# HG changeset patch
# User recetox
# Date 1751986127 0
# Node ID 07b7a10129168ebe19c4d19eb3c8aa9f4a6db4e7

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/wtv commit 99dee7aed6d881ca831d208a34d957b8b1f021d1

diff -r 000000000000 -r 07b7a1012916 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Jul 08 14:48:47 2025 +0000
@@ -0,0 +1,27 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.1.0</token>
+    
+    <xml name="creator">
+        <creator>
+            <person
+                givenName="Frank"
+                familyName="Acquaye"
+                url="https://github.com/acquayefrank"
+                identifier="0000-0002-9465-4018" />
+            <person
+                givenName="Helge"
+                familyName="Hecht"
+                url="https://github.com/hechth"
+                identifier="0000-0001-6744-996X" />
+            <organization
+                url="https://www.recetox.muni.cz/"
+                email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
+                name="RECETOX MUNI" />
+        </creator>
+    </xml>
+    <xml name="annotation">
+        <xrefs>
+            <xref type="bio.tools">wtv</xref>
+        </xrefs>
+    </xml>
+</macros>
\ No newline at end of file
diff -r 000000000000 -r 07b7a1012916 test-data/esi_spectra.msp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/esi_spectra.msp	Tue Jul 08 14:48:47 2025 +0000
@@ -0,0 +1,432 @@
+NAME: Hydrochlorothiazide
+SCANNUMBER: 1166
+RETENTIONTIME: 1.657244
+PRECURSORMZ: 297.9721
+PRECURSORTYPE: [M+H]+
+IONMODE: Positive
+SPECTRUMTYPE: Centroid
+FORMULA: C7H8ClN3O4S2
+INCHIKEY: JZUFKLXOESDKRF-UHFFFAOYSA-N
+INCHI: 
+SMILES: NS(=O)(=O)C1=CC2=C(NCNS2(=O)=O)C=C1Cl
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+COLLISIONENERGY: 
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+INSTRUMENTTYPE: LC-ESI-Orbitrap
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMMENT: 
+Num Peaks: 60
+87.22046	953
+90.03336	670
+90.03405	2282	"Theoretical m/z 90.034374, Mass diff 0 (0 ppm), Formula C6H4N"
+91.01784	9223
+91.04161	1407
+94.9298	975
+98.99949	2739
+104.95585	1568
+106.02885	1722	"Theoretical m/z 106.029289, Mass diff 0 (0 ppm), Formula C6H4NO"
+106.05258	2061
+107.99039	7366	"Theoretical m/z 107.990795, Mass diff 0 (0 ppm), Formula C5H2NS"
+113.88227	1438
+114.01056	5858	"Theoretical m/z 114.011052, Mass diff 0 (0 ppm), Formula C5H5ClN"
+114.99441	2017
+117.04485	2652	"Theoretical m/z 117.045273, Mass diff 0 (0 ppm), Formula C7H5N2"
+118.05248	9175
+121.03988	2581	"Theoretical m/z 121.040188, Mass diff 0 (0 ppm), Formula C6H5N2O"
+122.04753	2458
+122.09386	1520
+123.99489	4236	"Theoretical m/z 123.994851, Mass diff 0 (0.31 ppm), SMILES ClC1=CC=CC(N)=C1, Annotation [C6H6ClN-3H]+, Rule of HR True"
+124.00898	2045
+124.03937	2584	"Theoretical m/z 124.039853, Mass diff 0 (0 ppm), Formula C6H6NO2"
+125.0026	2665	"Theoretical m/z 125.002676, Mass diff 0 (0.61 ppm), SMILES ClC1=CC=CC(N)=C1, Annotation [C6H6ClN-2H]+, Rule of HR False"
+128.99747	3110	"Theoretical m/z 128.997003, Mass diff -0.001 (0 ppm), Formula H5N2O4S"
+129.02145	7805	"Theoretical m/z 129.021951, Mass diff 0 (0 ppm), Formula C5H6ClN2"
+130.00562	5031	"Theoretical m/z 130.005966, Mass diff 0 (0 ppm), Formula C5H5ClNO"
+131.9669	3817	"Theoretical m/z 131.967473, Mass diff 0 (0 ppm), Formula C4H3ClNS"
+139.9897	14215	"Theoretical m/z 139.990316, Mass diff 0 (0 ppm), Formula C6H3ClNO"
+141.95038	1025
+141.95129	2743	"Theoretical m/z 141.951823, Mass diff 0 (0 ppm), Formula C5HClNS"
+142.00533	16155	"Theoretical m/z 142.005966, Mass diff 0 (0 ppm), Formula C6H5ClNO"
+142.95927	6240
+142.98956	5304	"Theoretical m/z 142.989982, Mass diff 0 (0 ppm), Formula C6H4ClO2"
+143.96692	5824	"Theoretical m/z 143.967473, Mass diff 0 (0 ppm), Formula C5H3ClNS"
+147.92903	1713	"Theoretical m/z 147.929373, Mass diff 0 (0 ppm), Formula H3ClNO2S2"
+151.99007	1983	"Theoretical m/z 151.990316, Mass diff 0 (0 ppm), Formula C7H3ClNO"
+152.9978	22015
+154.0197	4571
+155.0006	5584	"Theoretical m/z 155.001215, Mass diff 0 (0 ppm), Formula C6H4ClN2O"
+155.9846	13898	"Theoretical m/z 155.985231, Mass diff 0 (0 ppm), Formula C6H3ClNO2"
+157.01656	15861	"Theoretical m/z 157.016865, Mass diff 0 (0 ppm), Formula C6H6ClN2O"
+158.00012	13511	"Theoretical m/z 158.000881, Mass diff 0 (0 ppm), Formula C6H5ClNO2"
+169.01605	2361	"Theoretical m/z 169.016865, Mass diff 0 (0 ppm), Formula C7H6ClN2O"
+170.00043	2572	"Theoretical m/z 170.000881, Mass diff 0 (0 ppm), Formula C7H5ClNO2"
+171.96185	8619	"Theoretical m/z 171.962387, Mass diff 0 (0 ppm), Formula C6H3ClNOS"
+172.94588	4072	"Theoretical m/z 172.945855, Mass diff 0 (0.14 ppm), SMILES O=S(=O)C=1C=CC=CC1Cl, Annotation [C6H5ClO2S-3H]+, Rule of HR True"
