Galaxy |

Changeset 7:a7162e5281c1 (2023-11-19)

Previous changeset 6:ffe46a9b1124 (2023-10-19) Next changeset 8:5f1db71eceb2 (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 ffe46a9b1124 -r a7162e5281c1 matchms_networking_wrapper.py
--- a/matchms_networking_wrapper.py Thu Oct 19 15:27:34 2023 +0000
+++ b/matchms_networking_wrapper.py Sun Nov 19 14:38:21 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 ffe46a9b1124 -r a7162e5281c1 test-data/networking/test9.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/networking/test9.json Sun Nov 19 14:38:21 2023 +0000

[

b'@@ -0,0 +1,1 @@\n+{"__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 HEA'..b'], [91.0, 2.09], [95.0, 4.84], [96.0, 34.11], [97.0, 70.76], [98.0, 39.72], [99.0, 38.18], [100.0, 10.63], [101.0, 2.64], [106.0, 2.45], [107.0, 9.09], [108.0, 3.77], [109.0, 7.22], [111.0, 2.23], [125.0, 3.44], [126.0, 8.91], [127.0, 2.05], [128.0, 3.52], [131.0, 18.48], [132.0, 57.96], [133.0, 22.12], [134.0, 40.71], [135.0, 10.45], [136.0, 7.81], [160.0, 31.84], [161.0, 5.2], [162.0, 50.47], [163.0, 5.2], [164.0, 22.81], [166.0, 5.57], [167.0, 4.1], [168.0, 2.56], [169.0, 3.63], [195.0, 3.59], [196.0, 99.99], [197.0, 9.68], [198.0, 91.34], [199.0, 7.07], [200.0, 28.42], [201.0, 2.09], [202.0, 3.04]]}], "n_row": 10, "n_col": 10, "row": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9], "col": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9], "data": [[1.0000000000000024, 75], [0.04114774674057928, 31], [0.17710152190705433, 21], [0.17085661959581475, 23], [0.11820489901801184, 20], [0.14391353368113288, 23], [0.13424518317585743, 22], [0.16302184623396593, 20], [0.21713328957565026, 35], [0.22391237572749612, 33], [0.04114774674057928, 31], [1.0, 64], [0.1692734165324067, 21], [0.37067924709578426, 26], [0.24122621725708923, 18], [0.34662690976657284, 25], [0.31547293125797937, 21], [0.14589071396910847, 17], [0.17015501057278729, 33], [0.1966303491285214, 36], [0.17710152190705433, 21], [0.1692734165324067, 21], [1.0000000000000004, 36], [0.8642820607867123, 34], [0.9366364793708947, 31], [0.795613402953013, 34], [0.8810755426623336, 33], [0.9969145604816481, 32], [0.24599606721524553, 29], [0.45520965921035, 34], [0.17085661959581475, 23], [0.37067924709578426, 26], [0.8642820607867123, 34], [1.0000000000000002, 44], [0.9027134288963568, 31], [0.9307825814728448, 39], [0.9659576988957936, 36], [0.8509129853304047, 32], [0.3444673514346889, 35], [0.5173844798552759, 40], [0.11820489901801184, 20], [0.24122621725708923, 18], [0.9366364793708947, 31], [0.9027134288963568, 31], [0.9999999999999999, 33], [0.9213275590672286, 33], [0.9533942663967058, 31], [0.9433967711878457, 29], [0.21528371907496652, 25], [0.43217303166982113, 32], [0.14391353368113288, 23], [0.34662690976657284, 25], [0.795613402953013, 34], [0.9307825814728448, 39], [0.9213275590672286, 33], [0.9999999999999999, 42], [0.9407506729068541, 36], [0.7880157905029312, 30], [0.29259279016389883, 34], [0.4692783216223206, 40], [0.13424518317585743, 22], [0.31547293125797937, 21], [0.8810755426623336, 33], [0.9659576988957936, 36], [0.9533942663967058, 31], [0.9407506729068541, 36], [1.0000000000000004, 37], [0.8807090225247666, 31], [0.3180741423660751, 29], [0.5085408652886422, 35], [0.16302184623396593, 20], [0.14589071396910847, 17], [0.9969145604816481, 32], [0.8509129853304047, 32], [0.9433967711878457, 29], [0.7880157905029312, 30], [0.8807090225247666, 31], [1.0, 32], [0.23122737562146575, 26], [0.4454070549740881, 30], [0.21713328957565026, 35], [0.17015501057278729, 33], [0.24599606721524553, 29], [0.3444673514346889, 35], [0.21528371907496652, 25], [0.29259279016389883, 34], [0.3180741423660751, 29], [0.23122737562146575, 26], [0.9999999999999998, 65], [0.9575222360551329, 53], [0.22391237572749612, 33], [0.1966303491285214, 36], [0.45520965921035, 34], [0.5173844798552759, 40], [0.43217303166982113, 32], [0.4692783216223206, 40], [0.5085408652886422, 35], [0.4454070549740881, 30], [0.9575222360551329, 53], [0.9999999999999993, 66]], "dtype": [["CosineGreedy_0.1_0.0_1.0_scores", "<f8"], ["CosineGreedy_0.1_0.0_1.0_matches", "<i8"]]}\n\\ No newline at end of file\n'