+            </output>
+            <output name="output_stats">
+                <assert_contents>
+                    <has_n_columns n="1"/>
+                    <has_n_lines n="39"/>
+                    <has_text text=" - Total shared found in hash 1: 37899"/>
+                    <has_text text=" - Total shared found in hash 2: 45921"/>
+                </assert_contents>
+            </output>
+        </test>
+
+        <!-- Test 04: Reads vs assembly with histogram outputs, PDF -->
+        <test expect_num_outputs="7">
+            <section name="input1">
+                <param name="files" value="ecoli_r1.1K.fastq" ftype="fastqsanger"/>
+            </section>
+            <section name="input2">
+                <param name="files" location="https://zenodo.org/records/20347489/files/EcoliK12.fasta" ftype="fasta"/>
+            </section>
+            <conditional name="input3">
+                <param name="use_input3" value="no"/>
+            </conditional>
+            <section name="kmer_options">
+                <param name="mer_len" value="27"/>
+            </section>
+            <section name="output_options">
+                <param name="output_type" value="pdf"/>
+                <param name="output_hists" value="true"/>
+            </section>
+            <output name="output_matrix">
+                <assert_contents>
+                    <has_n_columns n="1"/>
+                    <has_n_lines n="1013"/>
+                    <has_text text="# MaxVal:4485405"/>
+                </assert_contents>
+            </output>
+            <output name="output_plot_pdf">
+                <assert_contents>
+                    <has_size value="14721"/>
+                </assert_contents>
+            </output>
+            <output name="output_hist1">
+                <assert_contents>
+                    <has_size size="6010"/>
+                    <has_text text="# XLabel:27-mer frequency"/>
+                </assert_contents>
+            </output>
+            <output name="output_hist1_plot_pdf">
+                <assert_contents>
+                    <has_size value="11727"/>
+                </assert_contents>
+            </output>
+            <output name="output_hist2">
+                <assert_contents>
+                    <has_text text="# XLabel:27-mer frequency"/>
+                    <has_size size="6031"/>
+                </assert_contents>
+            </output>
+            <output name="output_hist1_plot_pdf">
+                <assert_contents>
+                    <has_size value="11727"/>
+                </assert_contents>
+            </output>
+            <output name="output_stats">
+                <assert_contents>
+                    <has_n_columns n="1"/>
+                    <has_n_lines n="39"/>
+                    <has_text text=" - Total shared found in hash 1: 37899"/>
+                    <has_text text=" - Total shared found in hash 2: 45921"/>
+                </assert_contents>
+            </output>
+        </test>
+
+        <!-- Test 05: Three datasets, custom bins and scaling, gzipped inputs -->
+        <test expect_num_outputs="6">
+            <section name="input1">
+                <param name="files" value="ecoli_r1.1K.fastq.gz" ftype="fastqsanger.gz"/>
+            </section>
+            <section name="input2">
+                <param name="files" value="ecoli_r2.1K.fastq.gz" ftype="fastqsanger.gz"/>
+            </section>
+            <conditional name="input3">
+                <param name="use_input3" value="yes"/>
+                <param name="files" location="https://zenodo.org/records/20347489/files/EcoliK12.fasta" ftype="fasta"/>
+            </conditional>
+            <section name="dataset_options">
+                <param name="d1_scale" value="0.5"/>
+                <param name="d2_scale" value="0.5"/>
+                <param name="d1_bins" value="500"/>
+                <param name="d2_bins" value="500"/>
+            </section>
+            <section name="kmer_options">
+                <param name="mer_len" value="21"/>
+            </section>
+            <section name="output_options">
+                <param name="output_type" value="png"/>
+            </section>
+            <output name="output_matrix">
+                <assert_contents>
+                    <has_n_columns n="1"/>
+                    <has_n_lines n="512"/>
+                    <has_text text="# MaxVal:60421"/>
+                    <has_size value="500312"/>
+                </assert_contents>
+            </output>
+            <output name="output_plot_png">
+                <assert_contents>
+                    <has_image_channels channels="4"/> 
+                    <has_image_height height="1800"/> 
+                    <has_image_width width="2400"/> 
+                </assert_contents>
+            </output>
+            <output name="kat_ends_matrix">
+                <assert_contents>
+                    <has_n_columns n="1"/>
+                    <has_n_lines n="502"/>
+                    <has_size value="500146"/>
+                </assert_contents>
+            </output>
+            <output name="kat_middle_matrix">
+                <assert_contents>
+                    <has_n_columns n="1"/>
+                    <has_n_lines n="502"/>
+                    <has_size value="500148"/>
+                </assert_contents>
+            </output>
+            <output name="kat_mixed_matrix">
+                <assert_contents>
+                    <has_n_columns n="1"/>
+                    <has_n_lines n="502"/>
+                    <has_size value="500177"/>
+                </assert_contents>
+            </output>
+             <output name="output_stats">
+                <assert_contents>
+                    <has_n_columns n="1"/>
+                    <has_n_lines n="42"/>
+                    <has_text text=" - Total shared found in hash 1: 17153"/>
+                    <has_text text=" - Total shared found in hash 2: 16531"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+
+    <help format="markdown"><![CDATA[
+**KAT Comp - K-mer Hash Comparison**
+
+KAT (K-mer Analysis Toolkit) Comp compares k-mer spectra from two (or optionally three) datasets, producing an intersection matrix and a visualisation plot.
