tools: add 3dtrees metadata wrapper

chemicaltoolbox/opsin/.shed.yml

@@ -0,0 +1,16 @@
+categories:
+  - Computational chemistry
+homepage_url: https://github.com/dan2097/opsin
+name: opsin
+owner: bgruening
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/opsin
+type: unrestricted
+repositories:
+  opsin:
+    description: OPSIN (Open Parser for Systematic IUPAC Nomenclature) IUPAC name-to-structure conversion
+    long_description: |
+      OPSIN is an Open Parser for Systematic IUPAC Nomenclature.
+      This suite provides tools to convert IUPAC chemical names into machine-readable structures,
+      including SMILES, CML, and InChI formats.
+    include:
+      - opsin.xml

chemicaltoolbox/opsin/opsin.xml

@@ -1,8 +1,11 @@
-<tool id="ctb_opsin" name="IUPAC name-to-structure" version="2.4.0">
-    <description>converter (OPSIN)</description>
+<tool id="ctb_opsin" name="opsin" version="@TOOL_VERSION@+galaxy0" profile="25.1">
+    <description>IUPAC name-to-structure</description>
+    <macros>
+        <token name="@TOOL_VERSION@">2.9.0</token>
+    </macros>
     <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" merge_outputs="outfile"></parallelism>
     <requirements>
-        <requirement type="package" version="2.4.0">opsin</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">opsin</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -13,15 +16,15 @@
     <command>
 <![CDATA[
         opsin
-            "${radicals}"
-            "${wildcards}"
+            ${radicals}
+            ${wildcards}
             -o$oformat
-            < "${infile}"
-            > "${outfile}"
+           < '${infile}'
+           > '${outfile}'
 ]]>
     </command>  
     <inputs>
-        <param format="tabular,text" name="infile" type="data" label="IUPAC names" help="Upload file with a list of IUPAC names, each on its own line."/>
+        <param format="tabular,txt" name="infile" type="data" label="IUPAC names" help="Upload file with a list of IUPAC names, each on its own line."/>
         <param name="oformat" type="select" label="Output format">
             <option value="smi">SMILES</option>
             <option value="cml">Chemical Markup Language</option>
@@ -53,7 +56,7 @@
 
 OPSIN_ is a IUPAC name-to-structure conversion tool offering high recall and precision on organic chemical nomenclature.
 
-.. _OPSIN: https://bitbucket.org/dan2097/opsin/overview
+.. _OPSIN: https://github.com/dan2097/opsin
 
 
 ]]>

tools/3dtrees_metadata/.shed.yml

@@ -0,0 +1,13 @@
+name: 3dtrees_metadata
+owner: bgruening
+description: Extract administrative and ecoregion metadata for 3Dtrees collections.
+homepage_url: https://github.com/3dTrees-earth/3dtrees_metadata
+long_description: |
+  Extracts administrative and ecoregion context for a 3Dtrees collection summary
+  by computing the collection centroid from collection_summary.json and
+  intersecting it with selected GADM and WWF Terrestrial Ecoregions v2.0 vector
+  datasets.
+remote_repository_url: https://github.com/3dTrees-earth/galaxytools/tree/3dtrees_metadata_v1_0_0/tools/3dtrees_metadata
+type: unrestricted
+categories:
+- "Geo Science"

