diff msmetaenhancer_wrapper.py @ 0:ce612a11b455 draft

"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msmetaenhancer_wrapper.py	Tue Mar 22 15:33:37 2022 +0000
@@ -0,0 +1,44 @@
+import argparse
+import asyncio
+import sys
+
+
+from MSMetaEnhancer import Application
+
+
+def main(argv):
+    parser = argparse.ArgumentParser(description="Annotate MSP file.")
+    parser.add_argument("--input_file", type=str, help="Path to query spectra file in MSP format.")
+    parser.add_argument("--output_file", type=str, help="Path to output spectra file.")
+    parser.add_argument("--jobs", type=str, help="Sequence of conversion jobs to be used.")
+    parser.add_argument("--log_file", type=str, help="Path to log with details of the annotation process.")
+    args = parser.parse_args()
+
+    app = Application(log_file=args.log_file)
+
+    # import .msp file
+    app.load_spectra(args.input_file, file_format='msp')
+
+    # curate given metadata
+    app.curate_spectra()
+
+    # specify requested services and jobs
+    services = ['PubChem', 'CTS', 'CIR', 'NLM', 'RDKit', 'IDSM', 'BridgeDB']
+
+    if len(args.jobs) != 0:
+        jobs = []
+        for job in args.jobs.split(","):
+            if len(job) != 0:
+                jobs.append(job.split())
+        asyncio.run(app.annotate_spectra(services, jobs))
+    else:
+        # execute without jobs parameter to run all possible jobs
+        asyncio.run(app.annotate_spectra(services))
+
+    # export .msp file
+    app.save_spectra(args.output_file, file_format="msp")
+    return 0
+
+
+if __name__ == "__main__":
+    main(argv=sys.argv[1:])