Add RayCloudTools

[hagreven]

This PR adds the Galaxy Tool XML file for 3Dtrees RayCloudTools (v1.1.1).

Introduces:

• full-parameter control
• returns results as a list collection that contains the segmented point cloud, terrain mesh, treefile and tree meshes (RCT-QSM)
• changes point cloud extra dimension name for instance IDs to PredInstance_RCT
• enables optional calculation of additional tree parameters in the treefile (--treeinfo)
• provides tests for collection output

---

Note

Low Risk
Low risk because this is an additive Galaxy tool XML; the main risk is mis-specified CLI args/output discovery patterns causing job failures or missing outputs at runtime.

Overview
Adds a new Galaxy tool definition tools/raycloudtools.xml that runs RayCloudTools (ghcr.io/3dtrees-earth/3dtrees_rct:1.1.1) for LiDAR tree instance segmentation, exposing key algorithm parameters plus optional --treeinfo, --branch-segmentation, and --branch-data flags.

Outputs are returned as list collections with dataset discovery patterns for segmented point clouds, tree text outputs (with/without tree attributes), and mesh files, and includes two collection-based tool tests covering default vs treeinfo execution.

^{Written by Cursor Bugbot for commit 77d0a8f. This will update automatically on new commits. Configure here.}

[cursor]

Cursor Bugbot has reviewed your changes and found 1 potential issue.

Bugbot Autofix prepared a fix for the issue found in the latest run.

• ✅ Fixed: Underscore in --branch_data flag mismatches parameter definition
  • Updated the command template to pass --branch-data so it matches the declared parameter argument and avoids argparse unrecognized-flag errors.

Or push these changes by commenting:

@cursor push 049f996b13

Preview (049f996b13)

diff --git a/tools/raycloudtools.xml b/tools/raycloudtools.xml
--- a/tools/raycloudtools.xml
+++ b/tools/raycloudtools.xml
@@ -33,7 +33,7 @@
         --treeinfo
         #end if
         #if $branch_data:
-        --branch_data
+        --branch-data
         #end if
         ]]>
     </command>

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[cursor]

Underscore in --branch_data flag mismatches parameter definition

High Severity

The command passes --branch_data (underscore) to run.py, but the parameter is declared with argument="--branch-data" (hyphen). Every other multi-word flag in the command uses hyphens consistently. If the Python script's argparse expects --branch-data, the underscore variant will be unrecognized and cause a runtime error when a user enables the branch data option.

Additional Locations (1)

• tools/raycloudtools.xml#L58-L59

 

[kgerb]

please create PR to the galaxytools repo :) galaxy is outdated