Repository 'matchms_fingerprint_similarity'
hg clone https://toolshed.g2.bx.psu.edu/repos/recetox/matchms_fingerprint_similarity

Changeset 20:1ffbd537984f (2025-08-14)
Previous changeset 19:fe9f3cd0b8dd (2025-06-30)
Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a57d984a9850c1faa44b6948981eb1303881ba9c
modified:
matchms_split.py
test-data/convert/ms_lima_output.msp
b
diff -r fe9f3cd0b8dd -r 1ffbd537984f matchms_split.py
--- a/matchms_split.py Mon Jun 30 13:00:39 2025 +0000
+++ b/matchms_split.py Thu Aug 14 12:38:51 2025 +0000
b
@@ -2,12 +2,11 @@
 import itertools
 import os
 
-import matchms
+from matchms import Metadata
 from matchms.exporting import save_as_msp
 from matchms.importing import load_from_msp
 
-
-matchms.Metadata.set_key_replacements({})
+Metadata.set_key_replacements({})
 
 
 def make_outdir(outdir: str):
@@ -43,7 +42,7 @@
 listarg.add_argument('--filename', type=str)
 listarg.add_argument('--method', type=str)
 listarg.add_argument('--outdir', type=str)
-listarg.add_argument('--parameter', type=int)
+listarg.add_argument('--parameter', type=int, required=False)
 args = listarg.parse_args()
 outdir = args.outdir
 filename = args.filename
b
diff -r fe9f3cd0b8dd -r 1ffbd537984f test-data/convert/ms_lima_output.msp
--- a/test-data/convert/ms_lima_output.msp Mon Jun 30 13:00:39 2025 +0000
+++ b/test-data/convert/ms_lima_output.msp Thu Aug 14 12:38:51 2025 +0000
b
b'@@ -1,4 +1,5 @@\n NAME: Acephate\n+IONMODE: positive\n FORMULA: C4H10NO3PS\n INCHIKEY: YASYVMFAVPKPKE-SECBINFHSA-N\n SMILES: COP(=O)(N=C(O)C)SC\n@@ -25,6 +26,7 @@\n 173.5094 2353.0\n \n NAME: Carbaryl\n+IONMODE: positive\n FORMULA: C12H11NO2\n INCHIKEY: CVXBEEMKQHEXEN-UHFFFAOYSA-N\n SMILES: CN=C(Oc1cccc2c1cccc2)O\n@@ -36,6 +38,7 @@\n 145.06491 1326147.0\n \n NAME: Dicrotophos\n+IONMODE: positive\n FORMULA: C8H16NO5P\n INCHIKEY: VEENJGZXVHKXNB-UHFFFAOYSA-N\n SMILES: COP(=O)(OC(=CC(=O)N(C)C)C)OC\n@@ -51,6 +54,7 @@\n 238.08437 2973124.0\n \n NAME: Dimethoate\n+IONMODE: positive\n FORMULA: C5H12NO3PS2\n INCHIKEY: MCWXGJITAZMZEV-UHFFFAOYSA-N\n SMILES: CN=C(CSP(=S)(OC)OC)O\n@@ -69,6 +73,7 @@\n 230.00722 497851.0\n \n NAME: Dimethomorph\n+IONMODE: positive\n FORMULA: C21H22NO4Cl\n INCHIKEY: QNBTYORWCCMPQP-UHFFFAOYSA-N\n SMILES: COc1cc(ccc1OC)C(=CC(=O)N1CCOCC1)c1ccc(cc1)Cl\n@@ -101,6 +106,7 @@\n 301.06311 4060551.0\n \n NAME: Methamidophos\n+IONMODE: positive\n FORMULA: C2H8NO2PS\n INCHIKEY: NNKVPIKMPCQWCG-ZCFIWIBFSA-N\n