+172.96968	6016	"Theoretical m/z 172.969074, Mass diff -0.001 (0 ppm), Formula CH5N2O4S2"
+173.01122	12248	"Theoretical m/z 173.01178, Mass diff 0 (0 ppm), Formula C6H6ClN2O2"
+173.99564	7545	"Theoretical m/z 173.995796, Mass diff 0 (0 ppm), Formula C6H5ClNO3"
+185.17621	1781
+187.95688	9648	"Theoretical m/z 187.95675, Mass diff 0 (0.69 ppm), SMILES O=S(=O)(N)C=1C=CC=CC1Cl, Annotation [C6H6ClNO2S-3H]+, Rule of HR True"
+188.96507	4401
+203.95193	6739	"Theoretical m/z 203.952217, Mass diff 0 (0 ppm), Formula C6H3ClNO3S"
+204.98299	11600	"Theoretical m/z 204.983295, Mass diff 0 (1.49 ppm), SMILES O=S(=O)(N)C1=CC=C(N)C=C1Cl, Annotation [C6H7ClN2O2S-H]+, Rule of HR True"
+220.97833	11703	"Theoretical m/z 220.978766, Mass diff 0 (0 ppm), Formula C6H6ClN2O3S"
+232.97527	1187
+232.97813	9081	"Theoretical m/z 232.978766, Mass diff 0 (0 ppm), Formula C7H6ClN2O3S"
+244.92268	1951
+252.94824	1201
+267.99866	3112
+
+COMPOUND_NAME: Levodopa_1
+SCANNUMBER: 727
+RETENTIONTIME: 0.7128666
+PRECURSORMZ: 198.0762
+PRECURSORTYPE: [M+H]+
+IONMODE: Positive
+SPECTRUMTYPE: Centroid
+FORMULA: C9H11NO4
+INCHIKEY: WTDRDQBEARUVNC-LURJTMIESA-N
+INCHI: 
+SMILES: N[C@@H](CC1=CC=C(O)C(O)=C1)C(O)=O
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+COLLISIONENERGY: 
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+INSTRUMENTTYPE: LC-ESI-Orbitrap
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMMENT: 
+Num Peaks: 15
+89.0386	25593
+91.05419	39312
+93.03366	93075	"Theoretical m/z 93.033489, Mass diff 0 (1.84 ppm), SMILES OC=1C=CC=CC1, Annotation [C6H6O-H]+, Rule of HR True"
+95.04929	41730	"Theoretical m/z 95.049139, Mass diff 0 (1.59 ppm), SMILES OC=1C=CC=CC1, Annotation [C6H6O+H]+, Rule of HR True"
+105.04477	33694
+106.06517	110237	"Theoretical m/z 106.065674, Mass diff 0 (0 ppm), Formula C7H8N"
+107.04907	537691
+109.02843	43567	"Theoretical m/z 109.028408, Mass diff 0 (0.2 ppm), SMILES OC=1C=CC=CC1O, Annotation [C6H6O2-H]+, Rule of HR True"
+111.04405	232622	"Theoretical m/z 111.044058, Mass diff 0 (0.07 ppm), SMILES OC=1C=CC=CC1O, Annotation [C6H6O2+H]+, Rule of HR True"
+117.03362	15773	"Theoretical m/z 117.033492, Mass diff 0 (1.09 ppm), SMILES OC1=CC=CC(=C1)CC, Annotation [C8H10O-5H]+, Rule of HR True"
+123.04398	28629
+134.05994	138556	"Theoretical m/z 134.060037, Mass diff 0 (0.72 ppm), SMILES OC1=CC=CC(=C1)CCN, Annotation [C8H11NO-3H]+, Rule of HR True"
+135.04385	178345
+139.03883	42804	"Theoretical m/z 139.039519, Mass diff 0 (0 ppm), Formula C7H7O3"
+152.07054	57178	"Theoretical m/z 152.070606, Mass diff 0 (0.43 ppm), SMILES OC1=CC=C(C=C1O)CCN, Annotation [C8H11NO2-H]+, Rule of HR True"
+
+NAME: Levodopa_2
+SCANNUMBER: 1076
+RETENTIONTIME: 1.048427
+PRECURSORMZ: 198.0762
+PRECURSORTYPE: [M+H]+
+IONMODE: Positive
+SPECTRUMTYPE: Centroid
+FORMULA: C9H11NO4
+INCHIKEY: WTDRDQBEARUVNC-LURJTMIESA-N
+INCHI: 
+SMILES: N[C@@H](CC1=CC=C(O)C(O)=C1)C(O)=O
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+COLLISIONENERGY: 
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+INSTRUMENTTYPE: LC-ESI-Orbitrap
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMMENT: 
+Num Peaks: 15
+89.0386	40545
+91.05419	69038
+93.03366	116301	"Theoretical m/z 93.033489, Mass diff 0 (1.84 ppm), SMILES OC=1C=CC=CC1, Annotation [C6H6O-H]+, Rule of HR True"
+95.04929	93288	"Theoretical m/z 95.049139, Mass diff 0 (1.59 ppm), SMILES OC=1C=CC=CC1, Annotation [C6H6O+H]+, Rule of HR True"
+105.04477	61069
+106.06517	201881	"Theoretical m/z 106.065674, Mass diff 0 (0 ppm), Formula C7H8N"
+107.04907	1016048
+109.02843	80781	"Theoretical m/z 109.028408, Mass diff 0 (0.2 ppm), SMILES OC=1C=CC=CC1O, Annotation [C6H6O2-H]+, Rule of HR True"
+111.04405	504774	"Theoretical m/z 111.044058, Mass diff 0 (0.07 ppm), SMILES OC=1C=CC=CC1O, Annotation [C6H6O2+H]+, Rule of HR True"
+117.03361	31769	"Theoretical m/z 117.033492, Mass diff 0 (1.01 ppm), SMILES OC1=CC=CC(=C1)CC, Annotation [C8H10O-5H]+, Rule of HR True"
+123.04398	47243
+134.05994	268309	"Theoretical m/z 134.060037, Mass diff 0 (0.72 ppm), SMILES OC1=CC=CC(=C1)CCN, Annotation [C8H11NO-3H]+, Rule of HR True"
+135.04385	343216
+139.03883	91801	"Theoretical m/z 139.039519, Mass diff 0 (0 ppm), Formula C7H7O3"
+152.07054	107058	"Theoretical m/z 152.070606, Mass diff 0 (0.43 ppm), SMILES OC1=CC=C(C=C1O)CCN, Annotation [C8H11NO2-H]+, Rule of HR True"
+
+NAME: Triamterene
+SCANNUMBER: 1192
+RETENTIONTIME: 2.533905
+PRECURSORMZ: 254.115
+PRECURSORTYPE: [M+H]+
+IONMODE: Positive
+SPECTRUMTYPE: Centroid
+FORMULA: C12H11N7
+INCHIKEY: FNYLWPVRPXGIIP-UHFFFAOYSA-N
+INCHI: 
+SMILES: NC1=NC(N)=C2N=C(C(N)=NC2=N1)C1=CC=CC=C1
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+COLLISIONENERGY: 
