test-data: rungc

workflow4metabolomics · Nov 14, 2024 · 769e93d · 769e93d
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Showing 9 changed files with 192 additions and 18 deletions.
diff --git a/tools/metams/test-data/dataMatrix.tsv b/tools/metams/test-data/dataMatrix.tsv
diff --git a/tools/metams/test-data/peakspectra.msp b/tools/metams/test-data/peakspectra.msp
@@ -1,10 +1,172 @@
-Name: Unknown 1
-DB.idx: -1
-rt: 13.956
-Class: Unknown
-rt.sd: 0.0027
-Num Peaks: 14
- 86 2339264; 87 294778; 133 1540615; 171 132778; 174 18213384;
- 175 3107052; 176 1420834; 177 242794; 246 324632; 248 3537056;
- 249 880866; 251 95357; 276 887971; 278 154526;
+Name: Glycine, 3TMS
+DB.idx: 4
+RI: 1302.682
+Formula: C11H29NO2Si3
+monoMW: 291.61
+std.rt: 13.965
+Class: Standard
+DB.idx: 4
+Num Peaks: 78
+ 57 316293; 58 608407; 59 2360607; 60 298845; 61 196310;
+ 70 169295; 71 161384; 72 648791; 73 11721138; 74 1113027;
+ 85 170795; 86 3075416; 87 384461; 88 151265; 95 64802;
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+ 104 33778; 105 72042; 108 20644; 111 54647; 113 112766;
+ 114 101832; 115 180609; 116 342635; 117 921701; 118 169096;
+ 119 269557; 129 117830; 130 783824; 131 770438; 132 312290;
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+ 145 119829; 146 281312; 147 4791240; 148 776758; 149 430714;
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+ 173 580616; 174 23638072; 175 4238967; 176 1802790; 177 316308;
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+ 203 40215; 204 134875; 222 19873; 246 373925; 247 132834;
+ 248 4524339; 249 1128021; 250 573219; 251 111802; 252 35632;
+ 271 12788; 274 10361; 275 53846; 276 1041597; 277 299864;
+ 278 137402; 279 34431; 367 3442;
+
+Name: Pyroglutamic acid, 2TMS
+DB.idx: 5
+RI: 1650.417
+Formula: C11H23NO3Si2
+monoMW: 273.477
+std.rt: 19.513
+Class: Standard
+DB.idx: 5
+Num Peaks: 158
+ 51 338626; 52 575985; 53 464956; 54 649153; 55 3336412;
+ 56 1197195; 57 2169449; 58 6685191; 59 9081136; 60 1387309;
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+ 96 309636; 97 359461; 98 945628; 99 1302033; 100 1977416;
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+ 106 78328; 107 721315; 109 119460; 110 547214; 111 389326;
+ 112 2669136; 113 919493; 114 1247351; 115 1018669; 116 429096;
+ 117 1634510; 118 277347; 119 446610; 120 209026; 121 3778822;
+ 122 441514; 124 186464; 125 92720; 126 589470; 127 446490;
+ 128 450712; 129 602449; 130 380558; 131 2567815; 132 768139;
+ 133 4538595; 134 605705; 135 383039; 136 55065; 138 106476;
+ 139 362925; 140 3322479; 141 1187929; 142 1007454; 143 317329;
+ 144 285466; 146 817699; 147 27946976; 148 4395199; 149 2777617;
+ 150 359788; 151 264840; 153 538648; 154 2958055; 156 201537792;
+ 157 26263368; 158 8572482; 159 854704; 161 112709; 165 38838;
+ 167 53444; 168 412158; 169 96591; 170 320590; 171 96076;
+ 172 334429; 173 104039; 174 482205; 175 165478; 182 63170;
+ 183 127405; 184 123256; 185 90504; 186 274650; 187 72726;
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+ 200 45080; 202 55194; 210 20123; 213 169498; 214 1336902;
+ 215 313400; 216 197429; 218 125726; 222 29111; 224 27879;
+ 225 68702; 227 103301; 228 1116292; 229 647341; 230 16641732;
+ 231 3538093; 232 1781749; 233 280558; 240 33947; 242 43021;
