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changeset 13:3dad3f53402f draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
author recetox
date Sun, 19 Nov 2023 14:36:56 +0000
parents 1e58bf51a0e5
children 184e5f0b4671
files matchms_networking_wrapper.py test-data/networking/test9.json
diffstat 2 files changed, 5 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/matchms_networking_wrapper.py	Thu Oct 19 15:23:20 2023 +0000
+++ b/matchms_networking_wrapper.py	Sun Nov 19 14:36:56 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/networking/test9.json	Sun Nov 19 14:36:56 2023 +0000
@@ -0,0 +1,1 @@
+{"__Scores__": true, "is_symmetric": false, "references": [{"synonym": "1-NITROPYRENE", "inchikey": "ALRLPDGCPYIVHP-UHFFFAOYSA-N", "formula": "C16H9NO2", "author": "KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH", "license": "CC BY-NC-SA", "instrument": "VARIAN MAT-44", "smiles": "[O-1][N+1](=O)c(c4)c(c1)c(c3c4)c(c2cc3)c(ccc2)c1", "inchi": "InChI=1S/C16H9NO2/c18-17(19)14-9-7-12-5-4-10-2-1-3-11-6-8-13(14)16(12)15(10)11/h1-9H", "smiles_2": "[H]C=1C([H])=C2C([H])=C([H])C3=C([H])C([H])=C(C=4C([H])=C([H])C(C1[H])=C2C34)N(=O)=O", "instrument_type": "EI-B", "ms_level": "MS1", "ionization_energy": "70 eV", "ion_type": "[M]+*", "ionization_mode": "positive", "last_auto-curation": "1495210335755", "molecular_formula": "C16H9NO2", "total_exact_mass": "247.063328528", "num_peaks": "75", "compound_name": "1-NITROPYRENE", "spectrum_id": "JP000001", "nominal_mass": "247.063328528", "precursor_mz": 0.0, "parent_mass": "247.06333", "peaks_json": [[51.0, 2.66], [55.0, 8.0], [57.0, 7.33], [58.0, 1.33], [59.0, 1.33], [60.0, 14.0], [61.0, 1.33], [62.0, 3.33], [63.0, 3.33], [66.0, 1.33], [68.0, 8.66], [70.0, 2.0], [72.0, 5.33], [73.0, 7.33], [74.0, 3.33], [75.0, 2.66], [76.0, 2.0], [78.0, 1.33], [80.0, 4.0], [81.0, 2.0], [82.0, 1.33], [83.0, 3.33], [86.0, 12.66], [87.0, 8.66], [92.0, 2.0], [93.0, 10.0], [94.0, 6.0], [98.0, 14.66], [99.0, 83.33], [100.0, 60.66], [104.0, 4.0], [107.0, 1.33], [108.0, 1.33], [110.0, 3.33], [112.0, 1.33], [113.0, 1.33], [115.0, 1.33], [116.0, 1.33], [120.0, 1.33], [122.0, 4.0], [123.0, 2.66], [124.0, 2.66], [125.0, 2.0], [126.0, 1.33], [134.0, 1.33], [135.0, 2.0], [137.0, 1.33], [147.0, 1.33], [149.0, 2.0], [150.0, 4.66], [151.0, 3.33], [159.0, 2.0], [162.0, 2.0], [163.0, 2.66], [173.0, 2.0], [174.0, 8.66], [175.0, 4.66], [177.0, 2.0], [187.0, 5.33], [188.0, 4.66], [189.0, 56.66], [190.0, 12.0], [191.0, 16.66], [198.0, 10.66], [199.0, 9.33], [200.0, 72.66], [201.0, 99.99], [202.0, 16.0], [203.0, 1.33], [207.0, 1.33], [214.0, 1.33], [217.0, 25.33], [218.0, 5.33], [247.0, 52.66], [248.0, 10.16]]}, {"synonym": "2,4-DINITROPHENOL", "inchikey": "UFBJCMHMOXMLKC-UHFFFAOYSA-N", "formula": "C6H4N2O5", "author": "KOGA M, UNIV. 