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Merge branch 'master' into add-credential-support-to-chatgpt-tool
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‎data_managers/data_manager_kmetashot/.shed.yml‎

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categories:
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- Data Managers
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- Metagenomics
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homepage_url: https://github.com/gdefazio/kMetaShot
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description: Data manager for kMetaShot reference data
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long_description: Data manager for kMetaShot reference data
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name: kmetashot_build_database
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owner: bgruening
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remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_kmetashot
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type: unrestricted

‎data_managers/data_manager_kmetashot/data_manager/kmetashot_datamanager.xml‎

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<tool id="kmetashot_build_database" name="kMetaShot" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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<description>database builder</description>
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<macros>
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<token name="@TOOL_VERSION@">2.0</token>
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<token name="@VERSION_SUFFIX@">0</token>
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<token name="@PROFILE@">24.1</token>
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</macros>
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<requirements>
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<requirement type="package" version="@TOOL_VERSION@">kmetashot</requirement>
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</requirements>
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<command><![CDATA[
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mkdir -p "$out_file.extra_files_path" &&
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#if $test != "true":
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#if $release == "1":
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wget "https://zenodo.org/records/17591095/files/kMetaShot_reference.h5" &&
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mv "kMetaShot_reference.h5" "$out_file.extra_files_path" &&
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#else:
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wget "https://zenodo.org/records/17375120/files/kMetaShot_bacteria_archaea_2025-05-22.h5" &&
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mv "kMetaShot_bacteria_archaea_2025-05-22.h5" "$out_file.extra_files_path" &&
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#end if
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#else:
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touch '$out_file.extra_files_path'/kMetaShot_bacteria_archaea_2025-05-22.h5 &&
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#end if
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cp "$dmjson" "$out_file"
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]]></command>
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<configfiles>
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<configfile name="dmjson"><![CDATA[
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{
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"data_tables":{
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"kmetashot":[
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{
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"dbkey":"kmetashot",
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"version":"${release}",
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#if $test == "true":
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"path":"${out_file.extra_files_path}/kMetaShot_bacteria_archaea_2025-05-22.h5",
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"name":"kMetaShot reference data 2025-05-22 - TEST",
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"value":"2025-05-22"
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#else:
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#if $release == "1":
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"path":"${out_file.extra_files_path}/kMetaShot_reference.h5",
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"name":"kMetaShot reference data 2022-07-31",
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"value":"2022-07-31"
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#else:
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"path":"${out_file.extra_files_path}/kMetaShot_bacteria_archaea_2025-05-22.h5",
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"name":"kMetaShot reference data 2025-05-22",
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"value":"2025-05-22"
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#end if
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#end if
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}
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]
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}
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}]]>
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</configfile>
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</configfiles>
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<inputs>
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<param name="release" type="select" multiple="false" label="kMetaShot reference data release">
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<option value="1">First release</option>
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<option value="2">Second release</option>
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</param>
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<param name="test" type="hidden" value="" checked="false" label="Run test"/>
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</inputs>
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<outputs>
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<data name="out_file" format="data_manager_json" />
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</outputs>
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<tests>
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<test expect_num_outputs="1">
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<param name="release" value="2"/>
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<param name="test" value="true"/>
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<output name="out_file">
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<assert_contents>
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<has_text text="25-05-22"/>
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<has_text text="kMetaShot reference data 2025-05-22 - TEST"/>
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</assert_contents>
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</output>
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</test>
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</tests>
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<help><![CDATA[
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Download and extract kMetaShot reference data.
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]]></help>
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<citations>
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<citation type="doi">10.1038/s41592-023-01940-w</citation>
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</citations>
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</tool>

‎data_managers/data_manager_kmetashot/data_manager_conf.xml‎

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<data_managers>
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<data_manager tool_file="data_manager/kmetashot_datamanager.xml" id="kmetashot_build_database">
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<data_table name="kmetashot">
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<output>
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<column name="value"/>
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<column name="dbkey"/>
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<column name="name"/>
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<column name="version"/>
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<column name="path" output_ref="out_file">
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<move type="file">
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<source>${path}</source>
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<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kmetashot/${value}/${path}</target>
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</move>
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<value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kmetashot/${value}/${path}</value_translation>
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<value_translation type="function">abspath</value_translation>
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</column>
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</output>
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</data_table>
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</data_manager>
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</data_managers>

‎data_managers/data_manager_kmetashot/test-data/kmetashot.loc‎

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25-05-22 kMetaShot-25-05-22 kMetaShot reference data 2025-05-22 2 /tmp/tmpf_hplx2a/galaxy-dev/tool-data/kmetashot/2/kMetaShot_bacteria_archaea_2025-05-22.h5

‎data_managers/data_manager_kmetashot/tool-data/kmetashot.loc.sample‎

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#This is a sample file distributed with Galaxy that enables tools
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#to use a the kMetaShot database.
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#You will need to create these data files using the following command
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#wget [selected version] [url_from_donwlaod]
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#The <version> column indicates the version from the kMetaShot ref data was downloaded
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#25-05-22 kMetaShot-25-05-22 kMetaShot reference data 2025-05-22 2 /mnt/galaxyIndices/kMetaShot_database/kMetaShot_bacteria_archaea_2025-05-22.h5

‎data_managers/data_manager_kmetashot/tool_data_table_conf.xml.sample‎

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<tables>
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<table name="kmetashot" comment_char="#" allow_duplicate_entries="False">
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<columns>value, dbkey, name, version, path</columns>
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<file path="tool-data/kmetashot.loc" />
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</table>
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</tables>