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+INSTRUMENTTYPE: LC-ESI-Orbitrap
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMMENT: 
+Num Peaks: 16
+104.04955	2668825	"Theoretical m/z 104.049472, Mass diff 0 (0.75 ppm), SMILES N=CC=1C=CC=CC1, Annotation [C7H7N-H]+, Rule of HR True"
+116.04969	358755	"Theoretical m/z 116.049478, Mass diff 0 (1.83 ppm), SMILES N=C(C=1C=CC=CC1)C, Annotation [C8H9N-3H]+, Rule of HR True"
+141.04509	292752	"Theoretical m/z 141.044723, Mass diff 0 (2.6 ppm), SMILES N=CCN=CC=1C=CC=CC1, Annotation [C9H10N2-5H]+, Rule of HR True"
+143.06067	1538683	"Theoretical m/z 143.060373, Mass diff 0 (2.08 ppm), SMILES N=CCN=CC=1C=CC=CC1, Annotation [C9H10N2-3H]+, Rule of HR True"
+168.05592	2335276	"Theoretical m/z 168.055627, Mass diff 0 (1.74 ppm), SMILES N=C1N=CC(=NC1)C2=CC=CC=C2, Annotation [C10H9N3-3H]+, Rule of HR True"
+183.06677	471766	"Theoretical m/z 183.066522, Mass diff 0 (1.35 ppm), SMILES N=C1N=C(N)C(=NC1)C2=CC=CC=C2, Annotation [C10H10N4-3H]+, Rule of HR True"
+185.08218	548064	"Theoretical m/z 185.082172, Mass diff 0 (0.04 ppm), SMILES N=C1N=C(N)C(=NC1)C2=CC=CC=C2, Annotation [C10H10N4-H]+, Rule of HR True"
+195.06664	4212438	"Theoretical m/z 195.066522, Mass diff 0 (0.61 ppm), SMILES N=C1N=C(N)C(=NC1=C)C2=CC=CC=C2, Annotation [C11H10N4-3H]+, Rule of HR True"
+210.07739	2065514	"Theoretical m/z 210.077417, Mass diff 0 (0.13 ppm), SMILES N=C1N=C(N)C(=NC1=CN)C2=CC=CC=C2, Annotation [C11H11N5-3H]+, Rule of HR True"
+212.09305	1847442	"Theoretical m/z 212.093067, Mass diff 0 (0.08 ppm), SMILES N=C1N=C(N)C(=NC1=CN)C2=CC=CC=C2, Annotation [C11H11N5-H]+, Rule of HR True"
+213.07713	471809
+220.06161	451533	"Theoretical m/z 220.061776, Mass diff 0 (0.76 ppm), SMILES N=1C=NC2=NC(N)=C(N=C2C1)C3=CC=CC=C3, Annotation [C12H9N5-3H]+, Rule of HR True"
+227.10378	739576	"Theoretical m/z 227.103962, Mass diff 0 (0.8 ppm), SMILES N=C(N=C1N=C(N)C(=NC1)C2=CC=CC=C2)N, Annotation [C11H12N6-H]+, Rule of HR True"
+237.0887	19002528	"Theoretical m/z 237.088321, Mass diff 0 (1.6 ppm), SMILES N1=CN=C(N)C2=NC(=C(N=C12)N)C3=CC=CC=C3, Annotation [C12H10N6-H]+, Rule of HR True"
+238.07248	224238
+254.11499	8105778	"Theoretical m/z 254.114866, Mass diff 0 (0.49 ppm), SMILES N1=C(N=C(N)C2=NC(=C(N=C12)N)C3=CC=CC=C3)N, Annotation [C12H11N7+H]+, Rule of HR True"
+
+NAME: Naproxen
+SCANNUMBER: 1575
+RETENTIONTIME: 6.590834
+PRECURSORMZ: 231.1017
+PRECURSORTYPE: [M+H]+
+IONMODE: Positive
+SPECTRUMTYPE: Centroid
+FORMULA: C14H14O3
+INCHIKEY: CMWTZPSULFXXJA-SECBINFHSA-N
+INCHI: 
+SMILES: COC1=CC2=CC=C(C=C2C=C1)[C@@H](C)C(O)=O
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+COLLISIONENERGY: 
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+INSTRUMENTTYPE: LC-ESI-Orbitrap
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMMENT: 
+Num Peaks: 22
+115.05428	163776	"Theoretical m/z 115.054775, Mass diff 0 (0 ppm), Formula C9H7"
+128.06198	81103	"Theoretical m/z 128.062058, Mass diff 0 (0.61 ppm), SMILES C=1C=CC=2C=CC=CC2C1, Annotation [C10H8]+, Rule of HR False"
+129.06979	94854	"Theoretical m/z 129.069883, Mass diff 0 (0.72 ppm), SMILES C=1C=CC=2C=CC=CC2C1, Annotation [C10H8+H]+, Rule of HR True"
+141.06979	155903	"Theoretical m/z 141.069873, Mass diff 0 (0.59 ppm), SMILES C=1C=CC=2C=C(C=CC2C1)C, Annotation [C11H10-H]+, Rule of HR True"
+142.07748	229986
+143.04916	46601	"Theoretical m/z 143.049137, Mass diff 0 (0.16 ppm), SMILES OC=1C=CC=2C=CC=CC2C1, Annotation [C10H8O-H]+, Rule of HR True"
+144.05682	18823
+152.06194	230737
+153.06989	594325	"Theoretical m/z 153.069879, Mass diff 0 (0.07 ppm), SMILES C=1C=CC=2C=C(C=CC2C1)CC, Annotation [C12H12-3H]+, Rule of HR True"
+154.07762	549550
+155.04921	55684	"Theoretical m/z 155.049142, Mass diff 0 (0.44 ppm), SMILES OC=1C=CC2=CC(=CC=C2C1)C, Annotation [C11H10O-3H]+, Rule of HR True"
+155.06009	20588
+155.08549	270234	"Theoretical m/z 155.085529, Mass diff 0 (0.25 ppm), SMILES C=1C=CC=2C=C(C=CC2C1)CC, Annotation [C12H12-H]+, Rule of HR True"
+156.0567	39024
+157.06454	21273
+158.07257	173416
+169.06493	332677	"Theoretical m/z 169.064798, Mass diff 0 (0.78 ppm), SMILES O(C=1C=CC2=CC(=CC=C2C1)C)C, Annotation [C12H12O-3H]+, Rule of HR True"
+170.07236	1450568
+171.0804	43243	"Theoretical m/z 171.080448, Mass diff 0 (0.28 ppm), SMILES O(C=1C=CC2=CC(=CC=C2C1)C)C, Annotation [C12H12O-H]+, Rule of HR True"
+181.07625	108177
+184.08809	31533
+185.09567	469414
+
+NAME: Hydroxychloroquine_1
+SCANNUMBER: 715
+RETENTIONTIME: 0.7305885
+PRECURSORMZ: 336.184
+PRECURSORTYPE: [M+H]+
+IONMODE: Positive
+SPECTRUMTYPE: Centroid
+FORMULA: C18H26ClN3O
+INCHIKEY: XXSMGPRMXLTPCZ-AWEZNQCLSA-N
+INCHI: 
+SMILES: CCN(CCO)CCC[C@H](C)NC1=C2C=CC(Cl)=CC2=NC=C1
