# HG changeset patch
# User francesco_lapi
# Date 1757066020 0
# Node ID 8a1213d1393d33e17214b7ac375fd76bd2e78c90
# Parent d2e36a8ab451a8437f6d4c6e00deec27b012be38
Uploaded
diff -r d2e36a8ab451 -r 8a1213d1393d COBRAxy/custom_data_generator.py
--- a/COBRAxy/custom_data_generator.py Fri Sep 05 09:32:38 2025 +0000
+++ b/COBRAxy/custom_data_generator.py Fri Sep 05 09:53:40 2025 +0000
@@ -36,15 +36,9 @@
parser.add_argument("--medium", type=str,
help="Custom medium file if medium_selector=Custom")
- parser.add_argument("--output_format", type=str, choices=["tabular", "xlsx"], required=True,
- help="Output format: CSV (tabular) or Excel (xlsx)")
-
parser.add_argument("--out_tabular", type=str,
help="Output file for the merged dataset (CSV or XLSX)")
- parser.add_argument("--out_xlsx", type=str,
- help="Output file for the merged dataset (CSV or XLSX)")
-
parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),
help="Tool directory (passed from Galaxy as $__tool_directory__)")
@@ -199,14 +193,6 @@
except Exception as e:
raise utils.DataErr(path, f"failed writing tabular output: {e}")
-def save_as_xlsx_df(df: pd.DataFrame, path: str) -> None:
- try:
- if not path.lower().endswith(".xlsx"):
- path += ".xlsx"
- os.makedirs(os.path.dirname(path) or ".", exist_ok=True)
- df.to_excel(path, index=False)
- except Exception as e:
- raise utils.DataErr(path, f"failed writing xlsx output: {e}")
###############################- ENTRY POINT -################################
def main(args:List[str] = None) -> None:
@@ -272,17 +258,11 @@
####
- # write only the requested output
- if ARGS.output_format == "xlsx":
- if not ARGS.out_xlsx:
- raise utils.ArgsErr("out_xlsx", "output path (--out_xlsx) is required when output_format == xlsx", ARGS.out_xlsx)
- save_as_xlsx_df(merged, ARGS.out_xlsx)
- expected = ARGS.out_xlsx
- else:
- if not ARGS.out_tabular:
- raise utils.ArgsErr("out_tabular", "output path (--out_tabular) is required when output_format == tabular", ARGS.out_tabular)
- save_as_tabular_df(merged, ARGS.out_tabular)
- expected = ARGS.out_tabular
+
+ if not ARGS.out_tabular:
+ raise utils.ArgsErr("out_tabular", "output path (--out_tabular) is required when output_format == tabular", ARGS.out_tabular)
+ save_as_tabular_df(merged, ARGS.out_tabular)
+ expected = ARGS.out_tabular
# verify output exists and non-empty
if not expected or not os.path.exists(expected) or os.path.getsize(expected) == 0:
diff -r d2e36a8ab451 -r 8a1213d1393d COBRAxy/custom_data_generator.xml
--- a/COBRAxy/custom_data_generator.xml Fri Sep 05 09:32:38 2025 +0000
+++ b/COBRAxy/custom_data_generator.xml Fri Sep 05 09:53:40 2025 +0000
@@ -4,20 +4,18 @@
marea_macros.xml
-
+
numpy
pandas
- cobra
+ cobra
lxml
- openpyxl
-
+
-
+
+
+
+
+
+
@@ -97,20 +93,6 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
@@ -118,16 +100,7 @@
-
-
-
-
-
+ optional="true"/>