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. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH", "license": "CC BY-NC-SA", "instrument": "VARIAN MAT-44", "smiles": "Oc(c1)cc(Cl)c(Cl)c1", "inchi": "InChI=1S/C6H4Cl2O/c7-5-2-1-4(9)3-6(5)8/h1-3,9H", "smiles_2": "[H]OC1=C([H])C([H])=C(Cl)C(Cl)=C1[H]", "instrument_type": "EI-B", "ms_level": "MS1", "ionization_energy": "70 eV", "ion_type": "[M]+*", "ionization_mode": "positive", "last_auto-curation": "1495210335820", "molecular_formula": "C6H4Cl2O", "total_exact_mass": "161.963920108", "num_peaks": "36", "compound_name": "3,4-DICHLOROPHENOL", "spectrum_id": "JP000003", "nominal_mass": "161.963920108", "precursor_mz": 0.0, "parent_mass": "161.96392", "peaks_json": [[51.0, 2.25], [53.0, 6.4], [60.0, 4.13], [61.0, 9.78], [62.0, 20.36], [63.0, 32.41], [64.0, 5.58], [71.0, 2.16], [72.0, 8.31], [73.0, 13.57], [74.0, 6.23], [75.0, 5.23], [81.0, 8.28], [82.0, 5.27], [83.0, 2.81], [91.0, 2.06], [97.0, 6.25], [98.0, 25.55], [99.0, 33.74], [100.0, 9.84], [101.0, 12.32], [107.0, 2.31], [109.0, 2.08], [126.0, 7.67], [127.0, 3.67], [128.0, 2.81], [133.0, 5.09], [134.0, 7.44], [135.0, 3.61], [136.0, 4.75], [161.0, 3.6], [162.0, 99.99], [163.0, 8.7], [164.0, 62.28], [165.0, 4.54], [166.0, 9.78]]}, {"synonym": "2,5-DICHLOROPHENOL", "inchikey": "RANCECPPZPIPNO-UHFFFAOYSA-N", "formula": "C6H4Cl2O", "author": "KOGA M, UNIV. 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OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH", "license": "CC BY-NC-SA", "instrument": "VARIAN MAT-44", "smiles": "Clc(c1)c(O)c(Cl)cc1", "inchi": "InChI=1S/C6H4Cl2O/c7-4-2-1-3-5(8)6(4)9/h1-3,9H", "smiles_2": "[H]OC=1C(Cl)=C([H])C([H])=C([H])C1Cl", "instrument_type": "EI-B", "ms_level": "MS1", "ionization_energy": "70 eV", "ion_type": "[M]+*", "ionization_mode": "positive", "last_auto-curation": "1495210335848", "molecular_formula": "C6H4Cl2O", "total_exact_mass": "161.963920108", "num_peaks": "33", "compound_name": "2,6-DICHLOROPHENOL", "spectrum_id": "JP000005", "nominal_mass": "161.963920108", "precursor_mz": 0.0, "parent_mass": "161.96392", "peaks_json": [[53.0, 7.25], [60.0, 3.0], [61.0, 8.88], [62.0, 17.84], [63.0, 70.92], [64.0, 8.02], [65.0, 2.01], [72.0, 5.48], [73.0, 12.35], [74.0, 4.63], [75.0, 4.81], [81.0, 6.73], [82.0, 4.37], [83.0, 2.09], [91.0, 3.83], [97.0, 7.27], [98.0, 34.04], [99.0, 15.04], [100.0, 13.17], [101.0, 4.37], [107.0, 2.61], [125.0, 2.01], [126.0, 33.42], [127.0, 3.34], [128.0, 11.41], [133.0, 3.34], [135.0, 2.17], [161.0, 2.35], [162.0, 99.99], [163.0, 8.23], [164.0, 63.43], [165.0, 4.35], [166.0, 9.91]]}, {"synonym": "2,3-DICHLOROPHENOL", "inchikey": "UMPSXRYVXUPCOS-UHFFFAOYSA-N", "formula": "C6H4Cl2O", "author": "KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH", "license": "CC