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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3Dtrees_standardization commit a46a7cd9cef25a6d34bcc268ba72d8afebfdf8c6
author bgruening
date Tue, 13 Jan 2026 07:41:37 +0000
parents e78c8c5ea3df
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0:e78c8c5ea3df 1:6524ef47a755
1 <tool id="3dtrees_standardization" name="3Dtrees: LAZ Standardization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2"> 1 <tool id="3dtrees_standardization" name="3DTrees: LAS/LAZ Standardization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
2 <description> 2 <description>Standardize LAS/LAZ files or validate collections for consistency</description>
3 laz file checks and standardization.
4 </description>
5 <macros> 3 <macros>
6 <token name="@TOOL_VERSION@">1.0.1</token> 4 <token name="@TOOL_VERSION@">1.1.0</token>
7 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">0</token>
8 </macros> 6 </macros>
9 <requirements> 7 <requirements>
10 <container type="docker">ghcr.io/3dtrees-earth/3dtrees-pc-standard:@TOOL_VERSION@</container> 8 <container type="docker">ghcr.io/3dtrees-earth/3dtrees-pc-standard:@TOOL_VERSION@</container>
11 </requirements> 9 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
13 ## needed because the Rscript is following symlinks 11 #if $mode.task == 'single_file':
14 cp '$input' /in/input.laz && 12 cp '$mode.input' input.laz &&
15 cd /src && 13 Rscript /src/run.R
16 Rscript run.R 14 --dataset-path ./input.laz
17 --dataset-path /in/input.laz 15 --output-dir ./
18 --output-dir . 16 --method single_file
19 --min-density 17 --min-density '$mode.min_density'
20 $min_density && 18 #if $mode.removeable_attributes:
21 mv /src/pc_standardized.laz '$pc_standardized' 19 --removeable_attributes '$mode.removeable_attributes'
22 ]]> 20 #end if
23 </command> 21 #else:
22 mkdir -p ./input_files &&
23 #for $f in $mode.input_collection
24 cp '$f' ./input_files/'${f.element_identifier}.laz' &&
25 #end for
26 Rscript /src/run.R
27 --dataset-path ./input_files/
28 --output-dir ./
29 --method collection
30 #end if
31 ]]></command>
32
24 <inputs> 33 <inputs>
25 <param name="input" type="data" format="laz" label="Point Cloud Dataset" help="LAZ point cloud to process"/> 34 <conditional name="mode">
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."/> 35 <param name="task" type="select" label="Mode">
36 <option value="single_file">Single File Standardization</option>
37 <option value="collection">Collection Validation</option>
38 </param>
39 <when value="single_file">
40 <param name="input" type="data" format="laz" label="Point Cloud File"
41 help="LAS/LAZ point cloud file to standardize (CRS validation, density check, format normalization)"/>
42 <param argument="--min-density" type="integer" min="1" max="10000" value="10"
43 label="Minimum Point Density"
44 help="Minimum acceptable point density in points per square meter. Default: 10 pts/m²"/>
45 <param argument="--removeable_attributes" type="text" value="" optional="true"
46 label="Attributes to Remove"
47 help="Space-separated list of attribute names to remove (e.g., 'Intensity UserData'). Leave empty for auto-detection."/>
48 </when>
49 <when value="collection">
50 <param name="input_collection" type="data" format="laz" multiple="true" label="Point Cloud Collection"
51 help="Multiple LAZ/LAS files to validate for consistency (CRS homogeneity, attribute consistency, overlaps)"/>
52 </when>
53 </conditional>
27 </inputs> 54 </inputs>
28 <outputs> 55 <outputs>
29 <data name="pc_standardized" format="laz" label="Standardized Point Cloud"/> 56 <data name="pc_standardized" format="laz" label="standardized" from_work_dir="input.laz">
57 <filter>mode['task'] == "single_file"</filter>
58 </data>
59 <data name="metadata_json" format="json" label="metadata" from_work_dir="input.json">
60 <filter>mode['task'] == "single_file"</filter>
61 </data>
62 <data name="convex_hull" format="geojson" label="convex_hull" from_work_dir="input_convex_hull_wgs84.GeoJSON">
63 <filter>mode['task'] == "single_file"</filter>
64 </data>
65 <data name="collection_summary" format="json" label="collection_summary" from_work_dir="collection_summary.json">
66 <filter>mode['task'] == "collection"</filter>
67 </data>
30 </outputs> 68 </outputs>
31 <tests> 69 <tests>
32 <test> 70 <test expect_num_outputs="3">
33 <param name="input" value="mikro.laz" ftype="laz"/> 71 <conditional name="mode">
34 <param name="min_density" value="10"/> 72 <param name="task" value="single_file"/>
35 <output name="pc_standardized"> 73 <param name="input" value="mikro.laz" ftype="laz"/>
74 <param name="min_density" value="10"/>
75 </conditional>
76 <output name="pc_standardized" ftype="laz">
36 <assert_contents> 77 <assert_contents>
37 <has_size value="100000" delta="50000"/> 78 <has_size min="1000"/>
79 </assert_contents>
80 </output>
81 <output name="convex_hull" ftype="geojson">
82 <assert_contents>
83 <has_json_property_with_text property="type" text="FeatureCollection"/>
84 </assert_contents>
85 </output>
86 <output name="metadata_json" ftype="json">
87 <assert_contents>
88 <has_text text='"point_count":[12917]'/>
89 <has_text text='"standardized":[true]'/>
90 </assert_contents>
91 </output>