+
+-----
+
+**What it does**
+
+There are three main use cases:
+
+1. **Reads vs reads** – Compares k-mer spectra from two read datasets. The intersection matrix is visualised as a density plot showing how related the two spectra are.
+
+2. **Reads vs assembly** – Compares k-mers from a read set (dataset 1) against those from an assembly (dataset 2). The matrix is visualised as a stacked spectra-cn histogram, revealing how well the assembly represents the read data and highlighting missing, duplicated, or collapsed content.
+
+3. **Filtered comparison** – A third dataset can be provided as a k-mer filter, restricting the comparison to only k-mers present in that set.
+
+-----
+
+**Inputs**
+
+- **Dataset 1**: One or more FASTA/FASTQ files (gzip accepted) or a pre-counted Jellyfish hash. For the reads-vs-assembly use case, provide reads here.
+- **Dataset 2**: One or more FASTA/FASTQ files (gzip accepted) or a pre-counted Jellyfish hash. For the reads-vs-assembly use case, provide the assembly here.
+- **Dataset 3** *(optional)*: A third dataset used as a k-mer filter. Only k-mers present in this set are considered during comparison.
+
+-----
+
+**Outputs**
+
+- **Comparison matrix** (`.mx`): Tab-separated matrix of intersected k-mer counts, with rows corresponding to dataset 1 bins and columns to dataset 2 bins.
+- **Plot**: Visualisation of the matrix in the selected format (PNG, PDF, or PostScript). A spectra-cn plot by default, or a density plot if selected.
+- **Histogram data and plots** *(optional)*: Per-dataset k-mer frequency histograms and corresponding plots, enabled via *Output histogram data and plots*.
+
+-----
+
+**Notes**
+
+- For the reads-vs-assembly use case, dataset 1 must be the **reads** and dataset 2 the **assembly**.
+- **Scaling factors** can be used to normalise coverage differences between datasets before comparison.
+- **5' trim** values can be specified per file using comma-separated integers (e.g. `5,5` for two files).
+- Use **Disable automatic hash growing** when working with large genomes or under strict memory limits.
+- If inputs are already Jellyfish hashes, k-mer length and hash size settings are ignored for those inputs.
