From ef1ca7d4591323931c9b34e1c09f92f3f9fa50f8 Mon Sep 17 00:00:00 2001 From: RJMW Date: Tue, 16 Jul 2024 15:33:20 +0100 Subject: [PATCH 01/19] Bump version Sirius to v5.8.6 and add credentials for login --- .../sirius_csifingerid/sirius_csifingerid.py | 24 ++-- .../sirius_csifingerid/sirius_csifingerid.xml | 112 ++++++++++-------- 2 files changed, 80 insertions(+), 56 deletions(-) diff --git a/tools/sirius_csifingerid/sirius_csifingerid.py b/tools/sirius_csifingerid/sirius_csifingerid.py index ba0b639..aebc96c 100644 --- a/tools/sirius_csifingerid/sirius_csifingerid.py +++ b/tools/sirius_csifingerid/sirius_csifingerid.py @@ -1,5 +1,6 @@ import argparse import csv +import json import glob import multiprocessing import os @@ -9,7 +10,6 @@ import uuid from collections import defaultdict - parser = argparse.ArgumentParser() parser.add_argument('--input_pth') parser.add_argument('--canopus_result_pth') @@ -32,6 +32,7 @@ parser.add_argument('--schema', default='msp') parser.add_argument('-a', '--adducts', action='append', nargs=1, required=False, default=[], help='Adducts used') +parser.add_argument('--credentials') args = parser.parse_args() print(args) @@ -39,6 +40,14 @@ print('Input file empty') exit() +with open(args.credentials) as f: + credentials = json.load(f) + +cmd_login = "sirius login " \ + "--user='{}' " \ + "--password='{}'".format(credentials["username"], credentials["password"]) +os.system(cmd_login) + if args.temp_dir: wd = os.path.join(args.temp_dir, 'temp_'+str(uuid.uuid4())) os.mkdir(wd) @@ -216,12 +225,13 @@ def run_sirius(meta_info, peaklist, args, wd, spectrac): # If possible always good to have the adduct in output as a column paramd['additional_details']['adduct'] = adduct - # ============== Create CLI cmd for metfrag =============================== + # ============== cmd for Sirius =============================== cmd = "sirius --cores {} --no-citations --ms2 {} --adduct {} " \ "--precursor {} -o {} " \ "formula -c {} --ppm-max {} --profile {} " \ - "structure --database {} canopus".format( - paramd["cli"]["--cores"], + "fingerprint " \ + "structure --database {} " \ + "canopus".format(paramd["cli"]["--cores"], paramd["cli"]["--ms2"], adduct, paramd["cli"]["--precursor"], @@ -312,9 +322,6 @@ def work(cmds): pnumlines = 0 plinesread = 0 - # end of file. Check if there is a MSP spectra to - # run metfrag on still - if plinesread and plinesread == pnumlines: if adducts_from_cli: for adduct in adducts_from_cli: @@ -349,7 +356,6 @@ def work(cmds): ###################################################################### # outputs might have different headers. Need to get a list of all the headers # before we start merging the files outfiles = [os.path.join(wd, f) for f in -# glob.glob(os.path.join(wd, "*_metfrag_result.csv"))] def concat_output(wd, filename, result_pth, level=2): if level == 2: @@ -404,7 +410,7 @@ def concat_output(wd, filename, result_pth, level=2): args.annotations_result_pth) concat_output(wd, - 'canopus_summary.tsv', + 'canopus_compound_summary.tsv', args.canopus_result_pth) concat_output(wd, diff --git a/tools/sirius_csifingerid/sirius_csifingerid.xml b/tools/sirius_csifingerid/sirius_csifingerid.xml index 24f8110..3ca11c9 100644 --- a/tools/sirius_csifingerid/sirius_csifingerid.xml +++ b/tools/sirius_csifingerid/sirius_csifingerid.xml @@ -1,57 +1,76 @@ + version="5.8.6+galaxy0" profile="24.0"> is used to identify metabolites using single and tandem mass spectrometry - - sirius-csifingerid + sirius-csifingerid Preferences -> Manage Information" + #end if + echo "Running Sirius as user: $username" && + export _JAVA_OPTIONS=-Duser.home=$__new_file_path__ && + python '$__tool_directory__/sirius_csifingerid.py' + --input_pth '$input' + --database $database + --profile $profile + --candidates $candidates + --ppm_max $ppm_max + --polarity $polarity + --out_dir $__new_file_path__ + --canopus_result_pth canopus_all_summary.tsv + --annotations_result_pth annotations_all_summary.tsv + --all_structures_result_pth structures_all_summary.tsv + --cores_top_level 1 + --cores_sirius \${GALAXY_SLOTS:-4} + --meta_select_col $meta_select_col + --min_MSMS_peaks $min_MSMS_peaks + --schema $schema + --temp_dir $__new_file_path__ + --credentials '$credentials' + + #if $adducts_cond.adducts_selector == 'select': + #for $a in $adducts_cond.adducts + --adducts $a + #end for + #elif $adducts_cond.adducts_selector == 'all': + #if $polarity == 'positive': + --adducts [M+H]+ + --adducts [M+NH4]+ + --adducts [M+Na]+ + --adducts [M+K]+ + --adducts [M+CH3OH+H]+ + --adducts [M+ACN+H]+ + --adducts [M+ACN+Na]+ + --adducts [M+2ACN+H]+ + #elif $polarity == 'negative': + --adducts [M-H]- + --adducts [M+Cl]- + --adducts [M+HCOO]- + --adducts [M+CH3COO]- + #end if + #end if ]]> + + + @@ -196,7 +215,6 @@ - ---------------- From ab15e3d23a4de75bb1814b254b6b63d7f6429c7f Mon Sep 17 00:00:00 2001 From: RJMW Date: Tue, 16 Jul 2024 15:33:58 +0100 Subject: [PATCH 02/19] Add example config file for user preferences --- config/user_preferences_extra_conf.yml | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 config/user_preferences_extra_conf.yml diff --git a/config/user_preferences_extra_conf.yml b/config/user_preferences_extra_conf.yml new file mode 100644 index 0000000..f9af05b --- /dev/null +++ b/config/user_preferences_extra_conf.yml @@ -0,0 +1,13 @@ +preferences: + sirius_account: + description: Sirius account + inputs: + - name: username + label: Username (email) + type: text + required: False + - name: password + label: Password + type: password + required: False + From a1232b7e8bdb01263d8f983180306e6c352b02a8 Mon Sep 17 00:00:00 2001 From: RJMW Date: Tue, 16 Jul 2024 15:37:46 +0100 Subject: [PATCH 03/19] Update tests --- .../annotation_CCMSLIB00000578155_result.tsv | 4 ++-- .../test-data/annotation_ML006801.tsv | 4 ++-- .../test-data/annotation_RP022611_result.tsv | 4 ++-- .../annotation_RP022611_result_all_adducts.tsv | 8 ++++---- .../test-data/annotation_generic.tsv | 12 ++++++------ .../test-data/canopus_CCMSLIB00000578155_result.tsv | 4 ++-- .../test-data/canopus_ML006801.tsv | 4 ++-- .../test-data/canopus_RP022611_result.tsv | 4 ++-- .../canopus_RP022611_result_all_adducts.tsv | 9 ++++----- .../sirius_csifingerid/test-data/canopus_generic.tsv | 12 ++++++------ 10 files changed, 32 insertions(+), 33 deletions(-) diff --git a/tools/sirius_csifingerid/test-data/annotation_CCMSLIB00000578155_result.tsv b/tools/sirius_csifingerid/test-data/annotation_CCMSLIB00000578155_result.tsv index 4cdabbd..1dcf421 100644 --- a/tools/sirius_csifingerid/test-data/annotation_CCMSLIB00000578155_result.tsv +++ b/tools/sirius_csifingerid/test-data/annotation_CCMSLIB00000578155_result.tsv @@ -1,2 +1,2 @@ -name adduct rank formulaRank #adducts #predictedFPs ConfidenceScore CSI:FingerIDScore ZodiacScore SiriusScore molecularFormula adduct InChIkey2D InChI name smiles xlogp pubchemids links dbflags ionMass retentionTimeInSeconds id -D-GLUCOSE-6-PHOSPHATE [M-H]- 1 1 1 1 0.2777991179997831 -40.17179067053119 N/A 17.8469785346642 C6H13O9P [M-H]- NBSCHQHZLSJFNQ InChI=1S/C6H13O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-10H,1H2,(H2,11,12,13) D-GLUCOSE-6-PHOSPHATE C(C1C(C(C(C(O1)O)O)O)O)OP(=O)(O)O -4.19999981 208;5958;65127;439198;439284;439404;439427;440100;447096;449526;4178491;4459709;9817215;9859975;10848963;12314997;11536233;10038266;12598269;11651816;11651817;11701643;10332946;10422797;10422798;11499884;16219407;21604864;21604865;23421197;23421199;23421200;25200774;25244236;24802166;42609823;44589902;44629605;46936284;51351673;51351674;59660207;59660208;66804219;72200063;71048769;70828590;90657928;90087729;92043642;89530481;89533633;92144442;92331698;92331699;92450038;102072969;101251820;100983220;124302956;124303605;129703999;129800866;133556303;134813555;135054589;135070792 HMDB:(1078 1401 3498);SuperNatural:(SN00005991 SN00006877 SN00368182 SN00005992);ZINC bio:(ZINC01529564 ZINC01532857 ZINC03869395 ZINC03869396 ZINC03869397 ZINC03869398 ZINC03875374 ZINC03875375 ZINC04096188 ZINC08551508 ZINC13540027);additional;MeSH:(65127 25244236);Plantcyc:(CPD-15711 GLC-6-P CPD-15712 CPD-1241 D-HEXOSE-6-PHOSPHATE MANNOSE-6P ALPHA-GLC-6-P);PubMed;NORMAN:(NS00015226);COCONUT:(CNP0093800 CNP0209092);KNApSAcK:(7307);Natural Products:(UNPD119019 UNPD208877);PubChem:(208 5958 65127 439198 439284 439404 439427 440100 447096 449526 4178491 4459709 9817215 9859975 10848963 12314997 11536233 10038266 12598269 11651816 11651817 11701643 10332946 10422797 10422798 11499884 16219407 21604864 21604865 23421197 23421199 23421200 25200774 25244236 24802166 42609823 44589902 44629605 46936284 51351673 51351674 59660207 59660208 66804219 72200063 71048769 70828590 90657928 90087729 92043642 89530481 89533633 92144442 92331698 92331699 92450038 102072969 101251820 100983220 124302956 124303605 129703999 129800866 133556303 134813555 135054589 135070792);CHEBI:(49728 91004 61548 58735 58247 134068 4170 4141 136602 58225 47944 43896 17719 48066 17665 61567 60332 61667 41076);PubChem class - bio and metabolites;KEGG:(C00275 C01172 C02965 C03735 C00668 C01113 C00092 C02962);YMDB:(2311 311 947 966 242);Training Set;Biocyc:(CPD-15711 GLC-6-P CPD-15712 CPD-1241 D-HEXOSE-6-PHOSPHATE MANNOSE-6P CPD1A0-6282 ALPHA-GLC-6-P SMA-0000014 SMA-0000409) 20965758 259.022 NaN 0_unknown_ +name adduct confidenceRank structurePerIdRank formulaRank #adducts #predictedFPs ConfidenceScore CSI:FingerIDScore ZodiacScore SiriusScore molecularFormula adduct InChIkey2D InChI name smiles xlogp pubchemids links dbflags ionMass retentionTimeInSeconds id featureId +D-GLUCOSE-6-PHOSPHATE [M-H]- 1 1 1 1 2 0.2798631164249337 -13.372705328911332 N/A 17.301255015582992 C6H13O9P [M-H]- NBSCHQHZLSJFNQ InChI=1S/C6H13O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-10H,1H2,(H2,11,12,13) D-GLUCOSE-6-PHOSPHATE C(C1C(C(C(C(O1)O)O)O)O)OP(=O)(O)O -4.19999981 208;5958;65127;439198;439284;439404;439427;440100;447096;449526;4178491;4459709;9817215;9859975;10848963;12314997;11536233;10038266;12598269;11651816;11651817;11701643;10332946;10422797;10422798;11499884;16219407;21604864;21604865;23421197;23421199;23421200;25200774;25244236;24802166;42609823;44589902;44629605;46936284;51351673;51351674;59660207;59660208;66804219;72200063;71048769;70828590;90657928;90087729;92043642;89530481;89533633;92144442;92331698;92331699;92450038;102072969;101251820;100983220;124302956;124303605;129703999;129800866;133556303;134813555;135054589;135070792 HMDB:(1078 1401 3498);SuperNatural:(SN00005991 SN00006877 SN00368182 SN00005992);ZINC bio:(ZINC01529564 ZINC01532857 ZINC03869395 ZINC03869396 ZINC03869397 ZINC03869398 ZINC03875374 ZINC03875375 ZINC04096188 ZINC08551508 ZINC13540027);additional;MeSH:(65127 25244236);Plantcyc:(CPD-15711 GLC-6-P CPD-15712 CPD-1241 D-HEXOSE-6-PHOSPHATE MANNOSE-6P ALPHA-GLC-6-P);PubMed;NORMAN:(NS00015226);COCONUT:(CNP0093800 CNP0209092);KNApSAcK:(7307);Natural Products:(UNPD119019 UNPD208877);PubChem:(208 5958 65127 439198 439284 439404 439427 440100 447096 449526 4178491 4459709 9817215 9859975 10848963 12314997 11536233 10038266 12598269 11651816 11651817 11701643 10332946 10422797 10422798 11499884 16219407 21604864 21604865 23421197 23421199 23421200 25200774 25244236 24802166 42609823 44589902 44629605 46936284 51351673 51351674 59660207 59660208 66804219 