From 817b97553ffe7f9edb66c6c6a468bfafe4e4afe3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= <berenice.batut@gmail.com>
Date: Thu, 22 Feb 2024 15:48:44 +0100
Subject: [PATCH] Add script to generate from tool table a YAML to install the
 tool

---
 bin/generate_tool_install_yaml.py | 58 +++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 bin/generate_tool_install_yaml.py

diff --git a/bin/generate_tool_install_yaml.py b/bin/generate_tool_install_yaml.py
new file mode 100644
index 00000000..5edabad1
--- /dev/null
+++ b/bin/generate_tool_install_yaml.py
@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+
+import argparse
+
+import pandas as pd
+import yaml
+
+COLUMNS = {
+    "Galaxy tool ids": "name",
+    "Galaxy wrapper owner": "owner",
+    "EDAM operation": "tool_panel_section_label",
+}
+
+
+def generate_install_yaml(
+    tsv_path: str,
+    output_path: str,
+) -> None:
+    df = pd.read_csv(tsv_path, sep="\t").assign(Expand=lambda df: "").fillna("")
+    if "To keep" in df.columns:
+        df["To keep"] = df["To keep"].replace("", False)
+        df = df.query("`To keep`")
+    df = df.loc[:, COLUMNS.keys()].reindex(columns=COLUMNS.keys()).rename(columns=COLUMNS)
+    df["name"] = df["name"].str.split(", ")
+    df = df.explode("name")
+    print(df)
+
+    tool_dict = {
+        "install_tool_dependencies": True,
+        "install_repository_dependencies": True,
+        "install_resolver_dependencies": True,
+        "tools": df.to_dict("records"),
+    }
+
+    with open(output_path, "w") as output:
+        yaml.dump(tool_dict, output, default_flow_style=False)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Generate the YAML to install the tools on a Galaxy server \
+            from TSV file"
+    )
+    parser.add_argument(
+        "--table",
+        "-ta",
+        required=True,
+        help="Path to TSV file with tools",
+    )
+    parser.add_argument(
+        "--output",
+        "-out",
+        required=True,
+        help="Path to YAML output",
+    )
+
+    args = parser.parse_args()
+    generate_install_yaml(args.table, args.output)