+
+
+    ]]></help>
+    <expand macro="citations"/>
+    <expand macro="creator"/>
+</tool>
\ No newline at end of file
diff --git a/tools/kat/kat_gcp.xml b/tools/kat/kat_gcp.xml
new file mode 100644
index 0000000000..93756c439a
--- /dev/null
+++ b/tools/kat/kat_gcp.xml
@@ -0,0 +1,261 @@
+<tool id="kat_gcp" name="KAT GCP" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>GC vs Coverage analysis of k-mers</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <stdio>
+        <regex match="corrupted double-linked list" source="stderr" level="warning" description="KAT C++ heap corruption — output files were still produced correctly"/>
+        <exit_code range="2:133" level="fatal" description="Error occurred"/>
+        <exit_code range="135:" level="fatal" description="Error occurred"/>
+        <exit_code range=":-1" level="fatal" description="Error occurred"/>
+    </stdio>
+    <version_command>echo @TOOL_VERSION@</version_command>
+    <command><![CDATA[
+        #if $input_type.type == 'fastx':
+            #for $i in range(len($input_type.input_files)):
+                #set $f = $input_type.input_files[$i]
+                @SET_EXT@
+                cp '$f' 'input_${i}${ext}' &&
+            #end for
+        #end if
+        kat gcp
+            -o kat-gcp
+            -t "\${GALAXY_SLOTS:-1}"
+            -x '$matrix_options.cvg_scale'
+            -y '$matrix_options.cvg_bins'
+            #if str($matrix_options.five_prime_trim).strip():
+                --5ptrim '$matrix_options.five_prime_trim'
+            #end if
+            -m '$kmer_options.mer_len'
+            -H '$kmer_options.hash_size'
+            $kmer_options.non_canonical
+            -v
+            -p '$output_options.output_type'
+            #if $input_type.type == 'fastx':
+                #for $i in range(len($input_type.input_files)):
+                    #set $f = $input_type.input_files[$i]
+                    @SET_EXT@
+                    'input_${i}${ext}'
+                #end for
+            #else:
+                '$input_type.jellyfish_hash'
+            #end if
+    ]]></command>
+    <inputs>
+        <conditional name="input_type">
+            <param name="type" type="select" label="Input type">
+                <option value="fastx" selected="true">FASTA/FASTQ files</option>
+                <option value="jellyfish">Jellyfish hash</option>
+            </param>
+            <when value="fastx">
+                <param name="input_files" type="data" format="fasta,fastqsanger,fasta.gz,fastqsanger.gz" multiple="true" label="Input FASTA/FASTQ files" help="One or more sequence files to analyse"/>
+            </when>
+            <when value="jellyfish">
+                <param name="jellyfish_hash" type="data" format="jellyfish" label="Jellyfish hash" help="Pre-computed jellyfish k-mer hash file"/>
+            </when>
+        </conditional>
+        <section name="kmer_options" title="K-mer Options" expanded="false">
+            <param argument="-m" name="mer_len" type="integer" value="27" min="1" label="K-mer length" help="Larger values provide more discriminating power between k-mers but require additional memory and lower coverage"/>
+            <param argument="-H" name="hash_size" type="integer" value="100000000" min="1" label="Hash size" help="If k-mer counting is required, use this value as the hash size. The hash will be doubled and recounted if it is too small, increasing runtime and memory usage"/>
+            <param argument="-N" name="non_canonical" type="boolean" truevalue="--non_canonical" falsevalue="" checked="false" label="Non-canonical k-mers" help="Store explicit k-mer as found. By default, canonical k-mers are stored, meaning both strands are counted"/>
+        </section>
+        <section name="matrix_options" title="Matrix Options" expanded="false">
+            <param argument="-x" name="cvg_scale" type="float" value="1" min="0" label="Coverage scale" help="Number of bins for the GC data when creating the contamination matrix"/>
+            <param argument="-y" name="cvg_bins" type="integer" value="1000" min="1" label="Coverage bins" help="Number of bins for the coverage data when creating the contamination matrix"/>
+            <expand macro="five_prime_trim_param"/>
+        </section>
+        <section name="output_options" title="Output Options" expanded="false">
+            <expand macro="output_type_param"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output_matrix" format="tabular" from_work_dir="kat-gcp.mx" label="${tool.name} on ${on_string}: GCP matrix"/>
+        <data name="output_plot" format="png" from_work_dir="kat-gcp.mx.png" label="${tool.name} on ${on_string}: GCP PNG Plot">
+            <filter>output_options['output_type'] == 'png'</filter>
+        </data>
+        <data name="output_pdf" format="pdf" from_work_dir="kat-gcp.mx.pdf" label="${tool.name} on ${on_string}: GCP PDF">
+            <filter>output_options['output_type'] == 'pdf'</filter>
+        </data>
+        <data name="output_stats" format="tabular" from_work_dir="kat-gcp.dist_analysis.json" label="${tool.name} on ${on_string}: JSON Stats"/>
+    </outputs>
+    <tests>
+        <!-- Test 01: Testing GCP matrix generation -->
+        <test expect_num_outputs="3">
+            <conditional name="input_type">
+                <param name="type" value="fastx"/>
+                <param name="input_files" location="https://zenodo.org/records/20347489/files/kat-input-subsampled.fastq.gz" ftype="fastqsanger.gz"/>
+            </conditional>
