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annotate standard.xml @ 0:e78c8c5ea3df draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3Dtrees_standardization commit ef08451cb2e70c234e44751684ef1eb35d1a93b8
author bgruening
date Tue, 09 Dec 2025 12:54:11 +0000
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children 6524ef47a755
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0
e78c8c5ea3df planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3Dtrees_standardization commit ef08451cb2e70c234e44751684ef1eb35d1a93b8
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1 <tool id="3dtrees_standardization" name="3Dtrees: LAZ Standardization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
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2 <description>
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3 laz file checks and standardization.
e78c8c5ea3df planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3Dtrees_standardization commit ef08451cb2e70c234e44751684ef1eb35d1a93b8
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4 </description>
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5 <macros>
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6 <token name="@TOOL_VERSION@">1.0.1</token>
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7 <token name="@VERSION_SUFFIX@">0</token>
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8 </macros>
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9 <requirements>
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10 <container type="docker">ghcr.io/3dtrees-earth/3dtrees-pc-standard:@TOOL_VERSION@</container>
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11 </requirements>
e78c8c5ea3df planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3Dtrees_standardization commit ef08451cb2e70c234e44751684ef1eb35d1a93b8
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12 <command detect_errors="exit_code"><![CDATA[
e78c8c5ea3df planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3Dtrees_standardization commit ef08451cb2e70c234e44751684ef1eb35d1a93b8
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13 ## needed because the Rscript is following symlinks
e78c8c5ea3df planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3Dtrees_standardization commit ef08451cb2e70c234e44751684ef1eb35d1a93b8
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14 cp '$input' /in/input.laz &&
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15 cd /src &&
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16 Rscript run.R
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17 --dataset-path /in/input.laz
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18 --output-dir .
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19 --min-density
e78c8c5ea3df planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3Dtrees_standardization commit ef08451cb2e70c234e44751684ef1eb35d1a93b8
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20 $min_density &&
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21 mv /src/pc_standardized.laz '$pc_standardized'
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22 ]]>
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23 </command>
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24 <inputs>
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25 <param name="input" type="data" format="laz" label="Point Cloud Dataset" help="LAZ point cloud to process"/>
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26 <param name="min_density" type="integer" value="500" min="1" max="10000" label="Minimum Point Density (points/m²)" help="Minimum required point density in points per square meter. Default: 500 for TLS data. Use lower values (e.g., 10-50) for ALS data."/>
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27 </inputs>
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28 <outputs>
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29 <data name="pc_standardized" format="laz" label="Standardized Point Cloud"/>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="input" value="mikro.laz" ftype="laz"/>
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34 <param name="min_density" value="10"/>
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35 <output name="pc_standardized">
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36 <assert_contents>
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37 <has_size value="100000" delta="50000"/>
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38 </assert_contents>
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39 </output>
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40 </test>
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41 </tests>
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42 <help>
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43 **What it does**
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44
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45 This tool performs a series of checks and standardizations on a LAS/LAZ point cloud file. It checks:
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46
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47 1. **Basic LAS Validation**
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48 - Validates the object using las_check()
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49 - Ensures the file has at least 100 points
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50
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51 2. **Bounding Box Consistency**
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52 - Updates header if bounding box doesn't match points
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53 - Validates spatial extent (all dimensions &gt; 1 meter)
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54 - Checks Z range is plausible (-100 to 5500 meters)
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55
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56 3. **Point Density Check**
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57 - Calculates point density using convex hull
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58 - Requires minimum point density (configurable, default: 500 points/m² for TLS)
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59
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60 4. **Extra Byte Data Type Check**
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61 - Validates extra byte attribute data types
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62 - Corrects mismatches if found
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63
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64 5. **CRS Validation**
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65 - Ensures CRS is specified
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66 - Validates transformation to EPSG:3857
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67
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68 6. **Point Data Format Check**
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69 - Downgrades format to 7 if necessary
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70 - Preserves NIR channel as extra attribute
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71
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72 7. **Land Coverage Validation**
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73 - Validates centroid is on land using Natural Earth data
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74
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75 8. **Output Writing**
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76 - Writes standardized LAZ file with Point Format ≤ 7
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77 </help>
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78 <creator>
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79 <person name="Julian Frey" email="julian.frey@wwd.uni-freiburg.de" url="https://orcid.org/0000-0001-7895-702X"/>
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80 <person name="Janusch Vajna-Jehle" email="janusch.jehle@geosense.uni-freiburg.de" url="https://orcid.org/0009-0002-0034-9387"/>
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81 <person name="Kilian Gerberding" email="kilian.gerberding@geosense.uni-freiburg.de" url="https://orcid.org/0009-0002-5001-2571"/>
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82 <organization name="3Dtrees-Team, University of Freiburg" url="https://github.com/3dTrees-earth"/>
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83 </creator>
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84 <citations>
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85 <citation type="bibtex">
e78c8c5ea3df planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3Dtrees_standardization commit ef08451cb2e70c234e44751684ef1eb35d1a93b8
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86 @misc{3dtrees_standard, title = {3D Trees Standardization}, author = {3D Trees Project}, year = {2025}}
e78c8c5ea3df planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3Dtrees_standardization commit ef08451cb2e70c234e44751684ef1eb35d1a93b8
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87 </citation>
e78c8c5ea3df planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3Dtrees_standardization commit ef08451cb2e70c234e44751684ef1eb35d1a93b8
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88 </citations>
e78c8c5ea3df planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3Dtrees_standardization commit ef08451cb2e70c234e44751684ef1eb35d1a93b8
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89 </tool>