From a622c5c52c06caa402cb77c9f29ce1affc9bdea6 Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Tue, 25 Feb 2025 21:45:31 +0000
Subject: [PATCH] Moved actual tool definition to submodule

---
 .devcontainer/devcontainer.json |  2 +-
 .shed.yml                       | 12 ------------
 .vscode/extensions.json         |  3 ++-
 .vscode/tasks.json              |  6 +++---
 auto-updated-tools-iuc          |  2 +-
 5 files changed, 7 insertions(+), 18 deletions(-)
 delete mode 100644 .shed.yml

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index ce3acb4..089aa83 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -3,7 +3,7 @@
 {
 	"name": "Python 3",
 	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
-	"image": "mcr.microsoft.com/devcontainers/python:1-3.12-bullseye",
+	"image": "mcr.microsoft.com/devcontainers/python:1-3.11-bullseye",
 
 	// Features to add to the dev container. More info: https://containers.dev/features.
 	// "features": {},
diff --git a/.shed.yml b/.shed.yml
deleted file mode 100644
index cff15f4..0000000
--- a/.shed.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-name: autobigs
-owner: iuc
-description: Automated MLST typing from PubMLST and InstitutPasteur.
-homepage_url: https://github.com/Syph-and-VPD-Lab/autoBIGS.cli
-long_description: |
-  A program that allows quickly batched requests for obtaining MLST 
-  profiles on multiple FASTA sequences and exporting it as a convenient 
-  CSV. Capable of querying a variety of MLST databases from both 
-  Institut Pasteur and PubMLST.
-remote_repository_url: https://github.com/Syph-and-VPD-Lab/autoBIGS.cli
-categories:
-- Sequence Analysis
\ No newline at end of file
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
index 02a917e..832b6fe 100644
--- a/.vscode/extensions.json
+++ b/.vscode/extensions.json
@@ -2,6 +2,7 @@
     "recommendations": [
         "mechatroner.rainbow-csv",
         "redhat.vscode-xml",
-        "ms-vscode.live-server"
+        "ms-vscode.live-server",
+        "davelopez.galaxy-tools"
     ]
 }
\ No newline at end of file
diff --git a/.vscode/tasks.json b/.vscode/tasks.json
index 29bd266..8ee5d77 100644
--- a/.vscode/tasks.json
+++ b/.vscode/tasks.json
@@ -6,19 +6,19 @@
         {
             "label": "lint",
             "type": "shell",
-            "command": "planemo lint",
+            "command": "planemo lint auto-updated-tools-iuc/tools/autobigs",
             "problemMatcher": []
         },
         {
             "label": "serve",
             "type": "shell",
-            "command": "planemo serve",
+            "command": "planemo serve auto-updated-tools-iuc/tools/autobigs",
             "problemMatcher": []
         },
         {
             "label": "run tests",
             "type": "shell",
-            "command": "planemo test autobigs-cli.xml --test_output_junit test_results/junit_results.xml --test_output_json test_results/results.json --test_output test_results/human.html",
+            "command": "planemo test auto-updated-tools-iuc/tools/autobigs/autobigs-cli.xml --test_output_junit test_results/junit_results.xml --test_output_json test_results/results.json --test_output test_results/human.html",
             "problemMatcher": []
         }
     ]
diff --git a/auto-updated-tools-iuc b/auto-updated-tools-iuc
index 9d6123a..98d0bee 160000
--- a/auto-updated-tools-iuc
+++ b/auto-updated-tools-iuc
@@ -1 +1 @@
-Subproject commit 9d6123a18805224b03c0558647cd079624886361
+Subproject commit 98d0beeb5cbb816e0e3ff38b9936340ba21bf683