72200063 71048769 70828590 90657928 90087729 92043642 89530481 89533633 92144442 92331698 92331699 92450038 102072969 101251820 100983220 124302956 124303605 129703999 129800866 133556303 134813555 135054589 135070792);CHEBI:(49728 91004 61548 58735 58247 134068 4170 4141 136602 58225 47944 43896 17719 48066 17665 61567 60332 61667 41076);PubChem class - bio and metabolites;KEGG:(C00275 C01172 C02965 C03735 C00668 C01113 C00092 C02962);YMDB:(2311 311 947 966 242);Training Set;Biocyc:(CPD-15711 GLC-6-P CPD-15712 CPD-1241 D-HEXOSE-6-PHOSPHATE MANNOSE-6P CPD1A0-6282 ALPHA-GLC-6-P SMA-0000014 SMA-0000409) 20965758 259.022 NaN 1_unknown_ N/A diff --git a/tools/sirius_csifingerid/test-data/annotation_ML006801.tsv b/tools/sirius_csifingerid/test-data/annotation_ML006801.tsv index 7d3209a..203cb38 100644 --- a/tools/sirius_csifingerid/test-data/annotation_ML006801.tsv +++ b/tools/sirius_csifingerid/test-data/annotation_ML006801.tsv @@ -1,2 +1,2 @@ -name adduct rank formulaRank #adducts #predictedFPs ConfidenceScore CSI:FingerIDScore ZodiacScore SiriusScore molecularFormula adduct InChIkey2D InChI name smiles xlogp pubchemids links dbflags ionMass retentionTimeInSeconds id -L-thialysine; LC-ESI-ITFT; MS2; CE: 50%; R=7500; [M+H]+ [M+H]+ 1 1 1 1 0.9560298733520203 -6.599755497315031 N/A 21.01043087165301 C5H12N2O2S [M+H]+ GHSJKUNUIHUPDF InChI=1S/C5H12N2O2S/c6-1-2-10-3-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9) L-thialysine; LC-ESI-ITFT; MS2; CE: 50%; R=7500; [M+H]+ C(CSCC(C(=O)O)N)N -3.70000005 20049;99558;6995002;12898158;54754416;57517225 HMDB:(29178 33518);SuperNatural:(SN00250912);ZINC bio:(ZINC01705407 ZINC01731787);additional;MeSH:(20049 99558);Plantcyc:(S-2-AMINOETHYL-L-CYSTEINE);PubMed;NORMAN:(NS00014577);COCONUT:(CNP0297414);Natural Products:(UNPD166389);PubChem:(20049 99558 6995002 12898158 54754416 57517225);CHEBI:(497734);PubChem class - bio and metabolites;Training Set;Biocyc:(S-2-AMINOETHYL-L-CYSTEINE) 20899950 165.0692 NaN 0_unknown_ +name adduct confidenceRank structurePerIdRank formulaRank #adducts #predictedFPs ConfidenceScore CSI:FingerIDScore ZodiacScore SiriusScore molecularFormula adduct InChIkey2D InChI name smiles xlogp pubchemids links dbflags ionMass retentionTimeInSeconds id featureId +L-thialysine; LC-ESI-ITFT; MS2; CE: 50%; R=7500; [M+H]+ [M+H]+ 1 1 1 1 1 0.7659760425325088 -5.475150599823154 N/A 25.850681523736977 C5H12N2O2S [M+H]+ GHSJKUNUIHUPDF InChI=1S/C5H12N2O2S/c6-1-2-10-3-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9) L-thialysine; LC-ESI-ITFT; MS2; CE: 50%; R=7500; [M+H]+ C(CSCC(C(=O)O)N)N -3.70000005 20049;99558;6995002;12898158;54754416;57517225 HMDB:(29178 33518);SuperNatural:(SN00250912);ZINC bio:(ZINC01705407 ZINC01731787);additional;MeSH:(20049 99558);Plantcyc:(S-2-AMINOETHYL-L-CYSTEINE);PubMed;NORMAN:(NS00014577);COCONUT:(CNP0297414);Natural Products:(UNPD166389);PubChem:(20049 99558 6995002 12898158 54754416 57517225);CHEBI:(497734);PubChem class - bio and metabolites;Training Set;Biocyc:(S-2-AMINOETHYL-L-CYSTEINE) 20899950 165.0692 NaN 1_unknown_ N/A diff --git a/tools/sirius_csifingerid/test-data/annotation_RP022611_result.tsv b/tools/sirius_csifingerid/test-data/annotation_RP022611_result.tsv index f79a8f7..1e895e3 100644 --- a/tools/sirius_csifingerid/test-data/annotation_RP022611_result.tsv +++ b/tools/sirius_csifingerid/test-data/annotation_RP022611_result.tsv @@ -1,2 +1,2 @@ -name adduct rank formulaRank #adducts #predictedFPs ConfidenceScore CSI:FingerIDScore ZodiacScore SiriusScore molecularFormula adduct InChIkey2D InChI name smiles xlogp pubchemids links dbflags ionMass retentionTimeInSeconds id -D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- [M-H]- 1 1 1 1 0.31290839506383084 -56.37857062945502 N/A 35.11438137495146 C6H12O6 [M-H]- WQZGKKKJIJFFOK InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2 D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- C(C1C(C(C(C(O1)O)O)O)O)O -2.5999999 206;5793;6036;18950;1549080;64689;79025;81696;657055;185698;439353;439357;439507;439583;439680;441032;441033;441034;441035;3000450;444314;448388;448702;451187;451188;451189;452245;455147;3034742;2724488;7018164;5104362;7043897;7044038;7098663;7098664;7157007;6102790;5319264;6321330;6323336;6400264;6560213;6971003;6971007;6971016;6971096;6971097;6971098;6992021;6992084;9794056;12003287;9815418;9834129;12193653;12285853;12285856;12285861;12285862;12285863;12285866;12285870;12285871;12285873;12285877;12285878;12285879;12285885;12285886;12285889;12285890;12285891;12285892;12285893;12285894;9899007;10899282;10035228;10954241;11571906;11571917;10081060;11600783;10103794;11019447;11030410;10130220;11651921;11672764;10197954;10219674;10219763;10313382;10329946;11344362;11959770;11367383;11970126;11412863;11480819;11492034;16211884;16211941;16211984;16211986;16212959;16212960;16212966;16213546;16213640;16213872;16217112;16219580;22825318;22836365;22836366;21355827;23424086;24802149;24802163;24802281;24892722;42626680;46188479;44328781;44328785;46780441;46897877;51340651;50939543;54445181;54445182;57197748;57288387;57483528;60052896;60078648;56845432;56845995;59034276;59036328;59040622;59083882;59105109;59125088;57691826;58594768;59146659;58595959;58618581;59503411;59503407;59383280;57973135;59445439;58969552;59886072;58070804;59965103;58265153;58265160;58265166;58265178;58265190;58265196;58300638;66629908;67518639;69528681;67615000;67615455;67641738;68167579;68324677;68334110;67938791;67944215;67944290;67950444;70543261;71777654;70443535;71309028;71309128;71309129;71309140;71309397;71309503;71309513;71309514;71309671;71309852;71309905;71309908;71309927;71317094;71317095;71317096;71317097;71317182;75357255;76973265;86278404;88547603;88255060;87297824;89000581;90057933;90781811;87929779;87931119;88974141;92043367;92043446;90159939;90895196;89200515;89332529;90346255;89374440;91057721;89742272;89424182;90470917;90472751;90472752;90472753;90472761;90472762;90472770;90473076;89855666;101015849;101033892;101513786;102089288;101254308;101254309;101254310;101254311;101254312;101254313;101254314;101254315;101718250;101718251;101796201;101469918;102601142;102601177;102601371;102601743;102601816;102447462;102447463;117064633;117064644;117065485;117633116;117768413;118797420;118797610;118797621;118797622;118855904;118855887;118855889;118855910;118855920;118855925;117938207;118924468;122522140;121494046;121494058;122360911;126704391;133119158;133119249;133121364;129629038;131698424;131698425;131698450;131699179;131706405;132939819;132939820;133662560;133662561;133662562;131842051;134695353;131966764;134860471;139025182;137554722 HMDB:(122 516 3345 1151 62202 12326 3449 169 33704 143 61922);PubChem class - food;SuperNatural:(SN00048687 SN00050524 SN00321479 SN00064345 SN00003330 SN00396363 SN00005681 SN00330500 SN00156785 SN00156795 SN00001876 SN00048690 SN00226998 SN00064344 SN00273897 SN00048679);ZINC bio:(ZINC00895026 ZINC00895055 ZINC00895084 ZINC00895350 ZINC00896168 ZINC00896169 ZINC00897147 ZINC00901155 ZINC01529206 ZINC01530434 ZINC01532520 ZINC01532549 ZINC02545114 ZINC02597049 ZINC03581097 ZINC03830678 ZINC03830679 ZINC03833800 ZINC03860903 ZINC03861213 ZINC04095659 ZINC04095660 ZINC04097150 ZINC04097151 ZINC04097152 ZINC04097153 ZINC04262018 ZINC04529488);additional;MeSH:(5793 6036 18950 79025 439357 439507 439680 441032 441033 441035 11030410);Plantcyc:(CPD-3607 ALPHA-D-GALACTOSE X-DMAN-HEX-);PubMed;NORMAN:(NS00007629);COCONUT:(CNP0082250 CNP0210547);KNApSAcK:(1126);Natural Products:(UNPD148053 UNPD130932 UNPD191130 UNPD175204 UNPD20367 UNPD175249 UNPD72621 UNPD116684 UNPD158921 UNPD175399 UNPD119270 UNPD83717);PubChem:(206 5793 6036 18950 1549080 64689 79025 81696 657055 185698 439353 439357 439507 439583 439680 441032 441033 441034 441035 3000450 444314 448388 448702 451187 451188 451189 452245 455147 3034742 2724488 7018164 5104362 7043897 7044038 7098663 7098664 7157007 6102790 5319264 6321330 6323336 6400264 6560213 6971003 6971007 6971016 6971096 6971097 6971098 6992021 6992084 9794056 12003287 9815418 9834129 12193653 12285853 12285856 12285861 12285862 12285863 12285866 12285870 12285871 12285873 12285877 12285878 12285879 12285885 12285886 12285889 12285890 12285891 12285892 12285893 12285894 9899007 10899282 10035228 10954241 11571906 11571917 10081060 11600783 10103794 11019447 11030410 10130220 11651921 11672764 10197954 10219674 10219763 10313382 10329946 11344362 11959770 11367383 11970126 11412863 11480819 11492034 16211884 16211941 16211984 16211986 16212959 16212960 16212966 16213546 16213640 16213872 16217112 16219580 22825318 22836365 22836366 21355827 23424086 24802149 24802163 24802281 24892722 42626680 46188479 44328781 44328785 46780441 46897877 51340651 50939543 54445181 54445182 57197748 57288387 57483528 60052896 60078648 56845432 56845995 59034276 59036328 59040622 59083882 59105109 59125088 57691826 58594768 59146659 58595959 58618581 59503411 59503407 59383280 57973135 59445439 58969552 59886072 58070804 59965103 58265153 58265160 58265166 58265178 58265190 58265196 58300638 66629908 67518639 69528681 67615000 67615455 67641738 68167579 68324677 68334110 67938791 67944215 67944290 67950444 70543261 71777654 70443535 71309028 71309128 71309129 71309140 71309397 71309503 71309513 71309514 71309671 71309852 71309905 71309908 71309927 71317094 71317095 71317096 71317097 71317182 75357255 76973265 86278404 88547603 88255060 87297824 89000581 90057933 90781811 87929779 87931119 88974141 92043367 92043446 90159939 90895196 89200515 89332529 90346255 89374440 91057721 89742272 89424182 90470917 90472751 90472752 90472753 90472761 90472762 90472770 90473076 89855666 101015849 101033892 101513786 102089288 101254308 101254309 101254310 101254311 101254312 101254313 101254314 101254315 101718250 101718251 101796201 101469918 102601142 102601177 102601371 102601743 102601816 102447462 102447463 117064633 117064644 117065485 117633116 117768413 118797420 118797610 118797621 118797622 118855904 118855887 118855889 118855910 118855920 118855925 117938207 118924468 122522140 121494046 121494058 122360911 126704391 133119158 133119249 133121364 129629038 131698424 131698425 131698450 131699179 131706405 132939819 132939820 133662560 133662561 133662562 131842051 134695353 131966764 134860471 139025182 137554722);CHEBI:(37686 80962 37692 28729 28563 72452 68462 27667 37680 37620 28102 63421 141392 42905 27517 15903 37677 27380 28061 18269 37706 59552 37630 4191 40656 37744 15444 59573 4093 37740 28100 4139 37679 4167 88300 18398 86059 37627 37619 83029 37704 37671 37631 27857 37693 18246 4208 43104 37741 17925);PubChem class - bio and metabolites;KEGG:(C00737 C01487 C06466 C06465 C15923 C06464 C00031 C06467 C00962 C02209 C00221 C21032 C01825 C00124 C00936 C00738 C00984 C21050 C00267 C00159);PubChem class - safety and toxic;YMDB:(273 146 894 286 72 846);Training Set;PubChem class - drug;Biocyc:(SMA-0000448 CPD-15625 CPD-15622 CPD-15758 ALPHA-GLUCOSE CPD-15628 SMA-0000188 CPD-3607 CPD-18461 CPD-12601 CPD-15627 SMA-0000654 CPD185E-2 SMA-0000436 CPD-13428 CPD-15624 Alpha-D-Talose CPD-15621 CPD-2361 CPD-11613 CPD-15762 CPD-15757 CPD-15761 GLC CPD-9918 D-AMINO-ACID GALACTOSE SMA-0000420 ALPHA-D-GALACTOSE CPD-15759 CPD-5725 SMA-0000670 L-GALACTOSE CPD-11611 CPD-13559) 255846782 179.0561 NaN 0_unknown_ +name adduct confidenceRank