+            <section name="kmer_options">
+                <param name="mer_len" value="27"/>
+            </section>
+            <output name="output_matrix" file="kat_gcp.mx">
+                <assert_contents>
+                    <has_text text="###"/>
+                    <has_text text="# Rows:27"/>
+                    <has_text text="27-mer frequency"/>
+                </assert_contents>
+            </output>
+            <output name="output_plot" file="kat_gcp.mx.png">
+                <assert_contents>
+                    <has_size value="238000" delta="10000"/>
+                </assert_contents>
+            </output>
+            <output name="output_stats" file="kat_gcp.dist_analysis.json">
+                <assert_contents>
+                    <has_size value="940"/>
+                    <has_text text="coverage"/>
+                    <has_text text="&quot;k&quot;: 27"/>
+                    <has_text text="nb_peaks"/>
+                    <has_text text="mean_gc"/>
+                    <has_text text="est_genome_size"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test 02: Uncompressed FASTQ input with k-mer length 21 -->
+        <test expect_num_outputs="3">
+            <conditional name="input_type">
+                <param name="type" value="fastx"/>
+                <param name="input_files" value="read_1.fastq" ftype="fastqsanger"/>
+            </conditional>
+            <section name="kmer_options">
+                <param name="mer_len" value="21"/>
+            </section>
+            <output name="output_matrix">
+                <assert_contents>
+                    <has_text text="###"/>
+                    <has_text text="# Rows:21"/>
+                    <has_text text="21-mer frequency"/>
+                    <has_text text="# Kmer value:21"/>
+                </assert_contents>
+            </output>
+            <output name="output_plot">
+                <assert_contents>
+                    <has_size value="190500" delta="10000"/>
+                </assert_contents>
+            </output>
+            <output name="output_stats">
+                <assert_contents>
+                    <has_size value="742"/>
+                    <has_text text="coverage"/>
+                    <has_text text="&quot;k&quot;: 21"/>
+                    <has_text text="nb_peaks"/>
+                    <has_text text="mean_gc"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test 03: Multiple paired FASTQ inputs with non-canonical k-mers -->
+        <test expect_num_outputs="3">
+            <conditional name="input_type">
+                <param name="type" value="fastx"/>
+                <param name="input_files" value="read1.fastq.gz,read2.fastq.gz" ftype="fastqsanger.gz"/>
+            </conditional>
+            <section name="kmer_options">
+                <param name="mer_len" value="27"/>
+                <param name="non_canonical" value="true"/>
+            </section>
+            <output name="output_matrix">
+                <assert_contents>
+                    <has_text text="###"/>
+                    <has_text text="# Rows:27"/>
+                    <has_text text="27-mer frequency"/>
+                    <has_text text="input_0.fastq.gz"/>
+                    <has_text text="input_1.fastq.gz"/>
+                </assert_contents>
+            </output>
+            <output name="output_plot">
+                <assert_contents>
+                    <has_size value="241727"/>
+                </assert_contents>
+            </output>
+            <output name="output_stats">
+                <assert_contents>
+                    <has_size value="745"/>
+                    <has_text text="coverage"/>
+                    <has_text text="&quot;k&quot;: 27"/>
+                    <has_text text="nb_peaks"/>
+                    <has_text text="mean_gc"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test 04: Custom coverage bins and PDF output -->
+        <test expect_num_outputs="3">
+            <conditional name="input_type">
+                <param name="type" value="fastx"/>
+                <param name="input_files" value="read1.fastq.gz" ftype="fastqsanger.gz"/>
+            </conditional>
+            <section name="kmer_options">
+                <param name="mer_len" value="27"/>
+            </section>
+            <section name="matrix_options">
+                <param name="cvg_bins" value="500"/>
+            </section>
+            <section name="output_options">
+                <param name="output_type" value="pdf"/>
+            </section>
+            <output name="output_matrix">
+                <assert_contents>
+                    <has_text text="###"/>
+                    <has_text text="# Rows:27"/>
+                    <has_text text="# Columns:501"/>
+                </assert_contents>
+            </output>
+            <output name="output_pdf">
+                <assert_contents>
+                    <has_size value="23700" delta="2000"/>
+                </assert_contents>
+            </output>
+            <output name="output_stats">
+                <assert_contents>
+                    <has_size value="742"/>
+                    <has_text text="coverage"/>
+                    <has_text text="&quot;k&quot;: 27"/>
+                    <has_text text="nb_peaks"/>
+                    <has_text text="mean_gc"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+**KAT GCP - GC vs Coverage Analysis**
+
+KAT (K-mer Analysis Toolkit) GCP compares GC content and k-mer coverage from sequence data.