+ 245 77511; 252 25529; 254 51583; 255 116747; 257 292195;
+ 258 16611026; 259 3425137; 260 1449116; 261 234399; 271 21809;
+ 272 77604; 273 680847; 274 170001; 275 63615; 343 5275;
+ 346 77810; 348 24720; 420 13841;
+
+Name: Alanine, 3TMS
+DB.idx: 6
+RI: 1360.504
+Formula: C12H31NO2Si3
+monoMW: 305.637
+std.rt: 15.323
+Class: Manual
+DB.idx: 6
+Num Peaks: 124
+ 54 89758; 55 274561; 56 190979; 57 472743; 58 1227701;
+ 59 8857202; 60 769050; 61 572383; 62 41693; 66 257757;
+ 68 50951; 70 467827; 71 357812; 72 1124052; 73 32258304;
+ 74 2673357; 75 2422084; 76 175458; 83 38410; 85 188547;
+ 86 367416; 87 252086; 88 60319; 94 41086; 96 32723;
+ 97 50677; 99 486943; 100 17472112; 101 1900147; 102 851052;
+ 103 361559; 105 143712; 106 17498; 107 26854; 111 34681;
+ 113 423231; 114 5383496; 115 1162939; 116 1080783; 117 1237291;
+ 118 240515; 119 435711; 121 43187; 125 15819; 128 174405;
+ 129 397688; 130 1744641; 131 1822916; 132 670119; 133 4839524;
+ 134 728488; 135 340438; 136 57257; 138 43976; 142 153189;
+ 143 64000; 144 108296; 146 293959; 147 10561822; 148 1491760;
+ 149 856234; 150 102563; 151 32670; 158 1009756; 159 218614;
+ 161 120212; 163 22096; 171 75896; 172 1056407; 173 301283;
+ 174 505863; 175 574319; 176 121867; 177 65048; 178 19944;
+ 180 22252; 182 39229; 184 102108; 185 246171; 187 618870;
+ 188 56198912; 189 10817010; 190 4731210; 191 1271570; 192 244376;
+ 194 20138; 197 17281; 199 14019; 200 191429; 201 75657;
+ 202 675342; 203 169524; 204 283190; 205 89690; 206 59625;
+ 216 134127; 221 102289; 222 29042; 224 7100; 232 122504;
+ 246 584093; 247 167296; 248 76389; 255 19200; 256 20821;
+ 259 85913; 261 123873; 262 9276494; 263 2565833; 264 1229448;
+ 265 215056; 266 50202; 275 20541; 276 49840; 277 30086;
+ 279 9403; 286 9243; 288 59278; 290 1507066; 291 370236;
+ 292 225705; 293 58740; 305 25278; 306 8768;
+
+Name: Aspartic acid, 2TMS
+DB.idx: 7
+RI: 1422.39
+Formula: C10H23NO4Si2
+monoMW: 277.465
+std.rt: 17.071
+Class: Manual
+DB.idx: 7
+Num Peaks: 116
+ 53 110556; 54 70748; 55 491989; 56 176719; 57 429061;
+ 58 867565; 59 1844082; 60 680229; 61 1783651; 62 153287;
+ 63 101630; 68 123735; 69 151943; 70 1623808; 71 339896;
+ 72 1895180; 73 30361752; 74 3806352; 75 9542434; 76 841470;
+ 77 445025; 83 92647; 84 134484; 85 157664; 87 326510;
+ 88 216697; 89 279460; 90 63265; 91 208179; 94 33994;
+ 97 52008; 98 185798; 99 316461; 100 1875360; 101 453860;
+ 102 861826; 103 388126; 104 99156; 105 69761; 107 25301;
+ 109 22961; 111 40850; 113 89550; 114 174059; 115 400852;
+ 116 8341494; 117 8393036; 118 1292305; 119 473023; 123 69069;
+ 126 81938; 127 106745; 128 686387; 129 693487; 130 9547276;
+ 131 1451533; 132 650288; 133 808761; 134 110943; 136 21502;
+ 142 86232; 143 144433; 144 1188715; 145 241754; 146 1021532;
+ 147 4643929; 148 865583; 149 641631; 150 89905; 151 34481;
+ 152 17594; 159 1417706; 160 23345888; 161 2689204; 162 1045742;
+ 163 83928; 170 49854; 172 332672; 173 99914; 187 144420;
+ 190 157941; 191 68491; 200 29189; 202 994060; 203 216078;
+ 204 126839; 216 88054; 217 155137; 220 834397; 221 158515;
+ 222 85032; 223 27191; 232 107424; 234 1972004; 235 400133;
+ 236 201912; 237 33541; 241 20022; 244 414185; 245 3084671;
+ 246 600419; 247 272617; 260 39656; 262 658881; 263 128316;