structurePerIdRank formulaRank #adducts #predictedFPs ConfidenceScore CSI:FingerIDScore ZodiacScore SiriusScore molecularFormula adduct InChIkey2D InChI name smiles xlogp pubchemids links dbflags ionMass retentionTimeInSeconds id featureId +D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- [M-H]- 1 1 1 1 1 0.26766749344403346 -18.744222610782234 N/A 33.159317785798166 C6H12O6 [M-H]- WQZGKKKJIJFFOK InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2 D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- C(C1C(C(C(C(O1)O)O)O)O)O -2.5999999 206;5793;6036;18950;1549080;64689;79025;81696;657055;185698;439353;439357;439507;439583;439680;441032;441033;441034;441035;3000450;444314;448388;448702;451187;451188;451189;452245;455147;3034742;2724488;7018164;5104362;7043897;7044038;7098663;7098664;7157007;6102790;5319264;6321330;6323336;6400264;6560213;6971003;6971007;6971016;6971096;6971097;6971098;6992021;6992084;9794056;12003287;9815418;9834129;12193653;12285853;12285856;12285861;12285862;12285863;12285866;12285870;12285871;12285873;12285877;12285878;12285879;12285885;12285886;12285889;12285890;12285891;12285892;12285893;12285894;9899007;10899282;10035228;10954241;11571906;11571917;10081060;11600783;10103794;11019447;11030410;10130220;11651921;11672764;10197954;10219674;10219763;10313382;10329946;11344362;11959770;11367383;11970126;11412863;11480819;11492034;16211884;16211941;16211984;16211986;16212959;16212960;16212966;16213546;16213640;16213872;16217112;16219580;22825318;22836365;22836366;21355827;23424086;24802149;24802163;24802281;24892722;42626680;46188479;44328781;44328785;46780441;46897877;51340651;50939543;54445181;54445182;57197748;57288387;57483528;60052896;60078648;56845432;56845995;59034276;59036328;59040622;59083882;59105109;59125088;57691826;58594768;59146659;58595959;58618581;59503411;59503407;59383280;57973135;59445439;58969552;59886072;58070804;59965103;58265153;58265160;58265166;58265178;58265190;58265196;58300638;66629908;67518639;69528681;67615000;67615455;67641738;68167579;68324677;68334110;67938791;67944215;67944290;67950444;70543261;71777654;70443535;71309028;71309128;71309129;71309140;71309397;71309503;71309513;71309514;71309671;71309852;71309905;71309908;71309927;71317094;71317095;71317096;71317097;71317182;75357255;76973265;86278404;88547603;88255060;87297824;89000581;90057933;90781811;87929779;87931119;88974141;92043367;92043446;90159939;90895196;89200515;89332529;90346255;89374440;91057721;89742272;89424182;90470917;90472751;90472752;90472753;90472761;90472762;90472770;90473076;89855666;101015849;101033892;101513786;102089288;101254308;101254309;101254310;101254311;101254312;101254313;101254314;101254315;101718250;101718251;101796201;101469918;102601142;102601177;102601371;102601743;102601816;102447462;102447463;117064633;117064644;117065485;117633116;117768413;118797420;118797610;118797621;118797622;118855904;118855887;118855889;118855910;118855920;118855925;117938207;118924468;122522140;121494046;121494058;122360911;126704391;133119158;133119249;133121364;129629038;131698424;131698425;131698450;131699179;131706405;132939819;132939820;133662560;133662561;133662562;131842051;134695353;131966764;134860471;139025182;137554722 HMDB:(122 516 3345 1151 62202 12326 3449 169 33704 143 61922);PubChem class - food;SuperNatural:(SN00048687 SN00050524 SN00321479 SN00064345 SN00003330 SN00396363 SN00005681 SN00330500 SN00156785 SN00156795 SN00001876 SN00048690 SN00226998 SN00064344 SN00273897 SN00048679);ZINC bio:(ZINC00895026 ZINC00895055 ZINC00895084 ZINC00895350 ZINC00896168 ZINC00896169 ZINC00897147 ZINC00901155 ZINC01529206 ZINC01530434 ZINC01532520 ZINC01532549 ZINC02545114 ZINC02597049 ZINC03581097 ZINC03830678 ZINC03830679 ZINC03833800 ZINC03860903 ZINC03861213 ZINC04095659 ZINC04095660 ZINC04097150 ZINC04097151 ZINC04097152 ZINC04097153 ZINC04262018 ZINC04529488);additional;MeSH:(5793 6036 18950 79025 439357 439507 439680 441032 441033 441035 11030410);Plantcyc:(CPD-3607 ALPHA-D-GALACTOSE X-DMAN-HEX-1:5_6:A CPD4FS-6 CPD-15762 ALPHA-GLUCOSE CPD-12601 CPD-15761 GLC L-GALACTOSE CPD-13559 GALACTOSE);PubMed;NORMAN:(NS00007629);COCONUT:(CNP0082250 CNP0210547);KNApSAcK:(1126);Natural Products:(UNPD148053 UNPD130932 UNPD191130 UNPD175204 UNPD20367 UNPD175249 UNPD72621 UNPD116684 UNPD158921 UNPD175399 UNPD119270 UNPD83717);PubChem:(206 5793 6036 18950 1549080 64689 79025 81696 657055 185698 439353 439357 439507 439583 439680 441032 441033 441034 441035 3000450 444314 448388 448702 451187 451188 451189 452245 455147 3034742 2724488 7018164 5104362 7043897 7044038 7098663 7098664 7157007 6102790 5319264 6321330 6323336 6400264 6560213 6971003 6971007 6971016 6971096 6971097 6971098 6992021 6992084 9794056 12003287 9815418 9834129 12193653 12285853 12285856 12285861 12285862 12285863 12285866 12285870 12285871 12285873 12285877 12285878 12285879 12285885 12285886 12285889 12285890 12285891 12285892 12285893 12285894 9899007 10899282 10035228 10954241 11571906 11571917 10081060 11600783 10103794 11019447 11030410 10130220 11651921 11672764 10197954 10219674 10219763 10313382 10329946 11344362 11959770 11367383 11970126 11412863 11480819 11492034 16211884 16211941 16211984 16211986 16212959 16212960 16212966 16213546 16213640 16213872 16217112 16219580 22825318 22836365 22836366 21355827 23424086 24802149 24802163 24802281 24892722 42626680 46188479 44328781 44328785 46780441 46897877 51340651 50939543 54445181 54445182 57197748 57288387 57483528 60052896 60078648 56845432 56845995 59034276 59036328 59040622 59083882 59105109 59125088 57691826 58594768 59146659 58595959 58618581 59503411 59503407 59383280 57973135 59445439 58969552 59886072 58070804 59965103 58265153 58265160 58265166 58265178 58265190 58265196 58300638 66629908 67518639 69528681 67615000 67615455 67641738 68167579 68324677 68334110 67938791 67944215 67944290 67950444 70543261 71777654 70443535 71309028 71309128 71309129 71309140 71309397 71309503 71309513 71309514 71309671 71309852 71309905 71309908 71309927 71317094 71317095 71317096 71317097 71317182 75357255 76973265 86278404 88547603 88255060 87297824 89000581 90057933 90781811 87929779 87931119 88974141 92043367 92043446 90159939 90895196 89200515 89332529 90346255 89374440 91057721 89742272 89424182 90470917 90472751 90472752 90472753 90472761 90472762 90472770 90473076 89855666 101015849 101033892 101513786 102089288 101254308 101254309 101254310 101254311 101254312 101254313 101254314 101254315 101718250 101718251 101796201 101469918 102601142 102601177 102601371 102601743 102601816 102447462 102447463 117064633 117064644 117065485 117633116 117768413 118797420 118797610 118797621 118797622 118855904 118855887 118855889 118855910 118855920 118855925 117938207 118924468 122522140 121494046 121494058 122360911 126704391 133119158 133119249 133121364 129629038 131698424 131698425 131698450 131699179 131706405 132939819 132939820 133662560 133662561 133662562 131842051 134695353 131966764 134860471 139025182 137554722);CHEBI:(37686 80962 37692 28729 28563 72452 68462 27667 37680 37620 28102 63421 141392 42905 27517 15903 37677 27380 28061 18269 37706 59552 37630 4191 40656 37744 15444 59573 4093 37740 28100 4139 37679 4167 88300 18398 86059 37627 37619 83029 37704 37671 37631 27857 37693 18246 4208 43104 37741 17925);PubChem class - bio and metabolites;KEGG:(C00737 C01487 C06466 C06465 C15923 C06464 C00031 C06467 C00962 C02209 C00221 C21032 C01825 C00124 C00936 C00738 C00984 C21050 C00267 C00159);PubChem class - safety and toxic;YMDB:(273 146 894 286 72 846);Training Set;PubChem class - drug;Biocyc:(SMA-0000448 CPD-15625 CPD-15622 CPD-15758 ALPHA-GLUCOSE CPD-15628 SMA-0000188 CPD-3607 CPD-18461 CPD-12601 CPD-15627 SMA-0000654 CPD185E-2 SMA-0000436 CPD-13428 CPD-15624 Alpha-D-Talose CPD-15621 CPD-2361 CPD-11613 CPD-15762 CPD-15757 CPD-15761 GLC CPD-9918 D-AMINO-ACID GALACTOSE SMA-0000420 ALPHA-D-GALACTOSE CPD-15759 CPD-5725 SMA-0000670 L-GALACTOSE CPD-11611 CPD-13559) 255846782 179.0561 NaN 1_unknown_ N/A diff --git a/tools/sirius_csifingerid/test-data/annotation_RP022611_result_all_adducts.tsv b/tools/sirius_csifingerid/test-data/annotation_RP022611_result_all_adducts.tsv index 1682c02..cbe39ae 100644 --- a/tools/sirius_csifingerid/test-data/annotation_RP022611_result_all_adducts.tsv +++ b/tools/sirius_csifingerid/test-data/annotation_RP022611_result_all_adducts.tsv @@ -1,4 +1,4 @@ -name adduct rank formulaRank #adducts #predictedFPs ConfidenceScore CSI:FingerIDScore ZodiacScore SiriusScore molecularFormula adduct InChIkey2D InChI name smiles xlogp pubchemids links dbflags ionMass retentionTimeInSeconds id -D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- [M-H]- 1 1 1 1 0.31290839506383084 -56.37857062945502 N/A 35.11438137495146 C6H12O6 [M-H]- WQZGKKKJIJFFOK InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2 D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- C(C1C(C(C(C(O1)O)O)O)O)O -2.5999999 206;5793;6036;18950;1549080;64689;79025;81696;657055;185698;439353;439357;439507;439583;439680;441032;441033;441034;441035;3000450;444314;448388;448702;451187;451188;451189;452245;455147;3034742;2724488;7018164;5104362;7043897;7044038;7098663;7098664;7157007;6102790;5319264;6321330;6323336;6400264;6560213;6971003;6971007;6971016;6971096;6971097;6971098;6992021;6992084;9794056;12003287;9815418;9834129;12193653;12285853;12285856;12285861;12285862;12285863;12285866;12285870;12285871;12285873;12285877;12285878;12285879;12285885;12285886;12285889;12285890;12285891;12285892;12285893;12285894;9899007;10899282;10035228;10954241;11571906;11571917;10081060;11600783;10103794;11019447;11030410;10130220;11651921;11672764;10197954;10219674;10219763;10313382;10329946;11344362;11959770;11367383;11970126;11412863;11480819;11492034;16211884;16211941;16211984;16211986;16212959;16212960;16212966;16213546;16213640;16213872;16217112;16219580;22825318;22836365;22836366;21355827;23424086;24802149;24802163;24802281;24892722;42626680;46188479;44328781;44328785;46780441;46897877;51340651;50939543;54445181;54445182;57197748;57288387;57483528;60052896;60078648;56845432;56845995;59034276;59036328;59040622;59083882;59105109;59125088;57691826;58594768;59146659;58595959;58618581;59503411;59503407;59383280;57973135;59445439;58969552;59886072;58070804;59965103;58265153;58265160;58265166;58265178;58265190;58265196;58300638;66629908;67518639;69528681;67615000;67615455;67641738;68167579;68324677;68334110;67938791;67944215;67944290;67950444;70543261;71777654;70443535;71309028;71309128;71309129;71309140;71309397;71309503;71309513;71309514;71309671;71309852;71309905;71309908;71309927;71317094;71317095;71317096;71317097;71317182;75357255;76973265;86278404;88547603;88255060;87297824;89000581;90057933;90781811;87929779;87931119;88974141;92043367;92043446;90159939;90895196;89200515;89332529;90346255;89374440;91057721;89742272;89424182;90470917;90472751;90472752;90472753;90472761;90472762;90472770;90473076;89855666;101015849;101033892;101513786;102089288;101254308;101254309;101254310;101254311;101254312;101254313;101254314;101254315;101718250;101718251;101796201;101469918;102601142;102601177;102601371;102601743;102601816;102447462;102447463;117064633;117064644;117065485;117633116;117768413;118797420;118797610;118797621;118797622;118855904;118855887;118855889;118855910;118855920;118855925;117938207;118924468;122522140;121494046;121494058;122360911;126704391;133119158;133119249;133121364;129629038;131698424;131698425;131698450;131699179;131706405;132939819;132939820;133662560;133662561;133662562;131842051;134695353;131966764;134860471;139025182;137554722 