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+COLLISIONENERGY: 
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+INSTRUMENTTYPE: LC-ESI-Orbitrap
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMMENT: 
+Num Peaks: 13
+90.09139	30131
+102.09145	269700	"Theoretical m/z 102.091343, Mass diff 0 (1.05 ppm), SMILES OCCN(C)CC, Annotation [C5H13NO-H]+, Rule of HR True"
+155.06026	15752	"Theoretical m/z 155.060923, Mass diff 0 (0 ppm), Formula C10H7N2"
+156.06787	34068
+158.15385	268527	"Theoretical m/z 158.153934, Mass diff 0 (0.53 ppm), SMILES OCCN(CC)CCCCC, Annotation [C9H21NO-H]+, Rule of HR True"
+164.02611	57566	"Theoretical m/z 164.026152, Mass diff 0 (0.25 ppm), SMILES ClC1=CC=C2C=CC=NC2=C1, Annotation [C9H6ClN+H]+, Rule of HR True"
+178.0289	14008	"Theoretical m/z 178.029221, Mass diff 0 (1.8 ppm), SMILES ClC=1C=CC=2C(=NC=CC2N)C1, Annotation [C9H7ClN2]+, Rule of HR False"
+179.03659	529838
+191.03661	374324
+192.04471	20156	"Theoretical m/z 192.044877, Mass diff 0 (0.87 ppm), SMILES ClC=1C=CC=2C(=NC=CC2NC)C1, Annotation [C10H9ClN2]+, Rule of HR False"
+205.05254	103967	"Theoretical m/z 205.052707, Mass diff 0 (0.82 ppm), SMILES ClC=1C=CC=2C(=NC=CC2NCC)C1, Annotation [C11H11ClN2-H]+, Rule of HR True"
+206.0602	15806	"Theoretical m/z 206.060532, Mass diff 0 (1.61 ppm), SMILES ClC=1C=CC=2C(=NC=CC2NCC)C1, Annotation [C11H11ClN2]+, Rule of HR False"
+247.09979	1130644	"Theoretical m/z 247.099659, Mass diff 0 (0.53 ppm), SMILES ClC=1C=CC=2C(=NC=CC2NC(C)CCC)C1, Annotation [C14H17ClN2-H]+, Rule of HR True"
+
+NAME: Carbidopa_2
+SCANNUMBER: 1055
+RETENTIONTIME: 1.111739
+PRECURSORMZ: 227.1028
+PRECURSORTYPE: [M+H]+
+IONMODE: Positive
+SPECTRUMTYPE: Centroid
+FORMULA: C10H14N2O4
+INCHIKEY: TZFNLOMSOLWIDK-JTQLQIEISA-N
+INCHI: 
+SMILES: C[C@@](CC1=CC=C(O)C(O)=C1)(NN)C(O)=O
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+COLLISIONENERGY: 
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+INSTRUMENTTYPE: LC-ESI-Orbitrap
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMMENT: 
+Num Peaks: 25
+91.05419	100027
+93.03343	210553
+95.04905	99586
+103.05414	118201
+105.03353	91361	"Theoretical m/z 105.033494, Mass diff 0 (0.34 ppm), SMILES OC1=CC=CC(=C1)C, Annotation [C7H8O-3H]+, Rule of HR True"
+105.0448	58763	"Theoretical m/z 105.045273, Mass diff 0 (0 ppm), Formula C6H5N2"
+105.06994	181885	"Theoretical m/z 105.070425, Mass diff 0 (0 ppm), Formula C8H9"
+107.0491	28371
+111.04408	1276960	"Theoretical m/z 111.044058, Mass diff 0 (0.2 ppm), SMILES OC=1C=CC=CC1O, Annotation [C6H6O2+H]+, Rule of HR True"
+117.05745	59901	"Theoretical m/z 117.057849, Mass diff 0 (0 ppm), Formula C8H7N"
+118.06524	995007	"Theoretical m/z 118.065674, Mass diff 0 (0 ppm), Formula C8H8N"
+119.04915	39761	"Theoretical m/z 119.04969, Mass diff 0 (0 ppm), Formula C8H7O"
+121.06458	23459
+123.04403	2045870	"Theoretical m/z 123.044056, Mass diff 0 (0.21 ppm), SMILES OC1=CC=C(C=C1O)C, Annotation [C7H8O2-H]+, Rule of HR True"
+131.04903	86907
+133.06456	118466
+139.03893	605185	"Theoretical m/z 139.039519, Mass diff 0 (0 ppm), Formula C7H7O3"
+146.05997	930734	"Theoretical m/z 146.060042, Mass diff 0 (0.5 ppm), SMILES OC1=CC=CC(=C1)CC(N)C, Annotation [C9H13NO-5H]+, Rule of HR True"
+149.04697	96239
+149.05966	61757	"Theoretical m/z 149.059701, Mass diff 0 (0.28 ppm), SMILES OC1=CC=C(C=C1O)CCC, Annotation [C9H12O2-3H]+, Rule of HR True"
+150.06746	97634	"Theoretical m/z 150.067526, Mass diff 0 (0.44 ppm), SMILES OC1=CC=C(C=C1O)CCC, Annotation [C9H12O2-2H]+, Rule of HR False"
+151.07504	237049
+164.07066	31856	"Theoretical m/z 164.070611, Mass diff 0 (0.3 ppm), SMILES OC1=CC=C(C=C1O)CC(N)C, Annotation [C9H13NO2-3H]+, Rule of HR True"
+181.09677	144151
+184.95612	25201
+
+NAME: Folic acid
+SCANNUMBER: 1090
+RETENTIONTIME: 3.005769
+PRECURSORMZ: 442.1473
+PRECURSORTYPE: [M+H]+
+IONMODE: Positive
+SPECTRUMTYPE: Centroid
+FORMULA: C19H19N7O6
+INCHIKEY: OVBPIULPVIDEAO-LBPRGKRZSA-N
+INCHI: 
+SMILES: NC1=NC(=O)C2=C(N1)N=CC(CNC1=CC=C(C=C1)C(=O)N[C@@H](CCC(O)=O)C(O)=O)=N2
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+COLLISIONENERGY: 
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+INSTRUMENTTYPE: LC-ESI-Orbitrap
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMMENT: 
+Num Peaks: 3
+295.09335	2026215	"Theoretical m/z 295.093799, Mass diff 0 (1.52 ppm), SMILES O=CC1=CC=C(C=C1)NCC=2N=C3C(=O)N=C(N)NC3=NC2, Annotation [C14H12N6O2-H]+, Rule of HR True"
+313.10416	106081	"Theoretical m/z 313.105694, Mass diff 0.002 (4.9 ppm), SMILES O=CC(N=CCNC1=CC=C(C=C1)C(=O)NC(C(=O)O)CC)=C, Annotation [C16H19N3O4-4H]+, Rule of HR False"
+442.14703	345611	"Theoretical m/z 442.146955, Mass diff 0 (0.17 ppm), SMILES O=C1N=C(N)NC2=NC=C(N=C12)CNC3=CC=C(C=C3)C(=O)NC(C(=O)O)CCC(=O)O, Annotation [C19H19N7O6+H]+, Rule of HR True"