+
+-----
+
+**What it does**
+
+This tool counts GC nucleotides for each distinct k-mer in the input and builds a matrix
+of GC count vs k-mer coverage. This matrix is useful for:
+
+- Distinguishing legitimate genomic content from contamination
+- Identifying unexpected sequence content
+- Analysing biological composition of a sequencing library
+
+-----
+
+**Inputs**
+
+- **FastA/FastQ files**: One or more sequence files (optionally gzip-compressed). KAT will perform k-mer counting internally.
+- **Jellyfish hash**: A pre-computed k-mer hash produced by Jellyfish.
+
+-----
+
+**Outputs**
+
+- **GCP matrix** (`.mx`): Tab-separated matrix of GC count vs k-mer coverage bins. Each cell contains the count of distinct k-mers with that GC/coverage combination.
+- **GCP plot**: A 2D density plot visualising the matrix, useful for detecting contamination or ploidy signals.
+- **Stats**: A JSON file with summary statistics for the run.
+
+-----
+
+**Tips**
+
+- For contamination screening, look for distinct clusters in the GCP plot that sit away from the main genomic peak.
+- Increase `--mer_len` for more specific k-mer discrimination (at the cost of memory).
+
+    ]]></help>
+    <expand macro="citations"/>
+    <expand macro="creator"/>
+</tool>
\ No newline at end of file
diff --git a/tools/kat/kat_hist.xml b/tools/kat/kat_hist.xml
new file mode 100644
index 0000000000..52254c71e0
--- /dev/null
+++ b/tools/kat/kat_hist.xml
@@ -0,0 +1,171 @@
+<tool id="kat_hist" name="KAT Histogram" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>creates a histogram of k-mer occurrences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <stdio>
+        <regex match="corrupted double-linked list" source="stderr" level="warning" description="KAT C++ heap corruption - output files were still produced correctly"/>
+        <exit_code range="2:133" level="fatal" description="Error occurred"/>
+        <exit_code range="135:" level="fatal" description="Error occurred"/>
+        <exit_code range=":-1" level="fatal" description="Error occurred"/>
+    </stdio>
+    <version_command>echo @TOOL_VERSION@</version_command>
+    <command><![CDATA[
+            #for $i in range(len($input_files)):
+                #set $f = $input_files[$i]
+                @SET_EXT@
+                cp '$f' 'input_${i}${ext}' &&
+            #end for
+            kat hist
+                -o kat_hist_out
+                -t "\${GALAXY_SLOTS:-1}"
+                --low $histogram_options.low
+                --high $histogram_options.high
+                --inc $histogram_options.inc
+                --mer_len $kmer_options.mer_len
+                --hash_size $kmer_options.hash_size
+                $kmer_options.non_canonical
+                @CMD_5PTRIM@
+                --output_type '$advanced_options.output_type'
+                #for $i in range(len($input_files)):
+                    #set $f = $input_files[$i]
+                    @SET_EXT@
+                    'input_${i}${ext}'
+                #end for
+        ]]></command>
+    <inputs>
+        <param name="input_files" type="data" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" multiple="true" label="Input files" help="One or more FastA/FastQ files (gzipped accepted), or a single Jellyfish hash file"/>
+        <section name="histogram_options" title="Histogram Options" expanded="true">
+            <param argument="--low" type="integer" value="1" min="1" label="Low count" help="Low count value of histogram"/>
+            <param argument="--high" type="integer" value="10000" min="1" label="High count" help="High count value of histogram"/>
+            <param argument="--inc" type="integer" value="1" min="1" label="Increment" help="Increment for each bin"/>
+        </section>
+        <expand macro="kmer_params"/>
+        <section name="advanced_options" title="Advanced Options" expanded="false">
+            <param name="trim_5p" argument="--5ptrim" type="text" value="" label="5' trim" help="Ignore the first X bases from reads. For multiple input files, provide comma-separated values (e.g. 5,10,0).">
+                <validator type="regex" message="Must be a number or comma-separated numbers">^[0-9]+(,[0-9]+)*$|^$</validator>
+            </param>
+            <expand macro="output_type_param"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output_hist" format="tabular" from_work_dir="kat_hist_out" label="${tool.name} on ${on_string}: Histogram"/>
+        <data name="output_plot" format="png" from_work_dir="kat_hist_out.png" label="${tool.name} on ${on_string}: PNG Plot">