HMDB:(122 516 3345 1151 62202 12326 3449 169 33704 143 61922);PubChem class - food;SuperNatural:(SN00048687 SN00050524 SN00321479 SN00064345 SN00003330 SN00396363 SN00005681 SN00330500 SN00156785 SN00156795 SN00001876 SN00048690 SN00226998 SN00064344 SN00273897 SN00048679);ZINC bio:(ZINC00895026 ZINC00895055 ZINC00895084 ZINC00895350 ZINC00896168 ZINC00896169 ZINC00897147 ZINC00901155 ZINC01529206 ZINC01530434 ZINC01532520 ZINC01532549 ZINC02545114 ZINC02597049 ZINC03581097 ZINC03830678 ZINC03830679 ZINC03833800 ZINC03860903 ZINC03861213 ZINC04095659 ZINC04095660 ZINC04097150 ZINC04097151 ZINC04097152 ZINC04097153 ZINC04262018 ZINC04529488);additional;MeSH:(5793 6036 18950 79025 439357 439507 439680 441032 441033 441035 11030410);Plantcyc:(CPD-3607 ALPHA-D-GALACTOSE X-DMAN-HEX-);PubMed;NORMAN:(NS00007629);COCONUT:(CNP0082250 CNP0210547);KNApSAcK:(1126);Natural Products:(UNPD148053 UNPD130932 UNPD191130 UNPD175204 UNPD20367 UNPD175249 UNPD72621 UNPD116684 UNPD158921 UNPD175399 UNPD119270 UNPD83717);PubChem:(206 5793 6036 18950 1549080 64689 79025 81696 657055 185698 439353 439357 439507 439583 439680 441032 441033 441034 441035 3000450 444314 448388 448702 451187 451188 451189 452245 455147 3034742 2724488 7018164 5104362 7043897 7044038 7098663 7098664 7157007 6102790 5319264 6321330 6323336 6400264 6560213 6971003 6971007 6971016 6971096 6971097 6971098 6992021 6992084 9794056 12003287 9815418 9834129 12193653 12285853 12285856 12285861 12285862 12285863 12285866 12285870 12285871 12285873 12285877 12285878 12285879 12285885 12285886 12285889 12285890 12285891 12285892 12285893 12285894 9899007 10899282 10035228 10954241 11571906 11571917 10081060 11600783 10103794 11019447 11030410 10130220 11651921 11672764 10197954 10219674 10219763 10313382 10329946 11344362 11959770 11367383 11970126 11412863 11480819 11492034 16211884 16211941 16211984 16211986 16212959 16212960 16212966 16213546 16213640 16213872 16217112 16219580 22825318 22836365 22836366 21355827 23424086 24802149 24802163 24802281 24892722 42626680 46188479 44328781 44328785 46780441 46897877 51340651 50939543 54445181 54445182 57197748 57288387 57483528 60052896 60078648 56845432 56845995 59034276 59036328 59040622 59083882 59105109 59125088 57691826 58594768 59146659 58595959 58618581 59503411 59503407 59383280 57973135 59445439 58969552 59886072 58070804 59965103 58265153 58265160 58265166 58265178 58265190 58265196 58300638 66629908 67518639 69528681 67615000 67615455 67641738 68167579 68324677 68334110 67938791 67944215 67944290 67950444 70543261 71777654 70443535 71309028 71309128 71309129 71309140 71309397 71309503 71309513 71309514 71309671 71309852 71309905 71309908 71309927 71317094 71317095 71317096 71317097 71317182 75357255 76973265 86278404 88547603 88255060 87297824 89000581 90057933 90781811 87929779 87931119 88974141 92043367 92043446 90159939 90895196 89200515 89332529 90346255 89374440 91057721 89742272 89424182 90470917 90472751 90472752 90472753 90472761 90472762 90472770 90473076 89855666 101015849 101033892 101513786 102089288 101254308 101254309 101254310 101254311 101254312 101254313 101254314 101254315 101718250 101718251 101796201 101469918 102601142 102601177 102601371 102601743 102601816 102447462 102447463 117064633 117064644 117065485 117633116 117768413 118797420 118797610 118797621 118797622 118855904 118855887 118855889 118855910 118855920 118855925 117938207 118924468 122522140 121494046 121494058 122360911 126704391 133119158 133119249 133121364 129629038 131698424 131698425 131698450 131699179 131706405 132939819 132939820 133662560 133662561 133662562 131842051 134695353 131966764 134860471 139025182 137554722);CHEBI:(37686 80962 37692 28729 28563 72452 68462 27667 37680 37620 28102 63421 141392 42905 27517 15903 37677 27380 28061 18269 37706 59552 37630 4191 40656 37744 15444 59573 4093 37740 28100 4139 37679 4167 88300 18398 86059 37627 37619 83029 37704 37671 37631 27857 37693 18246 4208 43104 37741 17925);PubChem class - bio and metabolites;KEGG:(C00737 C01487 C06466 C06465 C15923 C06464 C00031 C06467 C00962 C02209 C00221 C21032 C01825 C00124 C00936 C00738 C00984 C21050 C00267 C00159);PubChem class - safety and toxic;YMDB:(273 146 894 286 72 846);Training Set;PubChem class - drug;Biocyc:(SMA-0000448 CPD-15625 CPD-15622 CPD-15758 ALPHA-GLUCOSE CPD-15628 SMA-0000188 CPD-3607 CPD-18461 CPD-12601 CPD-15627 SMA-0000654 CPD185E-2 SMA-0000436 CPD-13428 CPD-15624 Alpha-D-Talose CPD-15621 CPD-2361 CPD-11613 CPD-15762 CPD-15757 CPD-15761 GLC CPD-9918 D-AMINO-ACID GALACTOSE SMA-0000420 ALPHA-D-GALACTOSE CPD-15759 CPD-5725 SMA-0000670 L-GALACTOSE CPD-11611 CPD-13559) 255846782 179.0561 NaN 0_unknown_ -D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- [M+HCOO]- 1 1 1 1 0.24088665114193236 -81.22229366045529 N/A 35.11438137495146 C5H10O4 [M+HCOO]- WDRISBUVHBMJEF InChI=1S/C5H10O4/c1-3(7)5(9)4(8)2-6/h2-5,7-9H,1H3 D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- CC(C(C(C=O)O)O)O -1.06286943 191114;13420529;11708064;18646774;45489773;53470544;57557847;88414315;92977673;98621168;135056775 PubChem:(191114 13420529 11708064 18646774 45489773 53470544 57557847 88414315 92977673 98621168 135056775);CHEBI:(62012);ZINC bio:(ZINC03652727 ZINC34194163 ZINC39644846);MeSH:(191114);Plantcyc:(CPD0-2167);Biocyc:(CPD0-2167);KEGG Mine 8590075942 179.0561 NaN 0_unknown_ -D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- [M+CH3COO]- 1 1 1 1 0.20584202493535325 -67.54430717221075 N/A 26.30175603007533 C4H8O4 [M+CH3COO]- YTBSYETUWUMLBZ InChI=1S/C4H8O4/c5-1-3(7)4(8)2-6/h1,3-4,6-8H,2H2 D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- C(C(C(C=O)O)O)O -2.20000005 94176;101561;439665;5460672;5460674;15559153;71774579;90145916;89822422;121493653;121493654;130699532;131879647;131883807;131887274 SuperNatural:(SN00394603);ZINC bio:(ZINC01760169 ZINC01760171 ZINC18185147);MeSH:(94176 101561 5460672);Plantcyc:(THREOSE);PubMed;NORMAN:(NS00032729);COCONUT:(CNP0166180);KNApSAcK:(7412);Natural Products:(UNPD167167);PubChem:(94176 101561 439665 5460672 5460674 15559153 71774579 90145916 89822422 121493653 121493654 130699532 131879647 131883807 131887274);YMDB Mine;CHEBI:(27904 28587 21405 21288);PubChem class - bio and metabolites;EcoCyc Mine;PubChem class - safety and toxic;Training Set;Biocyc:(ERYTHROSE THREOSE);KEGG Mine 60217026678 179.0561 NaN 0_unknown_ +name adduct confidenceRank structurePerIdRank formulaRank #adducts #predictedFPs ConfidenceScore CSI:FingerIDScore ZodiacScore SiriusScore molecularFormula adduct InChIkey2D InChI name smiles xlogp pubchemids links dbflags ionMass retentionTimeInSeconds id featureId +D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- [M-H]- 1 1 1 1 1 0.26766749344403346 -18.744222610782234 N/A 33.159317785798166 C6H12O6 [M-H]- WQZGKKKJIJFFOK InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2 D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- C(C1C(C(C(C(O1)O)O)O)O)O -2.5999999 206;5793;6036;18950;1549080;64689;79025;81696;657055;185698;439353;439357;439507;439583;439680;441032;441033;441034;441035;3000450;444314;448388;448702;451187;451188;451189;452245;455147;3034742;2724488;7018164;5104362;7043897;7044038;7098663;7098664;7157007;6102790;5319264;6321330;6323336;6400264;6560213;6971003;6971007;6971016;6971096;6971097;6971098;6992021;6992084;9794056;12003287;9815418;9834129;12193653;12285853;12285856;12285861;12285862;12285863;12285866;12285870;12285871;12285873;12285877;12285878;12285879;12285885;12285886;12285889;12285890;12285891;12285892;12285893;12285894;9899007;10899282;10035228;10954241;11571906;11571917;10081060;11600783;10103794;11019447;11030410;10130220;11651921;11672764;10197954;10219674;10219763;10313382;10329946;11344362;11959770;11367383;11970126;11412863;11480819;11492034;16211884;16211941;16211984;16211986;16212959;16212960;16212966;16213546;16213640;16213872;16217112;16219580;22825318;22836365;22836366;21355827;23424086;24802149;24802163;24802281;24892722;42626680;46188479;44328781;44328785;46780441;46897877;51340651;50939543;54445181;54445182;57197748;57288387;57483528;60052896;60078648;56845432;56845995;59034276;59036328;59040622;59083882;59105109;59125088;57691826;58594768;59146659;58595959;58618581;59503411;59503407;59383280;57973135;59445439;58969552;59886072;58070804;59965103;58265153;58265160;58265166;58265178;58265190;58265196;58300638;66629908;67518639;69528681;67615000;67615455;67641738;68167579;68324677;68334110;67938791;67944215;67944290;67950444;70543261;71777654;70443535;71309028;71309128;71309129;71309140;71309397;71309503;71309513;71309514;71309671;71309852;71309905;71309908;71309927;71317094;71317095;71317096;71317097;71317182;75357255;76973265;86278404;88547603;88255060;87297824;89000581;90057933;90781811;87929779;87931119;88974141;92043367;92043446;90159939;90895196;89200515;89332529;90346255;89374440;91057721;89742272;89424182;90470917;90472751;90472752;90472753;90472761;90472762;90472770;90473076;89855666;101015849;101033892;101513786;102089288;101254308;101254309;101254310;101254311;101254312;101254313;101254314;101254315;101718250;101718251;101796201;101469918;102601142;102601177;102601371;102601743;102601816;102447462;102447463;117064633;117064644;117065485;117633116;117768413;118797420;118797610;118797621;118797622;118855904;118855887;118855889;118855910;118855920;118855925;117938207;118924468;122522140;121494046;121494058;122360911;126704391;133119158;133119249;133121364;129629038;131698424;131698425;131698450;131699179;131706405;132939819;132939820;133662560;133662561;133662562;131842051;134695353;131966764;134860471;139025182;137554722 HMDB:(122 516 3345 1151 62202 12326 3449 169 33704 143 61922);PubChem class - food;SuperNatural:(SN00048687 SN00050524 SN00321479 SN00064345 SN00003330 SN00396363 SN00005681 SN00330500 SN00156785 SN00156795 SN00001876 SN00048690 SN00226998 SN00064344 SN00273897 SN00048679);ZINC bio:(ZINC00895026 ZINC00895055 ZINC00895084 ZINC00895350 ZINC00896168 ZINC00896169 ZINC00897147 ZINC00901155 ZINC01529206 ZINC01530434 ZINC01532520 ZINC01532549 ZINC02545114 ZINC02597049 ZINC03581097 ZINC03830678 ZINC03830679 ZINC03833800 ZINC03860903 ZINC03861213 ZINC04095659 ZINC04095660 ZINC04097150 ZINC04097151 ZINC04097152 ZINC04097153 ZINC04262018 ZINC04529488);additional;MeSH:(5793 6036 18950 79025 439357 439507 439680 441032 441033 441035 11030410);Plantcyc:(CPD-3607 ALPHA-D-GALACTOSE X-DMAN-HEX-1:5_6:A CPD4FS-6 CPD-15762 ALPHA-GLUCOSE CPD-12601 CPD-15761 GLC L-GALACTOSE CPD-13559 GALACTOSE);PubMed;NORMAN:(NS00007629);COCONUT:(CNP0082250 CNP0210547);KNApSAcK:(1126);Natural Products:(UNPD148053 UNPD130932 UNPD191130 UNPD175204 UNPD20367 UNPD175249 UNPD72621 UNPD116684 UNPD158921 UNPD175399 UNPD119270 UNPD83717);PubChem:(206 5793 6036 18950 1549080 64689 79025 81696 657055 185698 439353 439357 439507 439583 439680 441032 441033 441034 441035 3000450 444314 448388 448702 451187 451188 451189 452245 455147 3034742 2724488 7018164 5104362 7043897 7044038 7098663 7098664 7157007 6102790 5319264 6321330 6323336 6400264 6560213 6971003 