diff app_validate.py @ 0:6b226c5907a1 draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/app_validate.py	Fri Aug 07 06:17:31 2020 -0400
@@ -0,0 +1,32 @@
+import argparse
+
+import fastg2protlib.fastg2protlib as fg
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Run peptides for fastg")
+    parser.add_argument("msgf", help="Path MSGF+ tabular results.")
+    parser.add_argument(
+        "-d",
+        "--dbname",
+        default="results.db",
+        help="Name for the results database. Defaults to results.db",
+    )
+    parser.add_argument(
+        "-f",
+        "--fdr",
+        default=0.10,
+        type=float,
+        help="FDR cutoff for accepting PSM validation.",
+    )
+    parser.add_argument(
+        "-x",
+        "--decoy_header",
+        default="XXX_",
+        help="String used for marking decoy proteins.",
+    )
+
+    args = parser.parse_args()
+    fg.verified_proteins(
+        args.msgf, fdr_level=0.10, decoy_header="XXX_", db_name=args.dbname
+    )