+
+NAME: Tomoxetine
+SCANNUMBER: 1056
+RETENTIONTIME: 3.837629
+PRECURSORMZ: 256.1696
+PRECURSORTYPE: [M+H]+
+IONMODE: Positive
+SPECTRUMTYPE: Centroid
+FORMULA: C17H21NO
+INCHIKEY: VHGCDTVCOLNTBX-KRWDZBQOSA-N
+INCHI: 
+SMILES: CNCC[C@H](OC1=CC=CC=C1C)C1=CC=CC=C1
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+COLLISIONENERGY: 
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+INSTRUMENTTYPE: LC-ESI-Orbitrap
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMMENT: 
+Num Peaks: 4
+148.11182	244975
+241.9537	19711
+256.16953	880039	"Theoretical m/z 256.169584, Mass diff 0 (0.21 ppm), SMILES O(C=1C=CC=CC1C)C(C=2C=CC=CC2)CCNC, Annotation [C17H21NO+H]+, Rule of HR True"
+256.26309	14983
+
+NAME: Levetiracetam
+SCANNUMBER: 1064
+RETENTIONTIME: 1.391959
+PRECURSORMZ: 171.1127
+PRECURSORTYPE: [M+H]+
+IONMODE: Positive
+SPECTRUMTYPE: Centroid
+FORMULA: C8H14N2O2
+INCHIKEY: HPHUVLMMVZITSG-LURJTMIESA-N
+INCHI: 
+SMILES: CCC(N1CCCC1=O)C(=N)O
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+COLLISIONENERGY: 
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+INSTRUMENTTYPE: LC-ESI-Orbitrap
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMMENT: low MS2 spectra quality
+Num Peaks: 3
+98.06008	7534	"Theoretical m/z 98.060039, Mass diff 0 (0.42 ppm), SMILES O=C1N(C)CCC1, Annotation [C5H9NO-H]+, Rule of HR True"
+98.09631	37218	"Theoretical m/z 98.096422, Mass diff 0 (1.14 ppm), SMILES N(CCC)CCC, Annotation [C6H15N-3H]+, Rule of HR True"
+126.09106	260383	"Theoretical m/z 126.091343, Mass diff 0 (2.24 ppm), SMILES O=C1N(CCC)CCC1, Annotation [C7H13NO-H]+, Rule of HR True"
+
+NAME: Loratadine
+SCANNUMBER: 2177
+RETENTIONTIME: 6.992672
+PRECURSORMZ: 383.1527
+PRECURSORTYPE: [M+H]+
+IONMODE: Positive
+SPECTRUMTYPE: Centroid
+FORMULA: C22H23ClN2O2
+INCHIKEY: JCCNYMKQOSZNPW-UHFFFAOYSA-N
+INCHI: 
+SMILES: CCOC(=O)N1CCC(CC1)=C1C2=C(CCC3=C1N=CC=C3)C=C(Cl)C=C2
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+COLLISIONENERGY: 
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+INSTRUMENTTYPE: LC-ESI-Orbitrap
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMMENT: 
+Num Peaks: 37
+214.04152	1069392	"Theoretical m/z 214.041803, Mass diff 0 (1.32 ppm), SMILES ClC1=CC=CC(=C1)CCC=2C=NC=CC2, Annotation [C13H12ClN-3H]+, Rule of HR True"
+228.05782	1448834	"Theoretical m/z 228.057453, Mass diff 0 (1.61 ppm), SMILES ClC1=CC=C2C(=C1)CCC3=CC=CN=C3C2, Annotation [C14H12ClN-H]+, Rule of HR True"
+229.06494	1430824	"Theoretical m/z 229.065279, Mass diff 0 (1.48 ppm), SMILES ClC1=CC=C(C=C2CCNCC2)C(=C1)CC, Annotation [C14H18ClN-6H]+, Rule of HR False"
+230.09654	262614	"Theoretical m/z 230.096419, Mass diff 0 (0.52 ppm), SMILES N=1C=CC=C2C1C(=CCC)C=3C=CC=CC3CC2, Annotation [C17H17N-5H]+, Rule of HR True"
+231.104	849271
+232.11241	507223	"Theoretical m/z 232.112069, Mass diff 0 (1.47 ppm), SMILES N=1C=CC=C2C1C(=CCC)C=3C=CC=CC3CC2, Annotation [C17H17N-3H]+, Rule of HR True"
+233.11978	350605
+243.10422	861919
+244.1124	887622	"Theoretical m/z 244.112075, Mass diff 0 (1.33 ppm), SMILES N=1C=CC=C2C1C(C=3C=CC=CC3CC2)=C(C)CC, Annotation [C18H19N-5H]+, Rule of HR True"
+245.11966	693198
+246.12799	1448808	"Theoretical m/z 246.127725, Mass diff 0 (1.08 ppm), SMILES N=1C=CC=C2C1C(C=3C=CC=CC3CC2)=C(C)CC, Annotation [C18H19N-3H]+, Rule of HR True"
+247.13525	597984
+248.09418	566157
+252.05705	1180030	"Theoretical m/z 252.057458, Mass diff 0 (1.62 ppm), SMILES ClC1=CC=C2C(=CC)C3=NC=CC=C3CCC2=C1, Annotation [C16H14ClN-3H]+, Rule of HR True"
+253.06531	2100689	"Theoretical m/z 253.065283, Mass diff 0 (0.11 ppm), SMILES ClC1=CC=C2C(=CC)C3=NC=CC=C3CCC2=C1, Annotation [C16H14ClN-2H]+, Rule of HR False"
+257.1196	532621
+258.12839	5228206	"Theoretical m/z 258.127715, Mass diff 0.001 (2.61 ppm), SMILES N=1C=CC=C2C1C(C=3C=CC=CC3CC2)=C(CC)CC, Annotation [C19H21N-5H]+, Rule of HR True"
+259.13525	14287859
+266.07266	6656865	"Theoretical m/z 266.073114, Mass diff 0 (1.71 ppm), SMILES ClC1=CC=C2C(=CCC)C3=NC=CC=C3CCC2=C1, Annotation [C17H16ClN-3H]+, Rule of HR True"
+267.08072	25172082	"Theoretical m/z 267.080939, Mass diff 0 (0.82 ppm), SMILES ClC1=CC=C2C(=CCC)C3=NC=CC=C3CCC2=C1, Annotation [C17H16ClN-2H]+, Rule of HR False"
+268.08865	539589	"Theoretical m/z 268.088764, Mass diff 0 (0.42 ppm), SMILES ClC1=CC=C2C(=CCC)C3=NC=CC=C3CCC2=C1, Annotation [C17H16ClN-H]+, Rule of HR True"
+270.05496	675051	"Theoretical m/z 270.055503, Mass diff 0 (0 ppm), Formula C18H8NO2"
+278.07339	845156	"Theoretical m/z 278.073094, Mass diff 0 (1.06 ppm), SMILES ClC1=CC=C(C(=C1)C)C(C2=NC=CC=C2)=C(CC)CC, Annotation [C18H20ClN-7H]+, Rule of HR True"