6971007 6971016 6971096 6971097 6971098 6992021 6992084 9794056 12003287 9815418 9834129 12193653 12285853 12285856 12285861 12285862 12285863 12285866 12285870 12285871 12285873 12285877 12285878 12285879 12285885 12285886 12285889 12285890 12285891 12285892 12285893 12285894 9899007 10899282 10035228 10954241 11571906 11571917 10081060 11600783 10103794 11019447 11030410 10130220 11651921 11672764 10197954 10219674 10219763 10313382 10329946 11344362 11959770 11367383 11970126 11412863 11480819 11492034 16211884 16211941 16211984 16211986 16212959 16212960 16212966 16213546 16213640 16213872 16217112 16219580 22825318 22836365 22836366 21355827 23424086 24802149 24802163 24802281 24892722 42626680 46188479 44328781 44328785 46780441 46897877 51340651 50939543 54445181 54445182 57197748 57288387 57483528 60052896 60078648 56845432 56845995 59034276 59036328 59040622 59083882 59105109 59125088 57691826 58594768 59146659 58595959 58618581 59503411 59503407 59383280 57973135 59445439 58969552 59886072 58070804 59965103 58265153 58265160 58265166 58265178 58265190 58265196 58300638 66629908 67518639 69528681 67615000 67615455 67641738 68167579 68324677 68334110 67938791 67944215 67944290 67950444 70543261 71777654 70443535 71309028 71309128 71309129 71309140 71309397 71309503 71309513 71309514 71309671 71309852 71309905 71309908 71309927 71317094 71317095 71317096 71317097 71317182 75357255 76973265 86278404 88547603 88255060 87297824 89000581 90057933 90781811 87929779 87931119 88974141 92043367 92043446 90159939 90895196 89200515 89332529 90346255 89374440 91057721 89742272 89424182 90470917 90472751 90472752 90472753 90472761 90472762 90472770 90473076 89855666 101015849 101033892 101513786 102089288 101254308 101254309 101254310 101254311 101254312 101254313 101254314 101254315 101718250 101718251 101796201 101469918 102601142 102601177 102601371 102601743 102601816 102447462 102447463 117064633 117064644 117065485 117633116 117768413 118797420 118797610 118797621 118797622 118855904 118855887 118855889 118855910 118855920 118855925 117938207 118924468 122522140 121494046 121494058 122360911 126704391 133119158 133119249 133121364 129629038 131698424 131698425 131698450 131699179 131706405 132939819 132939820 133662560 133662561 133662562 131842051 134695353 131966764 134860471 139025182 137554722);CHEBI:(37686 80962 37692 28729 28563 72452 68462 27667 37680 37620 28102 63421 141392 42905 27517 15903 37677 27380 28061 18269 37706 59552 37630 4191 40656 37744 15444 59573 4093 37740 28100 4139 37679 4167 88300 18398 86059 37627 37619 83029 37704 37671 37631 27857 37693 18246 4208 43104 37741 17925);PubChem class - bio and metabolites;KEGG:(C00737 C01487 C06466 C06465 C15923 C06464 C00031 C06467 C00962 C02209 C00221 C21032 C01825 C00124 C00936 C00738 C00984 C21050 C00267 C00159);PubChem class - safety and toxic;YMDB:(273 146 894 286 72 846);Training Set;PubChem class - drug;Biocyc:(SMA-0000448 CPD-15625 CPD-15622 CPD-15758 ALPHA-GLUCOSE CPD-15628 SMA-0000188 CPD-3607 CPD-18461 CPD-12601 CPD-15627 SMA-0000654 CPD185E-2 SMA-0000436 CPD-13428 CPD-15624 Alpha-D-Talose CPD-15621 CPD-2361 CPD-11613 CPD-15762 CPD-15757 CPD-15761 GLC CPD-9918 D-AMINO-ACID GALACTOSE SMA-0000420 ALPHA-D-GALACTOSE CPD-15759 CPD-5725 SMA-0000670 L-GALACTOSE CPD-11611 CPD-13559) 255846782 179.0561 NaN 1_unknown_ N/A +D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- [M+HCOO]- 1 1 1 1 1 0.11953824052271411 -51.072129216820414 N/A 33.159317785798166 C5H10O4 [M+HCOO]- ZGOWPCHSOHJRIL InChI=1S/C5H10O4/c6-2-1-4(8)5(9)3-7/h3-6,8-9H,1-2H2 D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- C(CO)C(C(C=O)O)O -1.79999995 3035777;19076362;87374177;101407601;129115757;135054437 MeSH:(3035777);PubChem:(3035777 19076362 87374177 101407601 129115757 135054437);PubMed 70 179.0561 NaN 1_unknown_ N/A +D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- [M+CH3COO]- 1 1 1 1 1 0.1817841302932399 -38.37729715337194 N/A 25.031183734465845 C4H8O4 [M+CH3COO]- YTBSYETUWUMLBZ InChI=1S/C4H8O4/c5-1-3(7)4(8)2-6/h1,3-4,6-8H,2H2 D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- C(C(C(C=O)O)O)O -2.20000005 94176;101561;439665;5460672;5460674;15559153;71774579;90145916;89822422;121493653;121493654;130699532;131879647;131883807;131887274 SuperNatural:(SN00394603);ZINC bio:(ZINC01760169 ZINC01760171 ZINC18185147);MeSH:(94176 101561 5460672);Plantcyc:(THREOSE);PubMed;NORMAN:(NS00032729);COCONUT:(CNP0166180);KNApSAcK:(7412);Natural Products:(UNPD167167);PubChem:(94176 101561 439665 5460672 5460674 15559153 71774579 90145916 89822422 121493653 121493654 130699532 131879647 131883807 131887274);YMDB Mine;CHEBI:(27904 28587 21405 21288);PubChem class - bio and metabolites;EcoCyc Mine;PubChem class - safety and toxic;Training Set;Biocyc:(ERYTHROSE THREOSE);KEGG Mine 60217026678 179.0561 NaN 1_unknown_ N/A diff --git a/tools/sirius_csifingerid/test-data/annotation_generic.tsv b/tools/sirius_csifingerid/test-data/annotation_generic.tsv index 53e7ba8..8a5740f 100644 --- a/tools/sirius_csifingerid/test-data/annotation_generic.tsv +++ b/tools/sirius_csifingerid/test-data/annotation_generic.tsv @@ -1,6 +1,6 @@ -name adduct rank formulaRank #adducts #predictedFPs ConfidenceScore CSI:FingerIDScore ZodiacScore SiriusScore molecularFormula adduct InChIkey2D InChI name smiles xlogp pubchemids links dbflags ionMass retentionTimeInSeconds id -MZ:86.0606 | RT:1498 | XCMS_group:19 | file:1 | scan:NA [M+H]+ 1 1 1 1 0.26604529106484975 -118.22506236976034 N/A 23.3452897589273 C4H7NO [M+H]+ ABBZJHFBQXYTLU InChI=1S/C4H7NO/c1-2-3-4(5)6/h2H,1,3H2,(H2,5,6) MZ:86.0606 | RT:1498 | XCMS_group:19 | file:1 | scan:NA C=CCC(=O)N -0.100000001 541483;11105303 COCONUT:(CNP0292806);Natural Products:(UNPD154526);PubChem:(541483 11105303);SuperNatural:(SN00312732);ZINC bio:(ZINC02525865);PubChem class - bio and metabolites;PubMed 19963970 86.0606307983398 NaN 0_unknown_ -MZ:72.0815 | RT:1823 | XCMS_group:2 | file:1 | scan:NA [M+H]+ 1 1 1 1 0.20971889099889915 -122.29555245689393 N/A 21.957862557474318 C4H9N [M+H]+ IOXXVNYDGIXMIP InChI=1S/C4H9N/c1-3-4-5-2/h3,5H,1,4H2,2H3 MZ:72.0815 | RT:1823 | XCMS_group:2 | file:1 | scan:NA CNCC=C 0.400000006 69391;37888249 NORMAN:(NS00035152);PubChem class - safety and toxic;PubChem:(69391 37888249);PubMed 67371074 72.0815277099609 NaN 0_unknown_ -MZ:79.0219 | RT:177 | XCMS_group:9 | file:1 | scan:NA [M+H]+ 1 1 1 1 0.8516968844490043 -30.428891568077617 N/A 19.249416937845428 C2H6OS [M+H]+ IAZDPXIOMUYVGZ InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 MZ:79.0219 | RT:177 | XCMS_group:9 | file:1 | scan:NA CS(=O)C -0.600000024 679;75151;12206145;12264368;10103116;18594457;20151975;20719893;21022526;22345572;57247813;71309204;76973052;90811807;90817578 HMDB:(2151);PubChem class - food;Maconda:(CON00016);ZINC bio:(ZINC05224188);HSDB:(67-68-5);MeSH:(679);Plantcyc:(DMSO);PubMed;NORMAN:(NS00001957);Natural Products:(UNPD148866);PubChem:(679 75151 12206145 12264368 10103116 18594457 20151975 20719893 21022526 22345572 57247813 71309204 76973052 90811807 90817578);CHEBI:(28262);PubChem class - bio and metabolites;KEGG:(C11143);PubChem class - safety and toxic;PubChem class - drug;Biocyc:(DMSO) 252096366 79.0218658447266 NaN 0_unknown_ -MZ:79.0219 | RT:184 | XCMS_group:9 | file:1 | scan:NA [M+H]+ 1 1 1 1 0.8955620660537568 -41.80129625695348 N/A 14.61674883848477 C2H6OS [M+H]+ IAZDPXIOMUYVGZ InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 MZ:79.0219 | RT:184 | XCMS_group:9 | file:1 | scan:NA CS(=O)C -0.600000024 679;75151;12206145;12264368;10103116;18594457;20151975;20719893;21022526;22345572;57247813;71309204;76973052;90811807;90817578 HMDB:(2151);PubChem class - food;Maconda:(CON00016);ZINC bio:(ZINC05224188);HSDB:(67-68-5);MeSH:(679);Plantcyc:(DMSO);PubMed;NORMAN:(NS00001957);Natural Products:(UNPD148866);PubChem:(679 75151 12206145 12264368 10103116 18594457 20151975 20719893 21022526 22345572 57247813 71309204 76973052 90811807 90817578);CHEBI:(28262);PubChem class - bio and metabolites;KEGG:(C11143);PubChem class - safety and toxic;PubChem class - drug;Biocyc:(DMSO) 252096366 79.0218811035156 NaN 0_unknown_ -MZ:79.0219 | RT:212 | XCMS_group:9 | file:1 | scan:NA [M+H]+ 1 1 1 1 0.8320051497664187 -29.61962034150095 N/A 27.955014068311474 C2H6OS [M+H]+ IAZDPXIOMUYVGZ InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 MZ:79.0219 | RT:212 | XCMS_group:9 | file:1 | scan:NA CS(=O)C -0.600000024 679;75151;12206145;12264368;10103116;18594457;20151975;20719893;21022526;22345572;57247813;71309204;76973052;90811807;90817578 HMDB:(2151);PubChem class - food;Maconda:(CON00016);ZINC bio:(ZINC05224188);HSDB:(67-68-5);MeSH:(679);Plantcyc:(DMSO);PubMed;NORMAN:(NS00001957);Natural Products:(UNPD148866);PubChem:(679 75151 12206145 12264368 10103116 18594457 20151975 20719893 21022526 22345572 57247813 71309204 76973052 90811807 90817578);CHEBI:(28262);PubChem class - bio and metabolites;KEGG:(C11143);PubChem class - safety and toxic;PubChem class - drug;Biocyc:(DMSO) 252096366 79.0218887329102 NaN 0_unknown_ +name adduct confidenceRank structurePerIdRank formulaRank #adducts #predictedFPs ConfidenceScore CSI:FingerIDScore ZodiacScore SiriusScore molecularFormula adduct InChIkey2D InChI name smiles xlogp pubchemids links dbflags ionMass retentionTimeInSeconds id featureId +MZ:86.0606 | RT:1498 | XCMS_group:19 | file:1 | scan:NA [M+H]+ 1 1 1 1 1 0.246964170716151 -87.90262840670921 N/A 22.461314199360764 C4H7NO [M+H]+ HNJBEVLQSNELDL InChI=1S/C4H7NO/c6-4-2-1-3-5-4/h1-3H2,(H,5,6) MZ:86.0606 | RT:1498 | XCMS_group:19 | file:1 | scan:NA C1CC(=O)NC1 -0.0972428098 12025;3956071;12197590;12197592;10419134;20030003;20589568;18999930;58329813;90472990;91343693;101225382;101796586;123509162 HMDB:(2039);ZINC bio:(ZINC14684428);additional;HSDB:(616-45-5);MeSH:(12025);Plantcyc:(CPD-19607);PubMed;NORMAN:(NS00007032);COCONUT:(CNP0127855);KNApSAcK:(38233);Natural Products:(UNPD211738);PubChem:(12025 3956071 12197590 12197592 10419134 20030003 20589568 18999930 58329813 90472990 91343693 101225382 101796586 123509162);YMDB Mine;CHEBI:(36592);PubChem class - bio and metabolites;EcoCyc Mine;PubChem class - safety and toxic;Biocyc:(CPD-19607);KEGG Mine 60216486526 86.0606307983398 NaN 1_unknown_ N/A +MZ:72.0815 | RT:1823 | XCMS_group:2 | file:1 | scan:NA [M+H]+ 1 1 1 1 1 0.18725682827485585 -64.77612201011893 N/A 22.249117361045933 C4H9N [M+H]+ IOXXVNYDGIXMIP InChI=1S/C4H9N/c1-3-4-5-2/h3,5H,1,4H2,2H3 MZ:72.0815 | RT:1823 | XCMS_group:2 | file:1 | scan:NA CNCC=C 0.400000006 69391;37888249 NORMAN:(NS00035152);PubChem class - safety and toxic;PubChem:(69391 37888249);PubMed 67371074 72.0815277099609 NaN 1_unknown_ N/A +MZ:79.0219 | RT:177 | XCMS_group:9 | file:1 | scan:NA [M+H]+ 1 1 1 1 1 0.7922594558382015 -22.01296407905157 N/A 19.97137826965732 C2H6OS [M+H]+ IAZDPXIOMUYVGZ InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 MZ:79.0219 | RT:177 | XCMS_group:9 | file:1 | scan:NA CS(=O)C -0.600000024 679;75151;12206145;12264368;10103116;18594457;20151975;20719893;21022526;22345572;57247813;71309204;76973052;90811807;90817578 HMDB:(2151);PubChem class - food;Maconda:(CON00016);ZINC bio:(ZINC05224188);HSDB:(67-68-5);MeSH:(679);Plantcyc:(DMSO);PubMed;NORMAN:(NS00001957);Natural Products:(UNPD148866);PubChem:(679 75151 12206145 12264368 10103116 18594457 20151975 