amend db only and no trees help text

medema-group · Oct 25, 2024 · 10e4635 · 10e4635
1 parent fa80b83
commit 10e4635
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/big_scape/cli/cli_common_options.py b/big_scape/cli/cli_common_options.py
@@ -118,15 +118,17 @@ def common_all(fn):
             is_flag=True,
             default=False,
             help="Do not generate any output besides the data stored in the database. "
-            "Suitable for advanced users that work with the SQL database directly.",
+            "Suitable for advanced users that wish to only make use of the results "
+            "stored in the SQLite database.",
         ),
         click.option(
             "--no-trees",
             type=bool,
             is_flag=True,
             default=False,
             help="Do not generate any GCF newick trees. Suitable for users that do not "
-            "utilize our output visualization, but work with output tsv files directly.",
+            "utilize our output visualization, but only make use of the output stored "
+            "in the tsv files and/or SQLite database.",
         ),
         click.option(
             "--force-gbk",

diff --git a/big_scape/output/legacy_output.py b/big_scape/output/legacy_output.py
@@ -164,7 +164,7 @@ def legacy_prepare_output(
     click_context = click.get_current_context(silent=True)
 
     if click_context and click_context.obj["db_only_output"]:
-        logging.info("Skipping all output generation")
+        logging.info("Skipping all (non-SQLite db related) output generation")
         return
 
     copy_base_output_templates(output_dir)