tools/3dtrees_metadata/3dtrees_metadata.xml

@@ -0,0 +1,106 @@
+<tool id="3dtrees_metadata" name="3Dtrees: Metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
+    <description>Extract administrative and ecoregion metadata for a point-cloud collection</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_metadata:@TOOL_VERSION@</container>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$collection_summary' collection_summary.json &&
+        python -u /src/run.py
+        --collection-summary collection_summary.json
+        --metadata-layers '$metadata_layers'
+        --output-file additional_metadata.json
+        2>&1
+    ]]></command>
+    <inputs>
+        <param name="collection_summary" type="data" format="json" label="Collection summary" help="collection_summary.json from the 3Dtrees: LAS/LAZ Standardization collection mode."/>
+        <param argument="--metadata-layers" type="select" multiple="true" display="checkboxes" min="1" label="Metadata layers to extract" help="Choose at least one metadata layer. Both are selected by default.">
+            <option value="gadm" selected="true">GADM administrative boundaries</option>
+            <option value="ecoregion" selected="true">WWF Terrestrial Ecoregions v2.0</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="additional_metadata" format="json" label="additional_metadata" from_work_dir="additional_metadata.json"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="collection_summary" value="collection_summary.json" ftype="json"/>
+            <param name="metadata_layers" value="gadm,ecoregion"/>
+            <output name="additional_metadata" ftype="json">
+                <assert_contents>
+                    <has_text text='"matched": true'/>
+                    <has_text text='"selected_level": 1'/>
+                    <has_text text='"name": "Baden-Wuerttemberg"'/>
+                    <has_text text='"ecoregion_name": "Black Forest"'/>
+                    <has_text text='"biome_name": "Temperate Broadleaf &amp; Mixed Forests"'/>
+                    <has_text text='"is_forest_biome": true'/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="collection_summary" value="collection_summary.json" ftype="json"/>
+            <param name="metadata_layers" value="gadm"/>
+            <output name="additional_metadata" ftype="json">
+                <assert_contents>
+                    <has_text text='"admin"'/>
+                    <has_text text='"selected_level": 1'/>
+                    <has_text text='"name": "Baden-Wuerttemberg"'/>
+                    <not_has_text text='"ecoregion"'/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="collection_summary" value="collection_summary.json" ftype="json"/>
+            <param name="metadata_layers" value="ecoregion"/>
+            <output name="additional_metadata" ftype="json">
+                <assert_contents>
+                    <has_text text='"ecoregion_name": "Black Forest"'/>
+                    <has_text text='"is_forest_biome": true'/>
+                    <not_has_text text='"admin"'/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+**What it does**
+
+This tool reads a 3Dtrees `collection_summary.json`, computes the WGS84 centroid
+from `collection.multipolygon_wkt`, and intersects that point with the selected
+reference layers. GADM provides administrative context; WWF Terrestrial
+Ecoregions v2.0 data provides ecoregion, realm, and biome context.
+
+-----
+
+**Input**
+
+- **Collection summary**: `collection_summary.json` produced by the 3Dtrees
+  standardization tool in collection mode.
+- **Metadata layers to extract**: one or more internal reference layers. The tool
+  reads the selected reference datasets from the Docker image.
+
+-----
+
+**Output**
+
+The tool writes `additional_metadata.json` with:
+
+- GADM source details and checked layers
+- Collection centroid longitude/latitude in EPSG:4326
+- Whether the centroid matched a GADM feature
+- Selected administrative level and hierarchy
+- Raw matched GADM fields for downstream metadata enrichment
+- Optional WWF ecoregion name/id, realm, biome code/name, and forest-biome flag
+    ]]></help>
+    <creator>
+        <person name="Kilian Gerberding" email="kilian.gerberding@geosense.uni-freiburg.de" url="https://orcid.org/0009-0002-5001-2571"/>
+        <organization name="3Dtrees-Team, University of Freiburg" url="https://github.com/3dTrees-earth"/>
+    </creator>
+    <citations>
+        <citation type="bibtex">
+            @misc{3dtrees_metadata, title = {3Dtrees: Metadata}, author = {3Dtrees Project}, year = {2026}}
+        </citation>
+    </citations>
+</tool>

tools/3dtrees_metadata/test-data/collection_summary.json

@@ -0,0 +1,8 @@
+{
+  "collection": {
+    "multipolygon_wkt": "MULTIPOLYGON(((7.84 47.98, 7.86 47.98, 7.86 48.00, 7.84 48.00, 7.84 47.98)))"
+  },
+  "n_tiles": 2,
+  "homogeneous_crs": true,
+  "homogeneous_attribute_names": true
+}

tools/3dtrees_metadata/test-data/gadm_fixture.geojson

@@ -0,0 +1,35 @@
+{
+  "type": "FeatureCollection",
+  "name": "gadm_fixture",
+  "crs": {
+    "type": "name",
+    "properties": {
+      "name": "urn:ogc:def:crs:OGC:1.3:CRS84"
+    }
+  },
+  "features": [
+    {
+      "type": "Feature",
+      "properties": {
+        "GID_0": "DEU",
+        "COUNTRY": "Germany",
+        "GID_1": "DEU.1_1",
+        "NAME_1": "Baden-Wuerttemberg",
+        "TYPE_1": "Land",
+        "ENGTYPE_1": "State"
+      },
+      "geometry": {
+        "type": "Polygon",
+        "coordinates": [
+          [
+            [7.70, 47.80],
+            [8.00, 47.80],
+            [8.00, 48.20],
+            [7.70, 48.20],
+            [7.70, 47.80]
+          ]
+        ]
+      }
+    }
+  ]
+}

tools/3dtrees_metadata/test-data/wwf_ecoregions_fixture.geojson

@@ -0,0 +1,34 @@
+{
+  "type": "FeatureCollection",
+  "name": "wwf_ecoregions_fixture",
+  "crs": {
+    "type": "name",
+    "properties": {
+      "name": "urn:ogc:def:crs:OGC:1.3:CRS84"
+    }
+  },
+  "features": [
+    {
+      "type": "Feature",
+      "properties": {
+        "ECO_NAME": "Black Forest",
+        "ECO_ID": "PA0414",
+        "REALM": "PA",
+        "BIOME": 4,
+        "BIOME_DESC": "Temperate Broadleaf & Mixed Forests"
+      },
+      "geometry": {
+        "type": "Polygon",
+        "coordinates": [
+          [
+            [7.70, 47.80],
+            [8.00, 47.80],
+            [8.00, 48.20],
+            [7.70, 48.20],
+            [7.70, 47.80]
+          ]
+        ]
+      }
+    }
+  ]
+}

tools/3dtrees_raycloudtools/raycloudtools.xml

@@ -1,8 +1,8 @@
 <tool id="3dtrees_raycloudtools" name="3Dtrees: RayCloudTools" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.1" license="BSD-3-Clause">
     <description>Tree instance segmentation</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.1.1</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@TOOL_VERSION@">1.2.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
         <container type="docker">

tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_trees.txt

@@ -1,3 +1,3 @@
 # Tree file. Optional per-tree attributes (e.g. 'height,crown_radius, ') followed by 'x,y,z,radius' and any additional per-segment attributes:
 x,y,z,radius,parent_id,section_id
--0.0004,-0.0005,-0.0400,0.0525,-1,0, 0.0008,-0.0009,0.5044,0.0525,0,1, 0.0300,-0.0450,0.7800,0.0523,1,2, 0.0033,-0.0052,1.0377,0.0523,2,3, -0.0056,0.0493,1.2587,0.0384,3,4, 0.0203,-0.0530,1.2240,0.0356,3,5, -0.0260,0.1583,1.4181,0.0384,4,6, -0.0100,-0.0580,1.4800,0.0356,5,7, -0.0405,0.2458,1.5522,0.0384,6,8, -0.0133,-0.0633,1.7300,0.0356,7,9, -0.0558,0.3339,1.6914,0.0384,8,10, -0.0100,-0.0750,1.8750,0.0355,9,11, -0.0221,0.3834,1.8933,0.0319,10,12, -0.0650,0.4650,1.8400,0.0213,10,14, 0.0175,-0.1334,2.0886,0.0355,11,13, 0.0276,0.3805,2.0381,0.0319,12,15, -0.0950,0.5225,1.9500,0.0213,13,17, 0.0300,-0.1200,2.2040,0.0351,14,16, 0.0157,0.3912,2.1720,0.0319,15,18, -0.1050,0.6050,2.0400,0.0211,16,20, 0.0461,-0.1344,2.3103,0.0351,17,19, -0.0325,0.3050,2.3100,0.0316,18,21, -0.1200,0.6750,2.1250,0.0211,19,23, 0.0367,-0.2200,2.4633,0.0347,20,22, 0.0049,0.2169,2.5093,0.0313,21,24, -0.1633,0.7333,2.1900,0.0184,22,26, -0.1178,0.7124,2.2245,0.0103,22,30, 0.0550,-0.2675,2.5850,0.0267,23,25, 0.0640,-0.2840,2.5760,0.0222,23,28, 0.0450,0.1629,2.5958,0.0225,24,27, -0.0518,0.1240,2.6016,0.0214,24,32, -0.2225,0.8475,2.2725,0.0184,25,31, -0.1100,0.7225,2.3075,0.0103,26,36, 0.0750,-0.3200,2.7600,0.0267,27,29, 0.0520,-0.3640,2.7140,0.0222,28,34, 0.0250,0.2600,2.7400,0.0225,29,33, -0.0750,0.1250,2.7300,0.0214,30,38, -0.2650,0.9375,2.3500,0.0184,31,37, 0.1100,-0.3600,2.8850,0.0267,33,35, -0.0098,-0.4474,2.7674,0.0222,34,40, 0.0600,0.3567,2.8233,0.0225,35,39, -0.1075,0.1300,2.7900,0.0213,36,43, -0.2833,1.0000,2.4233,0.0152,37,42, -0.3100,0.9933,2.4167,0.0102,37,47, 0.1250,-0.4050,3.0050,0.0267,38,41, -0.0400,-0.5100,2.8120,0.0222,39,45, 0.0967,0.4467,2.8733,0.0191,40,44, 0.0497,0.4464,2.9199,0.0119,40,50, -0.1704,0.1585,2.8855,0.0213,41,49, -0.2948,1.0738,2.4693,0.0152,42,48, 0.1340,-0.4420,3.2000,0.0267,44,46, -0.1120,-0.6360,2.9080,0.0222,45,52, 0.0993,0.6170,2.8780,0.0191,46,51, 0.0800,0.4467,2.9733,0.0116,47,56, -0.2000,0.1500,2.9833,0.0201,48,55, -0.3100,1.1300,2.5450,0.0152,49,54, 0.1750,-0.4625,3.3275,0.0243,50,53, -0.1100,-0.7100,2.9833,0.0190,51,58, 0.2000,0.6350,2.9050,0.0180,52,57, 0.0900,0.4800,3.0500,0.0116,53,62, -0.2560,0.1200,3.1040,0.0201,54,61, -0.3287,1.1993,2.5983,0.0152,55,60, 0.1900,-0.4700,3.4467,0.0243,56,59, -0.1280,-0.7820,3.0440,0.0190,57,64, 0.2467,0.7000,2.9333,0.0180,58,63, 0.0833,0.5083,3.1149,0.0116,59,68, -0.2625,0.0650,3.1625,0.0189,60,67, -0.3500,1.2533,2.6300,0.0122,61,66, 0.2580,-0.4800,3.5500,0.0243,62,65, -0.1496,-0.8424,3.1172,0.0190,63,70, 0.3350,0.7950,2.9350,0.0178,64,69, 0.0575,0.5900,3.1525,0.0115,65,74, -0.2450,0.0000,3.2500,0.0182,66,73, -0.3833,1.3667,2.7500,0.0122,67,72, 0.2750,-0.4925,3.6600,0.0188,68,71, 0.3250,-0.4850,3.6100,0.0152,68,77, -0.1967,-0.9933,3.2467,0.0157,69,76, 0.4400,0.7833,2.9000,0.0174,70,75, 0.0900,0.5900,3.2100,0.0115,71,80, -0.2467,-0.0800,3.3333,0.0182,72,79, 0.2800,-0.5250,3.8425,0.0188,74,78, 0.4000,-0.4850,3.6600,0.0152,75,83, -0.2400,-1.0933,3.3033,0.0124,76,82, 0.4900,0.7500,2.8600,0.0174,77,81, -0.2300,-0.1800,3.3950,0.0181,79,85, 0.3033,-0.5533,3.9233,0.0154,80,84, 0.4600,-0.4900,3.7250,0.0120,81,87, 0.5050,0.7000,2.7900,0.0174,83,86, -0.2000,-0.2533,3.4767,0.0181,84,89, 0.3400,-0.5750,4.0200,0.0154,85,88, 0.4750,0.6700,2.7000,0.0169,87,90, -0.1250,-0.4350,3.5750,0.0181,88,92, 0.3550,-0.5975,4.1150,0.0119,89,91, 0.4000,0.6200,2.5833,0.0168,90,93, -0.1033,-0.6267,3.6833,0.0181,91,94, 0.3333,0.5367,2.5033,0.0168,93,95, 0.2625,0.4375,2.4475,0.0168,95,96
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