+279.08041	5262546	"Theoretical m/z 279.080914, Mass diff 0 (1.8 ppm), SMILES ClC1=CC=C2C(=C1)CCC3=CC=CN=C3C2=C(C)CC, Annotation [C18H18ClN-4H]+, Rule of HR False"
+280.08914	7022050	"Theoretical m/z 280.088739, Mass diff 0 (1.43 ppm), SMILES ClC1=CC=C2C(=C1)CCC3=CC=CN=C3C2=C(C)CC, Annotation [C18H18ClN-3H]+, Rule of HR True"
+281.09702	10365228	"Theoretical m/z 281.096564, Mass diff 0 (1.62 ppm), SMILES ClC1=CC=C2C(=C1)CCC3=CC=CN=C3C2=C(C)CC, Annotation [C18H18ClN-2H]+, Rule of HR False"
+282.104	4552220	"Theoretical m/z 282.104389, Mass diff 0 (1.38 ppm), SMILES ClC1=CC=C2C(=C1)CCC3=CC=CN=C3C2=C(C)CC, Annotation [C18H18ClN-H]+, Rule of HR True"
+283.06268	753392	"Theoretical m/z 283.063816, Mass diff 0.001 (0 ppm), Formula C16H12ClN2O"
+292.08813	2407086	"Theoretical m/z 292.089302, Mass diff 0.001 (0 ppm), Formula C19H15ClN"
+294.10406	7868947	"Theoretical m/z 294.104394, Mass diff 0 (1.14 ppm), SMILES ClC1=CC=C2C(=C1)CCC3=CC=CN=C3C2=C(CC)CC, Annotation [C19H20ClN-3H]+, Rule of HR True"
+302.14191	1312628
+311.1315	297924	"Theoretical m/z 311.130964, Mass diff 0.001 (1.72 ppm), SMILES ClC=1C=CC2=C(C1)CCC=3C=CC=NC3C2=C4CCNCC4, Annotation [C19H19ClN2+H]+, Rule of HR True"
+322.08487	1196748
+335.0939	324360	"Theoretical m/z 335.095116, Mass diff 0.001 (0 ppm), Formula C20H16ClN2O"
+337.10974	10984031	"Theoretical m/z 337.110218, Mass diff 0 (1.42 ppm), SMILES O=CN1CCC(=C2C=3N=CC=CC3CCC=4C=C(Cl)C=CC42)CC1, Annotation [C20H19ClN2O-H]+, Rule of HR True"
+339.16223	1170424	"Theoretical m/z 339.162801, Mass diff 0 (0 ppm), Formula C21H24ClN2"
+383.15204	420937	"Theoretical m/z 383.152082, Mass diff 0 (0.11 ppm), SMILES O=C(OCC)N1CCC(=C2C=3N=CC=CC3CCC=4C=C(Cl)C=CC42)CC1, Annotation [C22H23ClN2O2+H]+, Rule of HR True"
diff -r 000000000000 -r 07b7a1012916 test-data/filtered_ions.msp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filtered_ions.msp	Tue Jul 08 14:48:47 2025 +0000
@@ -0,0 +1,210 @@
+SCANNUMBER: 1166
+IONMODE: positive
+SPECTRUMTYPE: Centroid
+FORMULA: C7H8ClN3O4S2
+INCHIKEY: JZUFKLXOESDKRF-UHFFFAOYSA-N
+SMILES: NS(=O)(=O)C1=CC2=C(NCNS2(=O)=O)C=C1Cl
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMPOUND_NAME: Hydrochlorothiazide
+RETENTION_TIME: 1.657244
+PRECURSOR_MZ: 297.9721
+ADDUCT: [M+H]+
+INSTRUMENT_TYPE: LC-ESI-Orbitrap
+NUM PEAKS: 2
+220.97833   11703.0     "Theoretical m/z 220.978766, Mass diff 0 (0 ppm), Formula C6H6ClN2O3S"
+232.97813   9081.0      "Theoretical m/z 232.978766, Mass diff 0 (0 ppm), Formula C7H6ClN2O3S"
+
+SCANNUMBER: 727
+IONMODE: positive
+SPECTRUMTYPE: Centroid
+FORMULA: C9H11NO4
+INCHIKEY: WTDRDQBEARUVNC-LURJTMIESA-N
+SMILES: N[C@@H](CC1=CC=C(O)C(O)=C1)C(O)=O
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMPOUND_NAME: Levodopa_1
+RETENTION_TIME: 0.7128666
+PRECURSOR_MZ: 198.0762
+ADDUCT: [M+H]+
+INSTRUMENT_TYPE: LC-ESI-Orbitrap
+NUM PEAKS: 2
+107.04907   537691.0
+135.04385   178345.0
+
+SCANNUMBER: 1076
+IONMODE: positive
+SPECTRUMTYPE: Centroid
+FORMULA: C9H11NO4
+INCHIKEY: WTDRDQBEARUVNC-LURJTMIESA-N
+SMILES: N[C@@H](CC1=CC=C(O)C(O)=C1)C(O)=O
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMPOUND_NAME: Levodopa_2
+RETENTION_TIME: 1.048427
+PRECURSOR_MZ: 198.0762
+ADDUCT: [M+H]+
+INSTRUMENT_TYPE: LC-ESI-Orbitrap
+NUM PEAKS: 2
+134.05994   268309.0    "Theoretical m/z 134.060037, Mass diff 0 (0.72 ppm), SMILES OC1=CC=CC(=C1)CCN, Annotation [C8H11NO-3H]+, Rule of HR True"
+135.04385   343216.0
+
+SCANNUMBER: 1192
+IONMODE: positive
+SPECTRUMTYPE: Centroid
+FORMULA: C12H11N7
+INCHIKEY: FNYLWPVRPXGIIP-UHFFFAOYSA-N
+SMILES: NC1=NC(N)=C2N=C(C(N)=NC2=N1)C1=CC=CC=C1
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMPOUND_NAME: Triamterene
+RETENTION_TIME: 2.533905
+PRECURSOR_MZ: 254.115
+ADDUCT: [M+H]+
+INSTRUMENT_TYPE: LC-ESI-Orbitrap
+NUM PEAKS: 2
+237.0887    19002528.0  "Theoretical m/z 237.088321, Mass diff 0 (1.6 ppm), SMILES N1=CN=C(N)C2=NC(=C(N=C12)N)C3=CC=CC=C3, Annotation [C12H10N6-H]+, Rule of HR True"
+254.11499   8105778.0   "Theoretical m/z 254.114866, Mass diff 0 (0.49 ppm), SMILES N1=C(N=C(N)C2=NC(=C(N=C12)N)C3=CC=CC=C3)N, Annotation [C12H11N7+H]+, Rule of HR True"
+
+SCANNUMBER: 1575
+IONMODE: positive
+SPECTRUMTYPE: Centroid
+FORMULA: C14H14O3
+INCHIKEY: CMWTZPSULFXXJA-SECBINFHSA-N
+SMILES: COC1=CC2=CC=C(C=C2C=C1)[C@@H](C)C(O)=O
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMPOUND_NAME: Naproxen
+RETENTION_TIME: 6.590834
+PRECURSOR_MZ: 231.1017
+ADDUCT: [M+H]+
+INSTRUMENT_TYPE: LC-ESI-Orbitrap
+NUM PEAKS: 2
+170.07236   1450568.0
+185.09567   469414.0
+
+SCANNUMBER: 715
+IONMODE: positive
+SPECTRUMTYPE: Centroid
+FORMULA: C18H26ClN3O
+INCHIKEY: XXSMGPRMXLTPCZ-AWEZNQCLSA-N
+SMILES: CCN(CCO)CCC[C@H](C)NC1=C2C=CC(Cl)=CC2=NC=C1
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMPOUND_NAME: Hydroxychloroquine_1
