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