BY-NC-SA", "instrument": "VARIAN MAT-44", "smiles": "Oc(c1)c(Cl)c(Cl)cc1", "inchi": "InChI=1S/C6H4Cl2O/c7-4-2-1-3-5(9)6(4)8/h1-3,9H", "smiles_2": "[H]OC=1C([H])=C([H])C([H])=C(Cl)C1Cl", "instrument_type": "EI-B", "ms_level": "MS1", "ionization_energy": "70 eV", "ion_type": "[M]+*", "ionization_mode": "positive", "last_auto-curation": "1495210335870", "molecular_formula": "C6H4Cl2O", "total_exact_mass": "161.963920108", "num_peaks": "42", "compound_name": "2,3-DICHLOROPHENOL", "spectrum_id": "JP000006", "nominal_mass": "161.963920108", "precursor_mz": 0.0, "parent_mass": "161.96392", "peaks_json": [[51.0, 4.43], [53.0, 10.39], [60.0, 9.21], [61.0, 24.93], [62.0, 43.19], [63.0, 99.99], [64.0, 12.57], [65.0, 4.81], [66.0, 3.39], [71.0, 3.67], [72.0, 15.34], [73.0, 25.07], [74.0, 11.84], [75.0, 8.79], [81.0, 4.78], [82.0, 3.25], [83.0, 2.63], [84.0, 3.87], [85.0, 2.49], [87.0, 5.09], [89.0, 2.21], [91.0, 6.02], [96.0, 3.11], [97.0, 12.05], [98.0, 35.88], [99.0, 22.09], [100.0, 13.5], [101.0, 6.26], [107.0, 3.33], [109.0, 2.73], [125.0, 3.11], [126.0, 59.16], [127.0, 5.61], [128.0, 19.32], [133.0, 5.33], [135.0, 2.84], [161.0, 2.52], [162.0, 68.96], [163.0, 6.51], [164.0, 51.64], [165.0, 2.9], [166.0, 7.58]]}, {"synonym": "2,4-DICHLOROPHENOL", "inchikey": "HFZWRUODUSTPEG-UHFFFAOYSA-N", "formula": "C6H4Cl2O", "author": "KOGA M, UNIV. OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH", "license": "CC BY-NC-SA", "instrument": "VARIAN MAT-44", "smiles": "Oc(c1)c(Cl)cc(Cl)c1", "inchi": "InChI=1S/C6H4Cl2O/c7-4-1-2-6(9)5(8)3-4/h1-3,9H", "smiles_2": "[H]OC1=C([H])C([H])=C(Cl)C([H])=C1Cl", "instrument_type": "EI-B", "ms_level": "MS1", "ionization_energy": "70 eV", "ion_type": "[M]+*", "ionization_mode": "positive", "last_auto-curation": "1495210335864", "molecular_formula": "C6H4Cl2O", "total_exact_mass": "161.963920108", "num_peaks": "37", "compound_name": "2,4-DICHLOROPHENOL", "spectrum_id": "JP000007", "nominal_mass": "161.963920108", "precursor_mz": 0.0, "parent_mass": "161.96392", "peaks_json": [[51.0, 3.07], [53.0, 12.34], [60.0, 6.21], [61.0, 19.31], [62.0, 35.08], [63.0, 99.99], [64.0, 10.24], [66.0, 2.25], [71.0, 3.05], [72.0, 10.59], [73.0, 19.52], [74.0, 8.59], [75.0, 6.44], [81.0, 6.82], [82.0, 4.45], [83.0, 2.77], [84.0, 2.03], [91.0, 2.34], [96.0, 3.78], [97.0, 31.79], [98.0, 38.03], [99.0, 21.59], [100.0, 13.06], [101.0, 4.67], [125.0, 4.82], [126.0, 20.32], [127.0, 3.76], [128.0, 7.38], [133.0, 4.02], [134.0, 2.72], [135.0, 2.64], [161.0, 19.22], [162.0, 94.19], [163.0, 15.34], [164.0, 55.32], [165.0, 5.54], [166.0, 9.19]]}, {"synonym": "3,5-DICHLOROPHENOL", "inchikey": "VPOMSPZBQMDLTM-UHFFFAOYSA-N", "formula": "C6H4Cl2O", "author": "KOGA M, UNIV. 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\ No newline at end of file