+ 264 69923; 272 7826; 277 37715; 278 29889; 304 11423;
+ 306 12021; 349 5670; 373 27527; 374 9346; 393 4740;
+ 442 2912;
+
+Name: Tryptamine, 2TMS
+DB.idx: 8
+RI: 2224.531
+Formula: C16H28N2Si2
+monoMW: 304.578
+std.rt: 19.044
+Class: Manual
+DB.idx: 8
+Num Peaks: 125
+ 53 103908; 54 92348; 55 359811; 56 220319; 57 234375;
+ 58 577937; 59 3625396; 60 353747; 61 203780; 65 56054;
+ 67 128907; 68 288905; 69 270065; 70 189689; 71 186419;
+ 73 10021682; 74 951360; 80 62629; 81 55492; 82 148023;
+ 83 168514; 84 247841; 85 394058; 86 4374601; 87 491924;
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+ 115 207144; 116 578060; 117 600612; 118 157353; 119 73966;
+ 124 36333; 126 232163; 127 179149; 128 708154; 129 522829;
+ 130 1250999; 131 462746; 132 216417; 136 14172; 139 26745;
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+ 159 193798; 161 71597; 162 55797; 164 20330; 165 41274;
+ 167 134982; 168 3076559; 169 1236917; 170 382139; 171 175813;
+ 172 793755; 173 635083; 174 21999992; 175 3966143; 176 1668216;
+ 177 216481; 178 37373; 180 12735; 182 19976; 183 80285;
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+ 191 69447; 192 39714; 196 10899; 197 12167; 198 37741;
+ 199 62873; 200 203785; 201 477415; 202 156939; 213 29648;
+ 215 157180; 216 53881; 224 12789; 226 19959; 227 71824;
+ 240 19510; 241 100315; 242 61551; 253 33746; 256 52615;
+ 257 2699065; 258 663143; 259 242635; 260 53573; 273 158481;
+ 274 36775; 288 7723; 318 11318; 349 7175; 411 8416;
 
diff --git a/tools/metams/test-data/peakspectra_noDB.msp b/tools/metams/test-data/peakspectra_noDB.msp
@@ -0,0 +1,10 @@
+Name: Unknown 1
+DB.idx: -1
+rt: 13.956
+Class: Unknown
+rt.sd: 0.0027
+Num Peaks: 14
+ 86 2339264; 87 294778; 133 1540615; 171 132778; 174 18213384;
+ 175 3107052; 176 1420834; 177 242794; 246 324632; 248 3537056;
+ 249 880866; 251 95357; 276 887971; 278 154526;
+
diff --git a/tools/metams/test-data/peaktable.tsv b/tools/metams/test-data/peaktable.tsv
diff --git a/tools/metams/test-data/runGC.RData b/tools/metams/test-data/runGC.RData
diff --git a/tools/metams/test-data/sampleMetadata_noDB.tsv b/tools/metams/test-data/sampleMetadata_noDB.tsv
@@ -0,0 +1,3 @@
+sampleMetadata	class
+alg8	.
+alg2	.
diff --git a/tools/metams/test-data/variableMetadata.tsv b/tools/metams/test-data/variableMetadata.tsv
@@ -1,2 +1,6 @@
-Name	Class	rt.sd	rt
-Unknown 1	Unknown	0.0027	13.956
+Name	DB.idx	RI	Formula	monoMW	Class	std.rt	rt.sd	rt
+Glycine, 3TMS	4	1302.682	C11H29NO2Si3	291.61	Standard	13.965	0.0296	13.977
+Pyroglutamic acid, 2TMS	5	1650.417	C11H23NO3Si2	273.477	Standard	19.513	0.0453	19.513
+Alanine, 3TMS	6	1360.504	C12H31NO2Si3	305.637	Manual	15.323	0.0359	15.338
+Aspartic acid, 2TMS	7	1422.39	C10H23NO4Si2	277.465	Manual	17.071	NA	17.084
+Tryptamine, 2TMS	8	2224.531	C16H28N2Si2	304.578	Manual	19.044	0.0498	19.08
diff --git a/tools/metams/test-data/variableMetadata_noDB.tsv b/tools/metams/test-data/variableMetadata_noDB.tsv
@@ -0,0 +1,2 @@
+Name	Class	rt.sd	rt
+Unknown 1	Unknown	0.0027	13.956
diff --git a/tools/metams/test-data/xset.merged.sampleMetadata.tsv b/tools/metams/test-data/xset.merged.sampleMetadata.tsv
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		Name Class rt.sd rt
		Unknown 1 Unknown 0.0027 13.956