# HG changeset patch
# User goeckslab
# Date 1769205345 0
# Node ID f5b713d70f1aa262bdc59bcbd9e186507b676cb8
# Parent  f2877a8b54e4a20b854d6ef657965bc732173658
planemo upload for repository https://github.com/goeckslab/gleam commit 75eddf497315160aa1282ba1db839c4db0aed0c6

diff -r f2877a8b54e4 -r f5b713d70f1a base_model_trainer.py
--- a/base_model_trainer.py	Mon Jan 19 05:55:05 2026 +0000
+++ b/base_model_trainer.py	Fri Jan 23 21:55:45 2026 +0000
@@ -121,6 +121,30 @@
         self.target = names[target_index]
         sample_id_column = getattr(self, "sample_id_column", None)
         if sample_id_column:
+            if str(sample_id_column).isdigit():
+                idx = int(sample_id_column) - 1
+                if 0 <= idx < len(names):
+                    resolved = names[idx]
+                    if sample_id_column in names:
+                        LOG.warning(
+                            "Sample ID column value '%s' matches a header, but Galaxy data_column "
+                            "inputs are interpreted as 1-based indices; using column #%s header '%s'.",
+                            sample_id_column,
+                            idx + 1,
+                            resolved,
+                        )
+                    LOG.info(
+                        "Sample ID column '%s' not found; using column #%s header '%s' instead.",
+                        sample_id_column,
+                        idx + 1,
+                        resolved,
+                    )
+                    sample_id_column = resolved
+                else:
+                    raise ValueError(
+                        f"Sample ID column index {sample_id_column} is invalid. "
+                        f"Please select a number between 1 and {len(names)}."
+                    )
             sample_id_column = sample_id_column.replace(".", "_")
             self.sample_id_column = sample_id_column
         else: