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Changeset 5:811104b25490 (2023-11-19)

Previous changeset 4:73c902331bbc (2023-10-19) Next changeset 6:3fde8efbcf5a (2023-11-22)

Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e

modified:
matchms_networking_wrapper.py

added:
test-data/networking/test9.json

diff -r 73c902331bbc -r 811104b25490 matchms_networking_wrapper.py
--- a/matchms_networking_wrapper.py Thu Oct 19 15:24:22 2023 +0000
+++ b/matchms_networking_wrapper.py Sun Nov 19 14:39:19 2023 +0000

@@ -27,8 +27,11 @@
                                 score_cutoff=args.score_cutoff,
                                 link_method=args.link_method,
                                 keep_unconnected_nodes=args.keep_unconnected_nodes)
+    score_name = next((s for s in scores.score_names if args.score_name in s and "score" in s), None)
+    if score_name is None:
+        raise ValueError(f"Could not find any score name containing '{args.score_name}'.")

-    network.create_network(scores, args.score_name)
+    network.create_network(scores, score_name)
     network.export_to_file(filename=args.output_filename, graph_format=args.graph_format)

     return 0

diff -r 73c902331bbc -r 811104b25490 test-data/networking/test9.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/networking/test9.json Sun Nov 19 14:39:19 2023 +0000

[

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OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH", "license": "CC BY-NC-SA", "instrument": "VARIAN MAT-44", "smiles": "[O-1][N+1](=O)c(c1)cc([N+1]([O-1])=O)c(O)c1", "inchi": "InChI=1S/C6H4N2O5/c9-6-2-1-4(7(10)11)3-5(6)8(12)13/h1-3,9H", "smiles_2": "[H]OC1=C([H])C([H])=C(C([H])=C1N(=O)=O)N(=O)=O", "instrument_type": "EI-B", "ms_level": "MS1", "ionization_energy": "70 eV", "ion_type": "[M]+*", "ionization_mode": "positive", "last_auto-curation": "1495210335764", "molecular_formula": "C6H4N2O5", "total_exact_mass": "184.01202122799998", "num_peaks": "64", "compound_name": "2,4-DINITROPHENOL", "spectrum_id": "JP000002", "nominal_mass": "184.01202122799998", "precursor_mz": 0.0, "parent_mass": "184.01202", "peaks_json": [[51.0, 27.22], [52.0, 19.9], [53.0, 61.8], [54.0, 6.76], [55.0, 13.95], [56.0, 3.86], [57.0, 11.52], [60.0, 6.43], [61.0, 13.38], [62.0, 36.19], [63.0, 61.37], [64.0, 26.2], [65.0, 6.74], [66.0, 5.1], [67.0, 7.43], [68.0, 10.32], [69.0, 29.16], [70.0, 5.53], [71.0, 6.11], [73.0, 4.14], [74.0, 3.92], [75.0, 3.49], [76.0, 4.33], [77.0, 6.21], [78.0, 5.1], [79.0, 35.07], [80.0, 9.85], [81.0, 16.0], [82.0, 5.37], [83.0, 6.13], [84.0, 2.96], [85.0, 3.0], [90.0, 12.01], [91.0, 53.25], [92.0, 28.32], [93.0, 18.25], [94.0, 3.51], [95.0, 6.41], [96.0, 5.43], [97.0, 5.12], [98.0, 2.43], [105.0, 3.76], [106.0, 6.35], [107.0, 38.97], [108.0, 7.11], [109.0, 3.98], [111.0, 2.63], [120.0, 2.12], [121.0, 4.45], [122.0, 4.0], [123.0, 3.14], [126.0, 2.12], [136.0, 2.77], [137.0, 3.14], [138.0, 3.55], [149.0, 4.12], [153.0, 4.02], [154.0, 39.3], [155.0, 3.16], [168.0, 3.29], [183.0, 3.26], [184.0, 99.99], [185.0, 8.17], [186.0, 1.34]]}, {"synonym": "3,4-DICHLOROPHENOL", "inchikey": "WDNBURPWRNALGP-UHFFFAOYSA-N", "formula": "C6H4Cl2O", "author": "KOGA M, UNIV. 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