+RETENTION_TIME: 0.7305885
+PRECURSOR_MZ: 336.184
+ADDUCT: [M+H]+
+INSTRUMENT_TYPE: LC-ESI-Orbitrap
+NUM PEAKS: 2
+191.03661   374324.0
+247.09979   1130644.0   "Theoretical m/z 247.099659, Mass diff 0 (0.53 ppm), SMILES ClC=1C=CC=2C(=NC=CC2NC(C)CCC)C1, Annotation [C14H17ClN2-H]+, Rule of HR True"
+
+SCANNUMBER: 1055
+IONMODE: positive
+SPECTRUMTYPE: Centroid
+FORMULA: C10H14N2O4
+INCHIKEY: TZFNLOMSOLWIDK-JTQLQIEISA-N
+SMILES: C[C@@](CC1=CC=C(O)C(O)=C1)(NN)C(O)=O
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMPOUND_NAME: Carbidopa_2
+RETENTION_TIME: 1.111739
+PRECURSOR_MZ: 227.1028
+ADDUCT: [M+H]+
+INSTRUMENT_TYPE: LC-ESI-Orbitrap
+NUM PEAKS: 2
+123.04403   2045870.0   "Theoretical m/z 123.044056, Mass diff 0 (0.21 ppm), SMILES OC1=CC=C(C=C1O)C, Annotation [C7H8O2-H]+, Rule of HR True"
+146.05997   930734.0    "Theoretical m/z 146.060042, Mass diff 0 (0.5 ppm), SMILES OC1=CC=CC(=C1)CC(N)C, Annotation [C9H13NO-5H]+, Rule of HR True"
+
+SCANNUMBER: 1090
+IONMODE: positive
+SPECTRUMTYPE: Centroid
+FORMULA: C19H19N7O6
+INCHIKEY: OVBPIULPVIDEAO-LBPRGKRZSA-N
+SMILES: NC1=NC(=O)C2=C(N1)N=CC(CNC1=CC=C(C=C1)C(=O)N[C@@H](CCC(O)=O)C(O)=O)=N2
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMPOUND_NAME: Folic acid
+RETENTION_TIME: 3.005769
+PRECURSOR_MZ: 442.1473
+ADDUCT: [M+H]+
+INSTRUMENT_TYPE: LC-ESI-Orbitrap
+NUM PEAKS: 2
+295.09335   2026215.0   "Theoretical m/z 295.093799, Mass diff 0 (1.52 ppm), SMILES O=CC1=CC=C(C=C1)NCC=2N=C3C(=O)N=C(N)NC3=NC2, Annotation [C14H12N6O2-H]+, Rule of HR True"
+313.10416   106081.0    "Theoretical m/z 313.105694, Mass diff 0.002 (4.9 ppm), SMILES O=CC(N=CCNC1=CC=C(C=C1)C(=O)NC(C(=O)O)CC)=C, Annotation [C16H19N3O4-4H]+, Rule of HR False"
+
+SCANNUMBER: 1056
+IONMODE: positive
+SPECTRUMTYPE: Centroid
+FORMULA: C17H21NO
+INCHIKEY: VHGCDTVCOLNTBX-KRWDZBQOSA-N
+SMILES: CNCC[C@H](OC1=CC=CC=C1C)C1=CC=CC=C1
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMPOUND_NAME: Tomoxetine
+RETENTION_TIME: 3.837629
+PRECURSOR_MZ: 256.1696
+ADDUCT: [M+H]+
+INSTRUMENT_TYPE: LC-ESI-Orbitrap
+NUM PEAKS: 2
+256.16953   880039.0    "Theoretical m/z 256.169584, Mass diff 0 (0.21 ppm), SMILES O(C=1C=CC=CC1C)C(C=2C=CC=CC2)CCNC, Annotation [C17H21NO+H]+, Rule of HR True"
+256.26309   14983.0
+
+SCANNUMBER: 1064
+IONMODE: positive
+SPECTRUMTYPE: Centroid
+FORMULA: C8H14N2O2
+INCHIKEY: HPHUVLMMVZITSG-LURJTMIESA-N
+SMILES: CCC(N1CCCC1=O)C(=N)O
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMMENT: low MS2 spectra quality
+COMPOUND_NAME: Levetiracetam
+RETENTION_TIME: 1.391959
+PRECURSOR_MZ: 171.1127
+ADDUCT: [M+H]+
+INSTRUMENT_TYPE: LC-ESI-Orbitrap
+NUM PEAKS: 2
+98.09631    37218.0     "Theoretical m/z 98.096422, Mass diff 0 (1.14 ppm), SMILES N(CCC)CCC, Annotation [C6H15N-3H]+, Rule of HR True"
+126.09106   260383.0    "Theoretical m/z 126.091343, Mass diff 0 (2.24 ppm), SMILES O=C1N(CCC)CCC1, Annotation [C7H13NO-H]+, Rule of HR True"
+
+SCANNUMBER: 2177
+IONMODE: positive
+SPECTRUMTYPE: Centroid
+FORMULA: C22H23ClN2O2
+INCHIKEY: JCCNYMKQOSZNPW-UHFFFAOYSA-N
+SMILES: CCOC(=O)N1CCC(CC1)=C1C2=C(CCC3=C1N=CC=C3)C=C(Cl)C=C2
+AUTHORS: Biomarker Analytical Laboratories, RECETOX, Masaryk University (CZ)
+INSTRUMENT: LC Orbitrap Fusion Tribrid MS
+IONIZATION: ESI+
+LICENSE: CC BY-NC
+COMPOUND_NAME: Loratadine
+RETENTION_TIME: 6.992672
+PRECURSOR_MZ: 383.1527
+ADDUCT: [M+H]+
+INSTRUMENT_TYPE: LC-ESI-Orbitrap
+NUM PEAKS: 2
+267.08072   25172082.0  "Theoretical m/z 267.080939, Mass diff 0 (0.82 ppm), SMILES ClC1=CC=C2C(=CCC)C3=NC=CC=C3CCC2=C1, Annotation [C17H16ClN-2H]+, Rule of HR False"
+337.10974   10984031.0  "Theoretical m/z 337.110218, Mass diff 0 (1.42 ppm), SMILES O=CN1CCC(=C2C=3N=CC=CC3CCC=4C=C(Cl)C=CC42)CC1, Annotation [C20H19ClN2O-H]+, Rule of HR True"
+
diff -r 000000000000 -r 07b7a1012916 test-data/input_data_error_info.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_data_error_info.csv	Tue Jul 08 14:48:47 2025 +0000
@@ -0,0 +1,1 @@
+Name,error
diff -r 000000000000 -r 07b7a1012916 wtv.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wtv.xml	Tue Jul 08 14:48:47 2025 +0000
@@ -0,0 +1,78 @@
+<tool id="wtv" name="wtv" version="@TOOL_VERSION@+galaxy0" profile="23.0" license="MIT">
+    <description>ion selection based on intra-library specificity and retention properties</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="annotation"/>
+    <expand macro="creator"/>
+    <requirements>
+         <requirement type="package" version="@TOOL_VERSION@">wtv</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        wtv-cli --msp_path ${input_file} --outpath . --mz_min ${mz_min} --mz_max ${mz_max} --rt_window ${rt_window} --min_ion_intensity_percent ${min_ion_intensity_percent} --min_ion_num ${min_ion_num} --prefer_mz_threshold ${prefer_mz_threshold} --similarity_threshold ${similarity_threshold} --fr_factor ${fr_factor} --retention_time_max ${retention_time_max}  
