diff --git a/tools/metams/test-data/dataMatrix.tsv b/tools/metams/test-data/dataMatrix.tsv deleted file mode 100644 index a1f3a8130..000000000 --- a/tools/metams/test-data/dataMatrix.tsv +++ /dev/null @@ -1,2 +0,0 @@ -Name alg8 alg2 -Unknown 1 18213384 2907034 diff --git a/tools/metams/test-data/peakspectra.msp b/tools/metams/test-data/peakspectra.msp index 563087cf1..d42646fc8 100644 --- 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; + 99 95625; 100 1618532; 101 371473; 102 194300; 103 154892; + 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; + 133 1900199; 134 283305; 135 157747; 136 23715; 144 263144; + 145 119829; 146 281312; 147 4791240; 148 776758; 149 430714; + 150 54306; 158 362993; 159 154663; 170 31401; 171 108378; + 173 580616; 174 23638072; 175 4238967; 176 1802790; 177 316308; + 178 67581; 187 34267; 190 57883; 200 15557; 202 110221; + 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; + 61 2428274; 62 213258; 63 127195; 65 267956; 66 3568313; + 67 2222624; 68 882858; 69 747738; 70 2193333; 71 1770608; + 72 7657516; 73 113430768; 74 9750386; 75 13061012; 76 825056; + 77 513625; 78 129935; 80 363843; 81 191640; 82 453511; + 83 600419; 84 2544426; 85 1796955; 86 2593790; 87 747021; + 88 229333; 89 215309; 91 82213; 92 154229; 93 1177171; + 96 309636; 97 359461; 98 945628; 99 1302033; 100 1977416; + 101 558275; 102 493025; 103 670440; 104 122758; 105 306067; + 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; + 190 334303; 191 105635; 192 41986; 196 24884; 198 104267; + 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; + 88 246059; 89 759003; 90 111212; 91 59740; 94 122678; + 95 89278; 96 837410; 97 187069; 98 170686; 99 390831; + 100 1871628; 101 318302; 102 995646; 103 206161; 104 52138; + 109 26678; 110 48451; 112 304993; 113 209633; 114 416235; + 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; + 140 102888; 142 138543; 144 237406; 145 66218; 146 221104; + 150 26706; 151 32128; 152 81992; 153 61989; 158 328614; + 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; + 184 197718; 185 82742; 186 972896; 187 221998; 190 263894; + 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 new file mode 100644 index 000000000..563087cf1 --- /dev/null +++ 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 deleted file mode 100644 index d30cb1ed2..000000000 --- a/tools/metams/test-data/peaktable.tsv +++ /dev/null @@ -1,2 +0,0 @@ -"Name" "Class" "rt.sd" "rt" "alg8" "alg2" -"Unknown 1" "Unknown" 0.0027 13.956 18213384 2907034 diff --git a/tools/metams/test-data/runGC.RData b/tools/metams/test-data/runGC.RData deleted file mode 100644 index cdbfc9801..000000000 Binary files a/tools/metams/test-data/runGC.RData and /dev/null differ diff --git a/tools/metams/test-data/sampleMetadata_noDB.tsv b/tools/metams/test-data/sampleMetadata_noDB.tsv new file mode 100644 index 000000000..569d7a83f --- /dev/null +++ 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 index 25da9f7d1..1c7819c7c 100644 --- 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 new file mode 100644 index 000000000..25da9f7d1 --- /dev/null +++ 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 deleted file mode 100644 index b3b9c79f0..000000000 --- a/tools/metams/test-data/xset.merged.sampleMetadata.tsv +++ /dev/null @@ -1,3 +0,0 @@ -sample_name class polarity -alg8 . 0 -alg2 . 0