‎data_managers/data_manager_kmetashot/tool_data_table_conf.xml.test‎

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<tables>
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<!-- Location of kmetashot indexes for testing -->
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<table name="kmetashot" comment_char="#" allow_duplicate_entries="False">
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<columns>value, dbkey, name, version, path</columns>
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<file path="${__HERE__}/test-data/kmetashot.loc" />
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</table>
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</tables>

‎tools/3dtrees_overviews/overviews.xml‎

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<tool id="3dtrees_overviews" name="3Dtrees: Overviews" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
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<description>generates 3D overview images</description>
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<macros>
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<token name="@TOOL_VERSION@">1.0.0</token>
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<token name="@VERSION_SUFFIX@">1</token>
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<token name="@TOOL_VERSION@">1.0.1</token>
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<token name="@VERSION_SUFFIX@">0</token>
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</macros>
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<requirements>
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<container type="docker">ghcr.io/3dtrees-earth/tool_overviews:@TOOL_VERSION@</container>
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</requirements>
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<command detect_errors="exit_code"><![CDATA[
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export MPLCONFIGDIR=\$TMPDIR &&
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mkdir -p ./output_dir/ &&
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ln -s '$input' input.laz &&
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python -u /src/run.py
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mkdir -p ./output_dir/ &&
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ln -s '$input' input.laz &&
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python -u /src/run.py
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--dataset-path input.laz
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--max-points '$max_points'
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--section-width '$section_width'
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--image-width '$image_width'
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--image-height '$image_height'
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--top-views-deg '$top_views_deg'
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--cmap '$cmap'
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--camera-distance '$camera_distance'
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--camera-distance '$camera_distance'
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--output-dir ./output_dir/
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]]>
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]]>
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</command>
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<inputs>
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<param name="input" type="data" format="laz" label="Point Cloud Dataset" help="LAZ point cloud file to process"/>
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</test>
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</tests>
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<help format="markdown">
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**What it does**
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This tool generates 3D overview visualizations from point cloud dataset. It creates:
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1. **Top View Images**: A series of top-down views rotated around the point cloud center
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2. **Section Views**: Cross-sectional views from north-south and east-west directions
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3. **Overview Animation**: An animated GIF showing the rotation sequence
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The tool automatically handles large datasets by downsampling to a manageable number of points while preserving the overall structure and appearance.
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-----
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**Input**
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- **Point Cloud Dataset**: LAZ format point cloud file
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- **Maximum Points**: Limit for downsampling (default: 100M points)
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- **Section Width**: Width of cross-sectional views in meters
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- **Image Dimensions**: Width and height of output images in pixels
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- **Top View Rotation**: Angular step size for rotation sequence
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- **Color Map**: Visualization color scheme (height-based coloring)
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- **Camera Distance**: Distance from point cloud center for rendering
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-----
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**Output**
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- **Top View Images**: Collection of PNG images showing top-down views at different rotation angles
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- **Section View Images**: Collection of PNG images showing cross-sectional views
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- **Overview Animation**: GIF file showing the complete rotation sequence
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-----
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**Example**
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For a forest point cloud dataset, this tool will generate:
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- 36 top view images (every 10 degrees)
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- 2 section view images (north-south and east-west cuts)
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- 1 animated GIF showing the complete 360° rotation
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The images use height-based coloring to show terrain and vegetation structure.
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</help>
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**What it does**
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This tool generates 3D overview visualizations from point cloud dataset. It creates:
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1. **Top View Images**: A series of top-down views rotated around the point cloud center
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2. **Section Views**: Cross-sectional views from north-south and east-west directions
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3. **Overview Animation**: An animated GIF showing the rotation sequence
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The tool automatically handles large datasets by downsampling to a manageable number of points while preserving the overall structure and appearance.
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-----
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**Input**
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- **Point Cloud Dataset**: LAZ format point cloud file
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- **Maximum Points**: Limit for downsampling (default: 100M points)
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- **Section Width**: Width of cross-sectional views in meters
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- **Image Dimensions**: Width and height of output images in pixels
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- **Top View Rotation**: Angular step size for rotation sequence
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- **Color Map**: Visualization color scheme (height-based coloring)
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- **Camera Distance**: Distance from point cloud center for rendering
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-----
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**Output**
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- **Top View Images**: Collection of PNG images showing top-down views at different rotation angles
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- **Section View Images**: Collection of PNG images showing cross-sectional views
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- **Overview Animation**: GIF file showing the complete rotation sequence
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-----
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**Example**
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For a forest point cloud dataset, this tool will generate:
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- 36 top view images (every 10 degrees)
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- 2 section view images (north-south and east-west cuts)
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- 1 animated GIF showing the complete 360° rotation
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The images use height-based coloring to show terrain and vegetation structure.
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</help>
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<creator>
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<person name="Julian Frey" email="julian.frey@wwd.uni-freiburg.de" url="https://orcid.org/0000-0001-7895-702X"/>
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<person name="Kilian Gerberding" email="kilian.gerberding@geosense.uni-freiburg.de" url="https://orcid.org/0009-0002-5001-2571"/>

‎tools/3dtrees_py3dtiles/.shed.yml‎

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name: 3dtrees_py3dtiles
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owner: bgruening
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description: generates 3D tiles from point clouds
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homepage_url: https://github.com/3dTrees-earth/3dtrees_py3dtiles
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long_description: |
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generates 3D tiles from point clouds
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remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/3dtrees_py3dtiles
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type: unrestricted
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categories:
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- Geo Science

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