+    ]]></command>
+    <inputs>
+        <param type="data" name="input_file" format="msp" label="Input MSP file" help="MSP file to be processed." />
+        <param type="integer" name="mz_min" value="35" label="Minimum m/z value" help="Minimum m/z value (default: 35)." />
+        <param type="integer" name="mz_max" value="400" label="Maximum m/z value" help="Maximum m/z value (default: 400)." />
+        <param type="float" name="rt_window" value="2.00" label="Retention time window" help="Retention time window (default: 2.00).The units for rt_window match your retention time (RT) data, typically minutes." />
+        <param type="float" name="min_ion_intensity_percent" value="7" label="Minimum ion intensity percentage" help="Minimum ion intensity percentage (default: 7)." />
+        <param type="integer" name="min_ion_num" value="2" label="Minimum number of ions" help="Minimum number of ions (default: 2)." />
+        <param type="integer" name="prefer_mz_threshold" min="0" value="60" label="Preferred m/z threshold" help="Preferred m/z threshold (default: 60). Ions with m/z below this threshold are either set to 1 or deprioritised during ion selection and scoring." />
+        <param type="float" name="similarity_threshold" value="0.85" label="Similarity threshold" help="Similarity threshold (default: 0.85). The similarity_threshold is used to determine whether two compounds are considered similar based on their calculated similarity score."  min="0" max="1"/>
+        <param type="float" name="fr_factor" value="2.0" label="FR factor" help="FR factor (default: 2.0). FR (Fragment Ratio) helps assess the similarity of two spectra by comparing the relative intensities of shared ions, improving spectral discrimination when enough ions are shared." />
+        <param type="float" name="retention_time_max" value="68.80" label="Maximum retention time" help="Maximum retention time (default: 68.80)."  optional="true"/>
+        <section name="options" title="Options">
+            <param argument="log" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Export log files" help="Export log files with potential errors." />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="filtered_ions" from_work_dir="filtered_ions.msp" format="msp"/>
+        <data name="input_data_error_info" from_work_dir="input_data_error_info.csv" format="csv" label="Log file using wtv on ${on_string}">
+            <filter>options['log']</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="input_file" value="esi_spectra.msp" />
+            <section name="options">
+                <param name="log" value="TRUE"/>
+            </section>
+            <output name="filtered_ions" file="filtered_ions.msp" compare="sim_size"/>
+            <output name="input_data_error_info" file="input_data_error_info.csv" compare="sim_size"/>        </test>
+    </tests>
+    <help><![CDATA[
+**WTV Galaxy Tool**
+
+This tool provides a Galaxy interface for the `wtv-cli` command-line utility, which is used for ion selection in mass spectrometry.
+
+---
+
+**Inputs**
+
+- **Input MSP file**: The MSP file to be processed.
+- **Minimum m/z value**: Lower bound for m/z values to consider (default: 35).
+- **Maximum m/z value**: Upper bound for m/z values to consider (default: 400).
+- **Retention time window**: The window for retention time matching (default: 2.00).
+- **Minimum ion intensity percentage**: Minimum percentage for ion intensity (default: 7).
+- **Minimum number of ions**: Minimum number of ions required (default: 2).
+- **Preferred m/z threshold**: Threshold for preferred m/z (default: 60).
+- **Similarity threshold**: Minimum similarity score for matches (default: 0.85).
+- **FR factor**: Factor for fragment ratio calculations (default: 2.0).
+- **Maximum retention time**: Maximum retention time allowed (default: 68.80).
+
+---
+
+**Outputs**
+- The tool produces processed output files as specified by the `wtv-cli` utility.
+
+---
+
+**Acknowledgements**
+This project is based on the original work by Honglun Yuan, Yiding Jiangfang, Zhenhua Liu, Rong Rong Su, Qiao Li, Chuanying Fang, Sishu Huang, Xianqing Liu, Alisdair Robert Fernie, and Jie Luo, as published in [WTV_2.0](https://github.com/yuanhonglun/WTV_2.0) and [their associated publication](https://doi.org/10.1016/j.molp.2024.04.012).
+
+]]></help>
+    <citations>
+        <citation type="doi">10.1016/j.molp.2024.04.012</citation>
+    </citations>
+</tool>
\ No newline at end of file