SMILES: COP(=O)(SC)N\n@@ -115,6 +121,7 @@\n 127.99321 75837.0\n \n NAME: Mevinphos\n+IONMODE: positive\n FORMULA: C7H13O6P\n INCHIKEY: GEPDYQSQVLXLEU-UHFFFAOYSA-N\n SMILES: COC(=O)C=C(OP(=O)(OC)OC)C\n@@ -129,6 +136,7 @@\n 225.05209 101872.0\n \n NAME: Omethoate\n+IONMODE: positive\n FORMULA: C5H12NO4PS\n INCHIKEY: PZXOQEXFMJCDPG-UHFFFAOYSA-N\n SMILES: CN=C(CSP(=O)(OC)OC)O\n@@ -144,6 +152,7 @@\n 142.99275 4310988.0\n \n NAME: Temephos\n+IONMODE: positive\n FORMULA: C16H20O6P2S3\n INCHIKEY: WWJZWCUNLNYYAU-UHFFFAOYSA-N\n SMILES: COP(=S)(Oc1ccc(cc1)Sc1ccc(cc1)OP(=S)(OC)OC)OC\n@@ -198,6 +207,7 @@\n 387.9765 125383.0\n \n NAME: Trichlorfon\n+IONMODE: positive\n FORMULA: C4H8O4Cl3P\n INCHIKEY: NFACJZMKEDPNKN-VKHMYHEASA-N\n SMILES: COP(=O)(C(C(Cl)(Cl)Cl)O)OC\n@@ -212,6 +222,7 @@\n 127.01563 3150219.0\n \n NAME: Vamidothion\n+IONMODE: positive\n FORMULA: C8H18NO4PS2\n INCHIKEY: LESVOLZBIFDZGS-ZETCQYMHSA-N\n SMILES: CN=C(C(SCCSP(=O)(OC)OC)C)O\n@@ -225,6 +236,7 @@\n 288.04907 1456244.0\n \n NAME: Aldicarb sulfone\n+IONMODE: positive\n FORMULA: C7H14N2O4S\n INCHIKEY: YRRKLBAKDXSTNC-UHFFFAOYSA-N\n SMILES: CN=C(ON=CC(S(=O)(=O)C)(C)C)O\n@@ -244,6 +256,7 @@\n 223.07454 90546.0\n \n NAME: Benfuracarb\n+IONMODE: positive\n FORMULA: C20H30N2O5S\n INCHIKEY: FYZBOYWSHKHDMT-UHFFFAOYSA-N\n SMILES: CCOC(=O)CCN(C(C)C)SN(C(=O)Oc1cccc2c1OC(C2)(C)C)C\n@@ -276,6 +289,7 @@\n 195.04765 2265269.0\n \n NAME: Butoxycarboxim\n+IONMODE: positive\n FORMULA: C7H14N2O4S\n INCHIKEY: CTJBHIROCMPUKL-HOITVRGQSA-N\n SMILES: CN=C(ON=C(C(S(=O)(=O)C)C)C)O\n@@ -295,6 +309,7 @@\n 223.07454 90546.0\n \n NAME: Furathiocarb\n+IONMODE: positive\n FORMULA: C18H26N2O5S\n INCHIKEY: HAWJXYBZNNRMNO-UHFFFAOYSA-N\n SMILES: CCCCOC(=O)N(SN(C(=O)Oc1cccc2c1OC(C2)(C)C)C)C\n@@ -354,6 +369,7 @@\n 195.04765 11849349.0\n \n NAME: Methabenzthiazuron\n+IONMODE: positive\n FORMULA: C10H11N3OS\n INCHIKEY: RRVIAQKBTUQODI-UHFFFAOYSA-N\n SMILES: CN=C(N(c1nc2c(s1)cccc2)C)O\n@@ -372,6 +388,7 @@\n 165.04836 9598566.0\n \n NAME: Tebuthiuron\n+IONMODE: positive\n FORMULA: C9H16N4OS\n INCHIKEY: HBPDKDSFLXWOAE-UHFFFAOYSA-N\n SMILES: CN=C(N(c1nnc(s1)C(C)(C)C)C)O\n@@ -391,6 +408,7 @@\n 172.09081 12592908.0\n \n NAME: Thidiazuron\n+IONMODE: positive\n FORMULA: C9H8N4OS\n INCHIKEY: HFCYZXMHUIHAQI-UHFFFAOYSA-N\n SMILES: OC(=Nc1ccccc1)Nc1cnns1\n@@ -408,6 +426,7 @@\n 127.99126 615346.0\n \n NAME: Ethiofencarb\n+IONMODE: positive\n FORMULA: C11H15NO2S\n INCHIKEY: HEZNVIYQEUHLNI-UHFFFAOYSA-N\n