+            <filter>advanced_options['output_type'] == 'png'</filter>
+        </data>
+        <data name="output_pdf" format="pdf" from_work_dir="kat_hist_out.pdf" label="${tool.name} on ${on_string}: PDF Plot">
+            <filter>advanced_options['output_type'] == 'pdf'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- Test 01: Default options with PNG Output -->
+        <test expect_num_outputs="2">
+            <param name="input_files" location="https://zenodo.org/records/20347489/files/kat-input-subsampled.fastq.gz" ftype="fastqsanger.gz"/>
+            <section name="histogram_options">
+                <param name="low" value="1"/>
+                <param name="high" value="10000"/>
+                <param name="inc" value="1"/>
+            </section>
+            <output name="output_hist" file="kat_hist.out">
+                <assert_contents>
+                    <has_text text="# Kmer value:27"/>
+                    <has_n_lines n="10007"/>
+                </assert_contents>
+            </output>
+            <output name="output_plot" file="kat_hist.out.png" ftype="png">
+                <assert_contents>
+                    <has_image_channels channels="4"/> 
+                    <has_image_height height="1800"/> 
+                    <has_image_width width="2400"/> 
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test 02: Custom k-mer length with PDF Output -->
+        <test expect_num_outputs="2">
+            <param name="input_files" location="https://zenodo.org/records/20347489/files/kat-input-subsampled.fastq.gz" ftype="fastqsanger.gz"/>
+            <section name="kmer_options">
+                <param name="mer_len" value="21"/>
+            </section>
+            <section name="advanced_options">
+                <param name="output_type" value="pdf"/>
+            </section>
+            <output name="output_hist">
+                <assert_contents>
+                    <has_text text="# Kmer value:21"/>
+                    <has_n_lines n="10007"/>
+                </assert_contents>
+            </output>
+            <output name="output_pdf" ftype="pdf">
+                <assert_contents>
+                    <has_size size="13956"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test 03: 5' trim with PNG Output -->
+        <test expect_num_outputs="2">
+            <param name="input_files" location="https://zenodo.org/records/20347489/files/kat-input-subsampled.fastq.gz" ftype="fastqsanger.gz"/>
+            <section name="advanced_options">
+                <param name="trim_5p" value="5"/>
+            </section>
+            <output name="output_hist">
+                <assert_contents>
+                    <has_text text="# Kmer value:27"/>
+                    <has_n_lines n="10007"/>
+                </assert_contents>
+            </output>
+            <output name="output_plot" ftype="png">
+                <assert_contents>
+                    <has_image_channels channels="4"/> 
+                    <has_image_height height="1800"/> 
+                    <has_image_width width="2400"/> 
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+**KAT Histogram (kat hist)**
+
+Creates a histogram of k-mer occurrences from sequencing data.
+
+-----
+
+**What it does**
+
+The histogram shows how many k-mers appear at each frequency in the input data. Bucket *i* tallies k-mers with count *c* satisfying:
+
+```
+low + i*inc <= c < low + (i+1)*inc
+```
+
+The final bucket catches all k-mers with count >= the last bucket's lower bound.
+
+This tool is similar to the `histo` command in Jellyfish, but the output includes metadata that makes the histogram easier to plot and interpret.
+
+-----
+
+**Input**
+
+- One or more **FASTA** or **FASTQ** files (gzipped accepted)
+- Or a single pre-computed **Jellyfish hash** file
+
+-----
+
+**Outputs**
+
+1. **Histogram** (tabular) - tab-separated count/frequency table with metadata header lines prefixed with `#`.
+2. **Plot** (PNG/PDF) - visual plot of the k-mer frequency histogram.
+
+-----
+
+**Tips**
+
+- The default k-mer length of **27** works well for most short-read sequencing data.
+- For diploid or polyploid genomes, distinct peaks correspond to heterozygous and homozygous k-mers.
+- If the hash size is too small, KAT will automatically double it (increasing runtime and memory). Increase it if you expect many unique k-mers.
+- For multiple input files, provide different 5' trim values as comma-separated numbers (e.g. `5,10`).
+    ]]></help>
+    <expand macro="citations"/>
+    <expand macro="creator"/>
+</tool>
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