92 </test>
93 <test expect_num_outputs="1">
94 <conditional name="mode">
95 <param name="task" value="collection"/>
96 <param name="input_collection" value="mikro.laz,mikro2.laz" ftype="laz"/>
97 </conditional>
98 <output name="collection_summary" ftype="json">
99 <assert_contents>
100 <has_json_property_with_value property="n_tiles" value="2"/>
101 <has_json_property_with_value property="homogeneous_crs" value="true"/>
102 <has_json_property_with_value property="homogeneous_attribute_names" value="true"/>
38 </assert_contents> 103 </assert_contents>
39 </output> 104 </output>
40 </test> 105 </test>
41 </tests> 106 </tests>
42 <help>
43 **What it does**
44 107
45 This tool performs a series of checks and standardizations on a LAS/LAZ point cloud file. It checks: 108 <help><![CDATA[
109 **What it does**
46 110
47 1. **Basic LAS Validation** 111 This tool supports two modes:
48 - Validates the object using las_check()
49 - Ensures the file has at least 100 points
50 112
51 2. **Bounding Box Consistency** 113 **Single File Mode** (standardization):
52 - Updates header if bounding box doesn't match points 114 Standardizes a single LAS/LAZ file:
53 - Validates spatial extent (all dimensions &gt; 1 meter)
54 - Checks Z range is plausible (-100 to 5500 meters)
55 115
56 3. **Point Density Check** 116 1. **LAS Validation**: Runs ``las_check()`` and fixes header issues
57 - Calculates point density using convex hull 117 2. **Bounding Box**: Validates and corrects header bounding box
58 - Requires minimum point density (configurable, default: 500 points/m² for TLS) 118 3. **Point Density**: Checks density meets minimum threshold
119 4. **CRS Validation**: Verifies CRS is defined and transformable to EPSG:4978
120 5. **Land Check**: Confirms centroid is on land (using Natural Earth data)
121 6. **Format Normalization**: Downgrades Point Data Format to ≤7 for compatibility
122 7. **Attribute Cleanup**: Optionally removes specified attributes
59 123
60 4. **Extra Byte Data Type Check** 124 **Outputs (single file mode):**
61 - Validates extra byte attribute data types 125 - Standardized ``.laz`` file
62 - Corrects mismatches if found 126 - Metadata JSON with pre/post standardization info
127 - Convex hull GeoJSON in WGS84
63 128
64 5. **CRS Validation** 129 **Collection Mode** (validation):
65 - Ensures CRS is specified 130 Validates consistency of multiple LAS/LAZ files:
66 - Validates transformation to EPSG:3857
67 131
68 6. **Point Data Format Check** 132 - **CRS Homogeneity**: Checks if all files share the same coordinate reference system
69 - Downgrades format to 7 if necessary 133 - **Attribute Consistency**: Verifies attribute names and types across files
70 - Preserves NIR channel as extra attribute 134 - **Tile Geometry**: Detects overlaps and gaps between tiles
135 - **Global Statistics**: Computes aggregated statistics across all files
136 - **Removeable Attributes**: Identifies attributes that are all-NA or constant-zero
71 137
72 7. **Land Coverage Validation** 138 **Outputs (collection mode):**
73 - Validates centroid is on land using Natural Earth data 139 - ``collection_summary.json`` containing collection-level checks and flags, per-file metadata (CRS, attributes, point counts, convex hulls), and suggested removeable attributes for standardization
74 140
75 8. **Output Writing** 141 **Workflow Usage**
76 - Writes standardized LAZ file with Point Format ≤ 7 142
77 </help> 143 For collection-based workflows:
144 1. Run this tool with **Collection Validation** first to check consistency
145 2. Use the suggested ``removeable_attributes`` from the collection summary
146 3. Then run this tool with **Single File Standardization** (Galaxy maps over collection automatically) for standardization
147
148 ]]></help>
149
78 <creator> 150 <creator>
79 <person name="Julian Frey" email="julian.frey@wwd.uni-freiburg.de" url="https://orcid.org/0000-0001-7895-702X"/> 151 <person name="Julian Frey" email="julian.frey@wwd.uni-freiburg.de" url="https://orcid.org/0000-0001-7895-702X"/>
80 <person name="Janusch Vajna-Jehle" email="janusch.jehle@geosense.uni-freiburg.de" url="https://orcid.org/0009-0002-0034-9387"/> 152 <person name="Janusch Vajna-Jehle" email="janusch.jehle@geosense.uni-freiburg.de" url="https://orcid.org/0009-0002-0034-9387"/>
81 <person name="Kilian Gerberding" email="kilian.gerberding@geosense.uni-freiburg.de" url="https://orcid.org/0009-0002-5001-2571"/> 153 <person name="Kilian Gerberding" email="kilian.gerberding@geosense.uni-freiburg.de" url="https://orcid.org/0009-0002-5001-2571"/>
154 <person name="Mirko Mälicke" identifier="0000-0002-0424-2651"/>
82 <organization name="3Dtrees-Team, University of Freiburg" url="https://github.com/3dTrees-earth"/> 155 <organization name="3Dtrees-Team, University of Freiburg" url="https://github.com/3dTrees-earth"/>
83 </creator> 156 </creator>
157
84 <citations> 158 <citations>
85 <citation type="bibtex"> 159 <citation type="bibtex">
86 @misc{3dtrees_standard, title = {3D Trees Standardization}, author = {3D Trees Project}, year = {2025}} 160 @misc{3dtrees_standard, title = {3D Trees Standardization}, author = {3D Trees Project}, year = {2025}}
87 </citation> 161 </citation>
88 </citations> 162 </citations>