SMILES: CCSCc1ccccc1OC(=NC)O\n@@ -424,6 +443,7 @@\n 147.93529 2678.0\n \n NAME: Methiocarb\n+IONMODE: positive\n FORMULA: C11H15NO2S\n INCHIKEY: YFBPRJGDJKVWAH-UHFFFAOYSA-N\n SMILES: CN=C(Oc1cc(C)c(c(c1)C)SC)O\n@@ -438,6 +458,7 @@\n 226.08951 145633.0\n \n NAME: Carbofuran\n+IONMODE: positive\n FORMULA: C12H15NO3\n INCHIKEY: DUEPRVBVGDRKAG-UHFFFAOYSA-N\n SMILES: CN=C(Oc1cccc2c1OC(C2)(C)C)O\n@@ -458,6 +479,7 @@\n 147.08089 104307.0\n \n NAME: Chloroxuron\n+IONMODE: positive\n FORMULA: C15H15N2O2Cl\n INCHIKEY: IVUXTESCPZUGJC-UHFFFAOYSA-N\n SMILES: Clc1ccc(cc1)Oc1ccc(cc1)NC(=O)N(C)C\n@@ -502,6 +524,7 @@\n 249.18484 96150.0\n \n NAME: Chlortoluron\n+IONMODE: positive\n FORMULA: C10H13N2OCl\n INCHIK'..b'4,7 @@\n 184.99236 249943.0\n \n NAME: Triflumizole\n+IONMODE: positive\n FORMULA: C15H15N3OClF3\n INCHIKEY: HSMVPDGQOIQYSR-UHFFFAOYSA-N\n SMILES: CCCOCC(=Nc1ccc(cc1C(F)(F)F)Cl)n1cncc1\n@@ -4376,6 +4527,7 @@\n 346.09351 955540.0\n \n NAME: Triticonazole\n+IONMODE: positive\n FORMULA: C17H20N3OCl\n INCHIKEY: PPDBOQMNKNNODG-QGZVFWFLSA-N\n SMILES: OC1(Cn2ncnc2)C(=Cc2ccc(cc2)Cl)CCC1(C)C\n@@ -4445,6 +4597,7 @@\n 196.12456 74697.0\n \n NAME: Spinetoram L\n+IONMODE: positive\n FORMULA: C43H69NO10\n INCHIKEY: KWVYSEWJJXXTEZ-GDMNSMANSA-N\n SMILES: CCOC1C(OC)C(OC2CC3C(C2)C(=CC2C3C=C3C2CC(=O)OC(CC)CCCC(C(C3=O)C)OC2CCC(C(O2)C)N(C)C)C)OC(C1OC)C\n@@ -4476,6 +4629,7 @@\n 213.09132 89441.0\n \n NAME: Emamectin benzoate\n+IONMODE: positive\n FORMULA: C49H75NO13\n INCHIKEY: GCKZANITAMOIAR-XWVCPFKXSA-N\n SMILES: CCC(C1OC2(C=CC1C)OC1CC=C(C)C(OC3CC(OC)C(C(O3)C)OC3CC(OC)C(C(O3)C)NC)C(C)C=CC=C3C4(C(C(=O)OC(C2)C1)C=C(C)C(C4OC3)O)O)C\n@@ -4497,6 +4651,7 @@\n 173.50876 230972.0\n \n NAME: Fenpropimorph\n+IONMODE: positive\n FORMULA: C20H33NO\n INCHIKEY: RYAUSSKQMZRMAI-ALOPSCKCSA-N\n SMILES: CC(Cc1ccc(cc1)C(C)(C)C)CN1CC(C)OC(C1)C\n@@ -4521,6 +4676,7 @@\n 304.26379 2555976.0\n \n NAME: Spirodiclofen\n+IONMODE: positive\n FORMULA: C21H24O4Cl2\n INCHIKEY: DTDSAWVUFPGDMX-UHFFFAOYSA-N\n SMILES: CCC(C(=O)OC1=C(C(=O)OC21CCCCC2)c1cc(Cl)cc(c1)Cl)(C)C\n@@ -4534,6 +4690,7 @@\n 411.11246 2380661.0\n \n NAME: Spinosad\n+IONMODE: positive\n FORMULA: C41H65NO10\n INCHIKEY: SRJQTHAZUNRMPR-SFGMUSMWSA-N\n SMILES: CCC1CCCC(OC2CCC(C(O2)C)N(C)C)C(C)C(=O)C2=CC3C(C2CC(=O)O1)C=CC1C3CC(C1)OC1OC(C)C(C(C1OC)OC)OC\n@@ -4568,6 +4725,7 @@\n 225.09103 339682.0\n \n NAME: Spirotetramat\n+IONMODE: positive\n FORMULA: C21H27NO5\n INCHIKEY: CLSVJBIHYWPGQY-UHFFFAOYSA-N\n SMILES: CCOC(=O)OC1=C(C(=NC21CCC(CC2)OC)O)c1cc(C)ccc1C\n@@ -4603,6 +4761,7 @@\n 302.17508 467268.0\n \n NAME: Spinetoram J\n+IONMODE: positive\n FORMULA: C42H69NO10\n INCHIKEY: GOENIMGKWNZVDA-RWGFPKGXSA-N\n SMILES: CCOC1C(OC)C(OC2CC3C(C2)C2C=C4C(C2CC3)CC(=O)OC(CC)CCCC(C(C4=O)C)OC2CCC(C(O2)C)N(C)C)OC(C1OC)C\n@@ -4632,6 +4791,7 @@\n 217.12222 236328.0\n \n NAME: Hydramethylnon\n+IONMODE: positive\n FORMULA: C25H24N4F6\n INCHIKEY: IQVNEKKDSLOHHK-UHFFFAOYSA-N\n SMILES: CC1(C)CNC(=NC1)NN=C(C=Cc1ccc(cc1)C(F)(F)F)C=Cc1ccc(cc1)C(F)(F)F\n@@ -4690,6 +4850,7 @@\n 495.20059 2433116.0\n \n NAME: Aminocarb_1\n+IONMODE: positive\n FORMULA: C11H16N2O2\n INCHIKEY: IMIDOCRTMDIQIJ-UHFFFAOYSA-N\n SMILES: CN=C(Oc1ccc(c(c1)C)N(C)C)O\n@@ -4705,6 +4866,7 @@\n 152.10725 186336.0\n \n NAME: Aminocarb_2\n+IONMODE: positive\n FORMULA: C11H16N2O2\n INCHIKEY: IMIDOCRTMDIQIJ-UHFFFAOYSA-N\n SMILES: CN=C(Oc1ccc(c(c1)C)N(C)C)O\n@@ -4720,6 +4882,7 @@\n 152.10725 242082.0\n \n NAME: Propamocarb_1\n+IONMODE: positive\n FORMULA: C9H20N2O2\n INCHIKEY: WZZLDXDUQPOXNW-UHFFFAOYSA-N\n SMILES: CCCOC(=NCCCN(C)C)O\n@@ -4732,6 +4895,7 @@\n 102.05516 5038638.0\n \n NAME: Propamocarb_2\n+IONMODE: positive\n FORMULA: C9H20N2O2\n INCHIKEY: WZZLDXDUQPOXNW-UHFFFAOYSA-N\n SMILES: CCCOC(=NCCCN(C)C)O\n@@ -4744,6 +4908,7 @@\n 102.05516 2507023.0\n \n NAME: Formetanate_1\n+IONMODE: positive\n FORMULA: C11H15N3O2\n INCHIKEY: MYPKGPZHHQEODQ-UHFFFAOYSA-N\n SMILES: CN=C(Oc1cccc(c1)N=CN(C)C)O\n@@ -4767,6 +4932,7 @@\n 208.52768 2170.0\n \n NAME: Formetanate_2\n+IONMODE: positive\n FORMULA: C11H15N3O2\n INCHIKEY: MYPKGPZHHQEODQ-UHFFFAOYSA-N\n SMILES: CN=C(Oc1cccc(c1)N=CN(C)C)O\n@@ -4792,6 +4958,7 @@\n 165.1024 263802.0\n \n NAME: Mexacarbate\n+IONMODE: positive\n FORMULA: C12H18N2O2\n INCHIKEY: YNEVBPNZHBAYOA-UHFFFAOYSA-N\n SMILES: CN=C(Oc1cc(C)c(c(c1)C)N(C)C)O\n@@ -4807,6 +4974,7 @@\n 166.12282 1541928.0\n \n NAME: Monceren\n+IONMODE: positive\n FORMULA: C19H21N2OCl\n INCHIKEY: OGYFATSSENRIKG-UHFFFAOYSA-N\n SMILES: Clc1ccc(cc1)CN(C(=Nc1ccccc1)O)C1CCCC1\n@@ -4822,6 +4990,7 @@\n 125.01532 37442116.0\n \n NAME: Desmedipham\n+IONMODE: positive\n FORMULA: C16H16N2O4\n INCHIKEY: WZJZMXBKUWKXTQ-UHFFFAOYSA-N\n SMILES: CCOC(=Nc1cccc(c1)OC(=Nc1ccccc1)O)O\n@@ -4835,6 +5004,7 @@\n 182.08162 6480130.0\n \n NAME: Phenmedipham\n+IONMODE: positive\n FORMULA: C16H16N2O4\n INCHIKEY: IDOWTHOLJBTAFI-UHFFFAOYSA-N\n SMILES: COC(=Nc1cccc(c1)OC(=Nc1cccc(c1)C)O)O\n'