20719893 21022526 22345572 57247813 71309204 76973052 90811807 90817578);CHEBI:(28262);PubChem class - bio and metabolites;KEGG:(C11143);PubChem class - safety and toxic;PubChem class - drug;Biocyc:(DMSO) 252096366 79.0218658447266 NaN 1_unknown_ N/A +MZ:79.0219 | RT:184 | XCMS_group:9 | file:1 | scan:NA [M+H]+ 1 1 1 1 1 0.6210867138039745 -33.920592416531996 N/A 14.85848518016152 C2H6OS [M+H]+ IAZDPXIOMUYVGZ InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 MZ:79.0219 | RT:184 | XCMS_group:9 | file:1 | scan:NA CS(=O)C -0.600000024 679;75151;12206145;12264368;10103116;18594457;20151975;20719893;21022526;22345572;57247813;71309204;76973052;90811807;90817578 HMDB:(2151);PubChem class - food;Maconda:(CON00016);ZINC bio:(ZINC05224188);HSDB:(67-68-5);MeSH:(679);Plantcyc:(DMSO);PubMed;NORMAN:(NS00001957);Natural Products:(UNPD148866);PubChem:(679 75151 12206145 12264368 10103116 18594457 20151975 20719893 21022526 22345572 57247813 71309204 76973052 90811807 90817578);CHEBI:(28262);PubChem class - bio and metabolites;KEGG:(C11143);PubChem class - safety and toxic;PubChem class - drug;Biocyc:(DMSO) 252096366 79.0218811035156 NaN 1_unknown_ N/A +MZ:79.0219 | RT:212 | XCMS_group:9 | file:1 | scan:NA [M+H]+ 1 1 1 1 1 0.7676244132524646 -22.20830147238356 N/A 28.90460805630226 C2H6OS [M+H]+ IAZDPXIOMUYVGZ InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 MZ:79.0219 | RT:212 | XCMS_group:9 | file:1 | scan:NA CS(=O)C -0.600000024 679;75151;12206145;12264368;10103116;18594457;20151975;20719893;21022526;22345572;57247813;71309204;76973052;90811807;90817578 HMDB:(2151);PubChem class - food;Maconda:(CON00016);ZINC bio:(ZINC05224188);HSDB:(67-68-5);MeSH:(679);Plantcyc:(DMSO);PubMed;NORMAN:(NS00001957);Natural Products:(UNPD148866);PubChem:(679 75151 12206145 12264368 10103116 18594457 20151975 20719893 21022526 22345572 57247813 71309204 76973052 90811807 90817578);CHEBI:(28262);PubChem class - bio and metabolites;KEGG:(C11143);PubChem class - safety and toxic;PubChem class - drug;Biocyc:(DMSO) 252096366 79.0218887329102 NaN 1_unknown_ N/A diff --git a/tools/sirius_csifingerid/test-data/canopus_CCMSLIB00000578155_result.tsv b/tools/sirius_csifingerid/test-data/canopus_CCMSLIB00000578155_result.tsv index 9f30b8f..f838c68 100644 --- a/tools/sirius_csifingerid/test-data/canopus_CCMSLIB00000578155_result.tsv +++ b/tools/sirius_csifingerid/test-data/canopus_CCMSLIB00000578155_result.tsv @@ -1,2 +1,2 @@ -name adduct name molecularFormula adduct most specific class level 5 subclass class superclass all classifications -D-GLUCOSE-6-PHOSPHATE [M-H]- D-GLUCOSE-6-PHOSPHATE C6H13O9P [M-H]- Hexose phosphates Monosaccharides Carbohydrates and carbohydrate conjugates Organooxygen compounds Organic oxygen compounds Organic compounds; Organoheterocyclic compounds; Carbohydrates and carbohydrate conjugates; Alcohols and polyols; Ethers; Organic acids and derivatives; Organooxygen compounds; Organic phosphoric acids and derivatives; Phosphate esters; Hemiacetals; Hexoses; Monosaccharides; Monosaccharide phosphates; Secondary alcohols; Oxanes; Hexose phosphates; Polyols; Alkyl phosphates; Monoalkyl phosphates; Organic oxides; Oxacyclic compounds; Hydrocarbon derivatives; Organic oxygen compounds; Chemical entities +name adduct id molecularFormula adduct precursorFormula NPC#pathway NPC#pathway Probability NPC#superclass NPC#superclass Probability NPC#class NPC#class Probability ClassyFire#most specific class ClassyFire#most specific class Probability ClassyFire#level 5 ClassyFire#level 5 Probability ClassyFire#subclass ClassyFire#subclass Probability ClassyFire#class ClassyFire#class Probability ClassyFire#superclass ClassyFire#superclass probability ClassyFire#all classifications featureId +D-GLUCOSE-6-PHOSPHATE [M-H]- 1_unknown_ C6H13O9P [M-H]- C6H13O9P Carbohydrates 0.9452296495437622 Saccharides 0.9804683923721313 Monosaccharides 0.9375938177108765 Hexose phosphates 0.5990021228790283 Monosaccharides 0.9961119294166565 Carbohydrates and carbohydrate conjugates 0.9951272010803223 Organooxygen compounds 0.9999991655349731 Organic oxygen compounds 0.9999998807907104 Organic compounds; Organoheterocyclic compounds; Carbohydrates and carbohydrate conjugates; Alcohols and polyols; Organic acids and derivatives; Primary alcohols; Organooxygen compounds; Organic phosphoric acids and derivatives; Phosphate esters; Hexoses; Monosaccharides; Monosaccharide phosphates; Secondary alcohols; Oxanes; Acyloins; Hexose phosphates; Polyols; Alpha-hydroxy ketones; Beta-hydroxy ketones; Alkyl phosphates; Monoalkyl phosphates; Organic oxides; Oxacyclic compounds; Hydrocarbon derivatives; Organic oxygen compounds; Chemical entities N/A diff --git a/tools/sirius_csifingerid/test-data/canopus_ML006801.tsv b/tools/sirius_csifingerid/test-data/canopus_ML006801.tsv index cdd193e..152992a 100644 --- a/tools/sirius_csifingerid/test-data/canopus_ML006801.tsv +++ b/tools/sirius_csifingerid/test-data/canopus_ML006801.tsv @@ -1,2 +1,2 @@ -name adduct name molecularFormula adduct most specific class level 5 subclass class superclass all classifications -L-thialysine; LC-ESI-ITFT; MS2; CE: 50%; R=7500; [M+H]+ [M+H]+ L-thialysine; LC-ESI-ITFT; MS2; CE: 50%; R=7500; [M+H]+ C5H12N2O2S [M+H]+ L-alpha-amino acids Amino acids and derivatives Amino acids, peptides, and analogues Carboxylic acids and derivatives Organic acids and derivatives Organic compounds; Organosulfur compounds; Amino acids, peptides, and analogues; Alpha amino acids and derivatives; Organic acids and derivatives; Carboxylic acids and derivatives; Organonitrogen compounds; Organooxygen compounds; Amino acids and derivatives; Monoalkylamines; Monocarboxylic acids and derivatives; Thioethers; Carboxylic acids; Carbonyl compounds; Alpha amino acids; Amines; Primary amines; Sulfenyl compounds; Dialkylthioethers; Organic oxides; L-alpha-amino acids; Hydrocarbon derivatives; Amino acids; Cysteine and derivatives; Organopnictogen compounds; Organic oxygen compounds; Organic nitrogen compounds; Chemical entities +name adduct id molecularFormula adduct precursorFormula NPC#pathway NPC#pathway Probability NPC#superclass NPC#superclass Probability NPC#class NPC#class Probability ClassyFire#most specific class ClassyFire#most specific class Probability ClassyFire#level 5 ClassyFire#level 5 Probability ClassyFire#subclass ClassyFire#subclass Probability ClassyFire#class ClassyFire#class Probability ClassyFire#superclass ClassyFire#superclass probability ClassyFire#all classifications featureId +L-thialysine; LC-ESI-ITFT; MS2; CE: 50%; R=7500; [M+H]+ [M+H]+ 1_unknown_ C5H12N2O2S [M+H]+ C5H12N2O2S Amino acids and Peptides 0.9929136633872986 Small peptides 0.9823712706565857 Aminoacids 0.9485365748405457 L-alpha-amino acids 0.5713847875595093 Amino acids and derivatives 0.9991542100906372 Amino acids, peptides, and analogues 0.9991558790206909 Carboxylic acids and derivatives 0.9970132112503052 Organic acids and derivatives 0.9997649788856506 Organic compounds; Organosulfur compounds; Amino acids, peptides, and analogues; Alpha amino acids and derivatives; Organic acids and derivatives; Carboxylic acids and derivatives; Organonitrogen compounds; Organooxygen compounds; Amino acids and derivatives; Monoalkylamines; Monocarboxylic acids and derivatives; Thioethers; Carboxylic acids; Carbonyl compounds; Alpha amino acids; Amines; Primary amines; Sulfenyl compounds; Dialkylthioethers; Organic oxides; L-alpha-amino acids; Hydrocarbon derivatives; Amino acids; Cysteine and derivatives; Organopnictogen compounds; Organic oxygen compounds; Organic nitrogen compounds; Chemical entities N/A diff --git a/tools/sirius_csifingerid/test-data/canopus_RP022611_result.tsv b/tools/sirius_csifingerid/test-data/canopus_RP022611_result.tsv index 63d3802..25a9ef1 100644 --- a/tools/sirius_csifingerid/test-data/canopus_RP022611_result.tsv +++ b/tools/sirius_csifingerid/test-data/canopus_RP022611_result.tsv @@ -1,2 +1,2 @@ -name adduct name molecularFormula adduct most specific class level 5 subclass class superclass all classifications -D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- [M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- C6H12O6 [M-H]- Hexoses Monosaccharides Carbohydrates and carbohydrate conjugates Organooxygen compounds Organic oxygen compounds Organic compounds; Carbohydrates and carbohydrate conjugates; Aldehydes; Alcohols and polyols; Primary alcohols; Organooxygen compounds; Hexoses; Monosaccharides; Secondary alcohols; Carbonyl compounds; Polyols; Organic oxides; Hydrocarbon derivatives; Organic oxygen compounds; Chemical entities +name adduct id molecularFormula adduct precursorFormula NPC#pathway NPC#pathway Probability NPC#superclass NPC#superclass Probability NPC#class NPC#class Probability ClassyFire#most specific class ClassyFire#most specific class Probability ClassyFire#level 5 ClassyFire#level 5 Probability ClassyFire#subclass ClassyFire#subclass Probability ClassyFire#class ClassyFire#class Probability ClassyFire#superclass ClassyFire#superclass probability ClassyFire#all classifications featureId +D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- [M-H]- 1_unknown_ C6H12O6 [M-H]- C6H12O6 Carbohydrates 0.9183301329612732 Saccharides 0.8157960176467896 Monosaccharides 0.576671838760376 Monosaccharides 0.9366145133972168 Monosaccharides 0.9366145133972168 Carbohydrates and carbohydrate conjugates 0.9699927568435669 Organooxygen compounds 0.999981164932251 Organic oxygen compounds 0.9999126195907593 Organic compounds; Carbohydrates and carbohydrate conjugates; Alcohols and polyols; Primary alcohols; Organooxygen compounds; Monosaccharides; Secondary alcohols; Polyols; Hydrocarbon derivatives; Organic oxygen compounds; Chemical entities N/A diff --git a/tools/sirius_csifingerid/test-data/canopus_RP022611_result_all_adducts.tsv b/tools/sirius_csifingerid/test-data/canopus_RP022611_result_all_adducts.tsv index 6f4901f..45b5d39 100644 --- a/tools/sirius_csifingerid/test-data/canopus_RP022611_result_all_adducts.tsv +++ b/tools/sirius_csifingerid/test-data/canopus_RP022611_result_all_adducts.tsv @@ -1,5 +1,4 @@ -name adduct name molecularFormula adduct most specific class level 5 subclass class superclass all classifications -D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- [M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- C6H12O6 [M-H]- Hexoses Monosaccharides Carbohydrates and carbohydrate conjugates Organooxygen compounds Organic oxygen compounds Organic compounds; Carbohydrates and carbohydrate conjugates; Aldehydes; Alcohols and polyols; Primary alcohols; Organooxygen compounds; Hexoses; Monosaccharides; Secondary alcohols; Carbonyl compounds; Polyols; Organic oxides; Hydrocarbon derivatives; Organic oxygen compounds; Chemical entities -D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- [M+Cl]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- C4H10N5O [M+Cl]- Guanidines Guanidines Organonitrogen compounds Organic nitrogen compounds Organic compounds; Organoheterocyclic compounds; Organonitrogen compounds; Guanidines; Azacyclic compounds; Hydrocarbon derivatives; Organopnictogen compounds; Organic oxygen compounds; Organic nitrogen compounds; Chemical entities -D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- [M+HCOO]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- C5H10O4 [M+HCOO]- Monosaccharides Monosaccharides Carbohydrates and carbohydrate conjugates Organooxygen compounds Organic oxygen compounds Organic compounds; Aldehydes; Alcohols and polyols; Organooxygen compounds; Monosaccharides; Secondary alcohols; Carbonyl compounds; Polyols; Organic oxides; Hydrocarbon derivatives; Organic oxygen compounds; Chemical entities -D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- [M+CH3COO]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- C4H8O4 [M+CH3COO]- Monosaccharides Monosaccharides Carbohydrates and carbohydrate conjugates Organooxygen compounds Organic oxygen compounds Organic compounds; Carbohydrates and carbohydrate conjugates; Aldehydes; Alcohols and polyols; Primary alcohols; Organooxygen compounds; Monosaccharides; Secondary alcohols; Carbonyl compounds; Short-chain aldehydes; Polyols; Organic oxides; Hydrocarbon derivatives; Organic oxygen compounds; Chemical entities +name adduct id molecularFormula adduct precursorFormula NPC#pathway NPC#pathway Probability NPC#superclass NPC#superclass Probability NPC#class NPC#class Probability ClassyFire#most specific class ClassyFire#most specific class Probability ClassyFire#level 5 ClassyFire#level 5 Probability ClassyFire#subclass ClassyFire#subclass Probability ClassyFire#class ClassyFire#class Probability ClassyFire#superclass ClassyFire#superclass probability ClassyFire#all classifications featureId +D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- [M-H]- 1_unknown_ C6H12O6 [M-H]- C6H12O6 Carbohydrates 0.9183301329612732 Saccharides 0.8157960176467896 Monosaccharides 0.576671838760376 Monosaccharides 0.9366145133972168 Monosaccharides 0.9366145133972168 Carbohydrates and carbohydrate conjugates 0.9699927568435669 Organooxygen compounds 0.999981164932251 Organic oxygen compounds 0.9999126195907593 Organic compounds; Carbohydrates and carbohydrate conjugates; Alcohols and polyols; Primary alcohols; Organooxygen compounds; Monosaccharides; Secondary alcohols; Polyols; Hydrocarbon derivatives; Organic oxygen compounds; Chemical entities N/A +D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- [M+HCOO]- 1_unknown_ C5H10O4 [M+HCOO]- C6H12O6 Carbohydrates 0.8764852285385132 Saccharides 0.9348927736282349 Monosaccharides 0.7213488817214966 Monosaccharides 0.8771483898162842 Monosaccharides 0.8771483898162842 Carbohydrates and carbohydrate conjugates 0.9232270121574402 Organooxygen compounds 0.9999898672103882 Organic oxygen compounds 0.9999399185180664 Organic compounds; Organoheterocyclic compounds; Carbohydrates and carbohydrate conjugates; Alcohols and polyols; Ethers; Primary alcohols; Organooxygen compounds; Hemiacetals; Monosaccharides; Secondary alcohols; Oxanes; Polyols; Oxacyclic compounds; Hydrocarbon derivatives; Organic oxygen compounds; Chemical entities N/A +D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- [M+CH3COO]- 1_unknown_ C4H8O4 [M+CH3COO]- C6H12O6 Carbohydrates 0.8264330625534058 Saccharides 0.9152450561523438 Monosaccharides 0.7790881991386414 Monosaccharides 0.7968674898147583 Monosaccharides 0.7968674898147583 Carbohydrates and carbohydrate conjugates 0.8572495579719543 Organooxygen compounds 0.9999774694442749 Organic oxygen compounds 0.999927282333374 Organic compounds; Carbohydrates and carbohydrate conjugates; Alcohols and polyols; Ethers; Primary alcohols; Organooxygen compounds; Monosaccharides; Secondary alcohols; Short-chain aldehydes; Polyols; Hydrocarbon derivatives; Organic oxygen compounds; Chemical entities N/A diff --git a/tools/sirius_csifingerid/test-data/canopus_generic.tsv b/tools/sirius_csifingerid/test-data/canopus_generic.tsv index 5b4d4fb..c310028 100644 --- a/tools/sirius_csifingerid/test-data/canopus_generic.tsv +++ b/tools/sirius_csifingerid/test-data/canopus_generic.tsv @@ -1,6 +1,6 @@ -name adduct name molecularFormula adduct most specific class level 5 subclass class superclass all classifications -MZ:86.0606 | RT:1498 | XCMS_group:19 | file:1 | scan:NA [M+H]+ MZ:86.0606 | RT:1498 | XCMS_group:19 | file:1 | scan:NA C4H7NO [M+H]+ Carbonyl compounds Carbonyl compounds Organooxygen compounds Organic oxygen compounds Organic compounds; Organonitrogen compounds; Organooxygen compounds; Carbonyl compounds; Organic oxides; Hydrocarbon derivatives; Organopnictogen compounds; Organic oxygen compounds; Organic nitrogen compounds; Chemical entities -MZ:72.0815 | RT:1823 | XCMS_group:2 | file:1 | scan:NA [M+H]+ MZ:72.0815 | RT:1823 | XCMS_group:2 | file:1 | scan:NA C4H9N [M+H]+ Amines Amines Organonitrogen compounds Organic nitrogen compounds Organic compounds; Organonitrogen compounds; Amines; Hydrocarbon derivatives; Organopnictogen compounds; Organic nitrogen compounds; Chemical entities -MZ:79.0219 | RT:177 | XCMS_group:9 | file:1 | scan:NA [M+H]+ MZ:79.0219 | RT:177 | XCMS_group:9 | file:1 | scan:NA C2H6OS [M+H]+ Sulfoxides Sulfoxides Organosulfur compounds Organic compounds; Organosulfur compounds; Sulfoxides; Sulfinyl compounds; Organic oxides; Hydrocarbon derivatives; Organic oxygen compounds; Chemical entities -MZ:79.0219 | RT:184 | XCMS_group:9 | file:1 | scan:NA [M+H]+ MZ:79.0219 | RT:184 | XCMS_group:9 | file:1 | scan:NA C2H6OS [M+H]+ Sulfonyls Sulfonyls Organosulfur compounds Organic compounds; Organosulfur compounds; Sulfonyls; Organic oxides; Hydrocarbon derivatives; Organic oxygen compounds; Chemical entities -MZ:79.0219 | RT:212 | XCMS_group:9 | file:1 | scan:NA [M+H]+ MZ:79.0219 | RT:212 | XCMS_group:9 | file:1 | scan:NA C2H6OS [M+H]+ Sulfoxides Sulfoxides Organosulfur compounds Organic compounds; Organosulfur compounds; Sulfoxides; Sulfinyl compounds; Organic oxides; Hydrocarbon derivatives; Organic oxygen compounds; Chemical entities +name adduct id molecularFormula adduct precursorFormula NPC#pathway NPC#pathway Probability NPC#superclass NPC#superclass Probability NPC#class NPC#class Probability ClassyFire#most specific class ClassyFire#most specific class Probability ClassyFire#level 5 ClassyFire#level 5 Probability ClassyFire#subclass ClassyFire#subclass Probability ClassyFire#class ClassyFire#class Probability ClassyFire#superclass ClassyFire#superclass probability ClassyFire#all classifications featureId +MZ:86.0606 | RT:1498 | XCMS_group:19 | file:1 | scan:NA [M+H]+ 1_unknown_ C4H7NO [M+H]+ C4H7NO Fatty acids 0.8530412316322327 Fatty amides 0.775080144405365 Primary amides 0.8949538469314575 Carboxylic acid amides 0.5296071767807007 Carboxylic acid amides 0.5296071767807007 Carboxylic acid derivatives 0.40282538533210754 Carboxylic acids and derivatives 0.5522378087043762 Organic acids and derivatives 0.44322559237480164 Organic compounds; Organoheterocyclic compounds; Carboxylic acids and derivatives; Organonitrogen compounds; Organooxygen compounds; Carboxylic acid amides; Carbonyl compounds; Organic oxides; Azacyclic compounds; Hydrocarbon derivatives; Organopnictogen compounds; Organic oxygen compounds; Organic nitrogen compounds; Chemical entities N/A +MZ:72.0815 | RT:1823 | XCMS_group:2 | file:1 | scan:NA [M+H]+ 1_unknown_ C4H9N [M+H]+ C4H9N Fatty acids 0.6732514500617981 Fatty acyls 0.714306116104126 Hydrocarbons 0.11661990731954575 Amines 0.7185161709785461 Amines 0.7185161709785461 Organonitrogen compounds 0.9983186721801758 Organic nitrogen compounds 0.9996323585510254 Organic compounds; Organonitrogen compounds; Amines; Organic cations; Hydrocarbon derivatives; Organopnictogen compounds; Organic nitrogen compounds; Chemical entities N/A +MZ:79.0219 | RT:177 | XCMS_group:9 | file:1 | scan:NA [M+H]+ 1_unknown_ C2H6OS [M+H]+ C2H6OS Fatty acids 0.8569706678390503 Fatty acyls 0.986767590045929 Fatty alcohols 0.1375749558210373 Sulfoxides 0.9073586463928223 Sulfoxides 0.9073586463928223 Organosulfur compounds 0.9998962879180908 Organic compounds; Organosulfur compounds; Sulfoxides; Sulfinyl compounds; Organic oxides; Hydrocarbon derivatives; Organic oxygen compounds; Chemical entities N/A +MZ:79.0219 | RT:184 | XCMS_group:9 | file:1 | scan:NA [M+H]+ 1_unknown_ C2H6OS [M+H]+ C2H6OS Fatty acids 0.6974629759788513 Fatty acyls 0.9201967120170593 Oxygenated hydrocarbons 0.13950756192207336 Sulfoxides 0.6846614480018616 Sulfoxides 0.6846614480018616 Organosulfur compounds 0.9995274543762207 Organic compounds; Organosulfur compounds; Sulfoxides; Sulfinyl compounds; Organic oxides; Hydrocarbon derivatives; Organic oxygen compounds; Chemical entities N/A +MZ:79.0219 | RT:212 | XCMS_group:9 | file:1 | scan:NA [M+H]+ 1_unknown_ C2H6OS [M+H]+ C2H6OS Fatty acids 0.8569149971008301 Fatty acyls 0.9876387119293213 Fatty alcohols 0.14616914093494415 Sulfoxides 0.9139788746833801 Sulfoxides 0.9139788746833801 Organosulfur compounds 0.9999037981033325 Organic compounds; Organosulfur compounds; Sulfoxides; Sulfinyl compounds; Organic oxides; Hydrocarbon derivatives; Organic oxygen compounds; Chemical entities N/A From e6ba3db68e5fc6caa6b383466cbdf1c8df05080a Mon Sep 17 00:00:00 2001 From: RJMW Date: Tue, 16 Jul 2024 15:46:27 +0100 Subject: [PATCH 04/19] Remove Travis testing --- .travis.yml | 118 ---------------------------------------------------- 1 file changed, 118 deletions(-) delete mode 100644 .travis.yml diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 0cf3f9e..0000000 --- a/.travis.yml +++ /dev/null @@ -1,118 +0,0 @@ -# 'sudo required' will give us 7,5 GB memory, but has slower startup times, as we start a VM instead of a Container -sudo: required -language: python -cache: pip - -python: 3.6 - -jobs: - include: - - stage: lint - addons: {} - before_install: skip - install: - - pip install flake8 flake8-import-order planemo - - planemo --version - - git diff --quiet "$TRAVIS_COMMIT_RANGE" -- ; GIT_DIFF_EXIT_CODE=$? - - | - if [ "$GIT_DIFF_EXIT_CODE" -gt 1 ] ; then - git remote set-branches --add origin master - git fetch - TRAVIS_COMMIT_RANGE=origin/master... - fi - - echo $TRAVIS_COMMIT_RANGE - - | - planemo ci_find_repos --exclude_from .tt_skip \ - --changed_in_commit_range "$TRAVIS_COMMIT_RANGE" \ - --output changed_repositories.list - - cat changed_repositories.list - script: - - set -e - - cd "$TRAVIS_BUILD_DIR" && flake8 --exclude=.git,./deprecated/ . - - while read -r DIR; do planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive "$DIR"; done < changed_repositories.list - - - stage: test - env: CHUNK=0 - - - stage: deploy - if: (type = push) AND (branch = master) - addons: {} - before_install: skip - install: - - pip install planemo - - planemo --version - - git diff --quiet "$TRAVIS_COMMIT_RANGE" -- ; GIT_DIFF_EXIT_CODE=$? - - | - if [ "$GIT_DIFF_EXIT_CODE" -gt 1 ] ; then - git remote set-branches --add origin master - git fetch - TRAVIS_COMMIT_RANGE=origin/master... - fi - - echo $TRAVIS_COMMIT_RANGE - - | - planemo ci_find_repos --exclude_from .tt_skip \ - --changed_in_commit_range "$TRAVIS_COMMIT_RANGE" \ - --output changed_repositories.list - - cat changed_repositories.list - script: - - set -e - - | - if [ "$TRAVIS_PULL_REQUEST" == "false" -a "$TRAVIS_BRANCH" == "master" ]; then - #while read -r DIR; do planemo shed_update --shed_target testtoolshed --shed_email "$SHED_EMAIL" --shed_password "$SHED_PASSWORD" --force_repository_creation "$DIR" || exit 1; done < changed_repositories.list - while read -r DIR; do planemo shed_update --shed_target toolshed --shed_email "$SHED_EMAIL" --shed_password "$SHED_PASSWORD" --force_repository_creation "$DIR" || exit 1; done < changed_repositories.list - fi - -before_install: - - export GALAXY_REPO=https://github.com/galaxyproject/galaxy - - export GALAXY_RELEASE=release_19.09 - # - export PLANEMO_CONDA_PREFIX="$HOME/conda" - - unset JAVA_HOME - -install: - - pip install planemo - # - planemo conda_init - # - export PATH="$PLANEMO_CONDA_PREFIX/bin:$PATH" - # - conda install -y -c conda-forge conda=4.6.8 - - planemo --version - # - conda --version - - git diff --quiet "$TRAVIS_COMMIT_RANGE" -- ; GIT_DIFF_EXIT_CODE=$? - - | - if [ "$GIT_DIFF_EXIT_CODE" -gt 1 ] ; then - git remote set-branches --add origin master - git fetch - TRAVIS_COMMIT_RANGE=origin/master... - fi - - echo $TRAVIS_COMMIT_RANGE - - | - planemo ci_find_repos --exclude packages \ - --exclude_from .tt_skip \ - --changed_in_commit_range "$TRAVIS_COMMIT_RANGE" \ - --output changed_repositories.list - - touch changed_repositories_chunk.list changed_tools_chunk.list - - | - if [ -s changed_repositories.list ]; then - if [ $(wc -l < changed_repositories.list) -eq 1 ]; then - planemo ci_find_tools --chunk_count 1 --chunk "${CHUNK}" \ - --output changed_tools_chunk.list \ - $(cat changed_repositories.list) - else - planemo ci_find_repos --chunk_count 1 --chunk "${CHUNK}" \ - --output changed_repositories_chunk.list \ - $(cat changed_repositories.list) - fi - fi - - cat changed_repositories.list - - cat changed_repositories_chunk.list - - cat changed_tools_chunk.list - -script: - - - set -e - - | - if [ -s changed_tools_chunk.list ]; then - planemo test --galaxy_branch "$GALAXY_RELEASE" --galaxy_python_version 3.7 --galaxy_source "$GALAXY_REPO" $(cat changed_tools_chunk.list) - elif [ -s changed_repositories_chunk.list ]; then - while read -r DIR; do - planemo test --galaxy_branch "$GALAXY_RELEASE" --galaxy_python_version 3.7 --galaxy_source "$GALAXY_REPO" "$DIR" - done < changed_repositories_chunk.list - fi From 189364e0058a979bfb1ccd71e06f3b9046fc6154 Mon Sep 17 00:00:00 2001 From: RJMW Date: Tue, 16 Jul 2024 16:28:56 +0100 Subject: [PATCH 05/19] Fix pylint --- .../sirius_csifingerid/sirius_csifingerid.py | 23 ++++++++++--------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/tools/sirius_csifingerid/sirius_csifingerid.py b/tools/sirius_csifingerid/sirius_csifingerid.py index aebc96c..b7ea07f 100644 --- a/tools/sirius_csifingerid/sirius_csifingerid.py +++ b/tools/sirius_csifingerid/sirius_csifingerid.py @@ -1,7 +1,7 @@ import argparse import csv -import json import glob +import json import multiprocessing import os import re @@ -45,7 +45,8 @@ cmd_login = "sirius login " \ "--user='{}' " \ - "--password='{}'".format(credentials["username"], credentials["password"]) + "--password='{}'".format(credentials["username"], + credentials["password"]) os.system(cmd_login) if args.temp_dir: @@ -232,15 +233,15 @@ def run_sirius(meta_info, peaklist, args, wd, spectrac): "fingerprint " \ "structure --database {} " \ "canopus".format(paramd["cli"]["--cores"], - paramd["cli"]["--ms2"], - adduct, - paramd["cli"]["--precursor"], - paramd["cli"]["--output"], - paramd["cli"]["--candidates"], - paramd["cli"]["--ppm-max"], - paramd["cli"]["--profile"], - paramd["cli"]["--database"] - ) + paramd["cli"]["--ms2"], + adduct, + paramd["cli"]["--precursor"], + paramd["cli"]["--output"], + paramd["cli"]["--candidates"], + paramd["cli"]["--ppm-max"], + paramd["cli"]["--profile"], + paramd["cli"]["--database"] + ) print(cmd) paramds[paramd["SampleName"]] = paramd From 694d36fd4cbbb32f097e2568a85c3fa237c17df7 Mon Sep 17 00:00:00 2001 From: RJMW Date: Tue, 16 Jul 2024 16:39:04 +0100 Subject: [PATCH 06/19] Update github workflow --- .github/workflows/pr.yaml | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index d8d282a..a47eb43 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -2,13 +2,13 @@ name: Galaxy Tool Linting and Tests for push and PR on: [push, pull_request] env: GALAXY_FORK: galaxyproject - GALAXY_BRANCH: release_21.09 + GALAXY_BRANCH: release_24.1 MAX_CHUNKS: 4 MAX_FILE_SIZE: 1M concurrency: - # group runs by PR, but keep runs on master separate + # group runs by PR, but keep runs on main separate # because we do not want to cancel toolshed uploads - group: pr-${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main') && github.run_number || github.ref }} + group: pr-${{ (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/main') && github.run_number || github.ref }} cancel-in-progress: true jobs: # the setup job does two things: @@ -19,6 +19,7 @@ jobs: # - a file containing the list of changed repositories # which are needed in subsequent steps. setup: + name: Setup cache and determine changed repositories runs-on: ubuntu-latest outputs: @@ -171,7 +172,7 @@ jobs: - uses: actions/checkout@v2 with: fetch-depth: 1 - - uses: r-lib/actions/setup-r@master + - uses: r-lib/actions/setup-r@main with: r-version: ${{ matrix.r-version }} - name: Cache R packages @@ -350,7 +351,7 @@ jobs: deploy: name: Deploy needs: [setup, lint, flake8, lintr] - if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'computational-metabolomics' }} + if: ${{ (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'computational-metabolomics' }} runs-on: ubuntu-latest strategy: matrix: @@ -387,7 +388,7 @@ jobs: determine-success: name: Check workflow success needs: [setup, lint, flake8, lintr, file_sizes] - if: ${{ always() && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/main' }} + if: ${{ always() && github.ref != 'refs/heads/main' && github.ref != 'refs/heads/main' }} runs-on: ubuntu-latest steps: - name: Check tool lint status @@ -404,4 +405,4 @@ jobs: run: exit 1 # - name: Check tool test status # if: ${{ needs.combine_outputs.result != 'success' && needs.combine_outputs.result != 'skipped' }} -# run: exit 1 \ No newline at end of file +# run: exit 1 From 43e4fad8e65a48038ed35fafd2978430c876b772 Mon Sep 17 00:00:00 2001 From: RJMW Date: Tue, 16 Jul 2024 16:51:57 +0100 Subject: [PATCH 07/19] Update github workflow (2) --- .github/workflows/pr.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index a47eb43..cd79865 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -31,7 +31,7 @@ jobs: commit-range: ${{ steps.discover.outputs.commit-range }} strategy: matrix: - python-version: ['3.7'] + python-version: ['3.11'] steps: - name: Print github context properties run: | @@ -97,7 +97,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.7'] + python-version: ['3.11'] steps: # checkout the repository # and use it as the current working directory @@ -135,7 +135,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.7'] + python-version: ['3.11'] steps: - uses: actions/checkout@v2 with: @@ -258,7 +258,7 @@ jobs: fail-fast: false matrix: chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }} - python-version: ['3.7'] + python-version: ['3.11'] services: postgres: image: postgres:11 @@ -317,7 +317,7 @@ jobs: # runs-on: ubuntu-latest # strategy: # matrix: -# python-version: ['3.7'] +# python-version: ['3.11'] # steps: # - uses: actions/download-artifact@v2 # with: @@ -355,7 +355,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.7'] + python-version: ['3.11'] steps: - uses: actions/checkout@v2 with: From 66132b932a6b0f60cc92de562f1f38d1c8c6afaa Mon Sep 17 00:00:00 2001 From: Ralf Weber Date: Tue, 16 Jul 2024 20:14:51 +0100 Subject: [PATCH 08/19] Update github workflow (2, lintr) --- .github/workflows/pr.yaml | 50 ++++++++++++--------------------------- 1 file changed, 15 insertions(+), 35 deletions(-) diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index cd79865..a52652f 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -167,52 +167,32 @@ jobs: strategy: matrix: os: [ubuntu-20.04] - r-version: ['4.0.1'] + r-version: ['release'] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 with: fetch-depth: 1 - - uses: r-lib/actions/setup-r@main + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.r-version }} - name: Cache R packages - uses: actions/cache@v2 + uses: actions/cache@v4 with: path: ${{ env.R_LIBS_USER }} key: r_cache_${{ matrix.os }}_${{ matrix.r-version }} - - name: Install non-R lintr dependencies - run: sudo apt-get install libcurl4-openssl-dev - - name: Install lintr - run: | - install.packages('remotes') - remotes::install_cran("lintr") - shell: Rscript {0} - - name: Save repositories to file - run: echo '${{ needs.setup.outputs.repository-list }}' > repository_list.txt + - name: Install packages + uses: r-lib/actions/setup-r-dependencies@v2 + with: + packages: | + any::argparse + any::styler - name: lintr run: | - library(lintr) - linters <- with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL) - con <- file("repository_list.txt", "r") - status <- 0 - while (TRUE) { - repo <- readLines(con, n = 1) - if (length(repo) == 0) { - break - } - lnt <- lint_dir(repo, relative_path=T, linters=linters) - if (length(lnt) > 0) { - status <- 1 - for (l in lnt) { - rel_path <- paste(repo, l$filename, sep="/") - write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message), stderr()) - write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message), "rlint_report.txt", append=TRUE) - } - } - } - quit(status = status) - shell: Rscript {0} - - uses: actions/upload-artifact@v2 + set -eo pipefail + echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' -n 1 ./.github/styler.R --dry off + git status + git diff --exit-code | tee rlint_report.txt + - uses: actions/upload-artifact@v4 if: ${{ failure() }} with: name: 'R linting output' From dcfb320edc1f5a2249a7e7d5d83192f864a83195 Mon Sep 17 00:00:00 2001 From: Ralf Weber Date: Tue, 16 Jul 2024 20:22:48 +0100 Subject: [PATCH 09/19] Add styler.R (to complete set of scripts for testing) --- .github/styler.R | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 .github/styler.R diff --git a/.github/styler.R b/.github/styler.R new file mode 100644 index 0000000..c5c0cb5 --- /dev/null +++ b/.github/styler.R @@ -0,0 +1,36 @@ +#!/usr/bin/env Rscript + +library("argparse") +library("styler") + +parser <- ArgumentParser(description = "Call styler") +parser$add_argument("dir", + metavar = "DIR", type = "character", + help = "File to parse" +) +parser$add_argument("--dry", + choices = c("off", "on"), default = "on" +) +args <- parser$parse_args() + +file_info <- file.info(args$dir) +is_directory <- file_info$isdir + +if (is_directory) { + captured_output <- capture.output({ + result <- style_dir(args$dir, indent_by = 4, dry = args$dry, recursive = TRUE) + }) +} else { + captured_output <- capture.output({ + result <- style_file(args$dir, indent_by = 4, dry = args$dry) + }) +} + +n <- nrow(subset(result, changed == TRUE)) +if (n > 0) { + if (args$dry == "off") { + print(paste("Changed", n, "files")) + } else { + stop(paste("Linting failed for", n, "files")) + } +} From 3b1503830d35ea031a6a912f742a472d26d74dde Mon Sep 17 00:00:00 2001 From: RJMW Date: Tue, 16 Jul 2024 20:54:28 +0100 Subject: [PATCH 10/19] Chmod 755 styler.R --- .github/styler.R | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 .github/styler.R diff --git a/.github/styler.R b/.github/styler.R old mode 100644 new mode 100755 From acfa1e0f69b7ec2a26fe64d36a2e149b98c5e5fc Mon Sep 17 00:00:00 2001 From: Ralf Weber Date: Wed, 17 Jul 2024 17:03:16 +0100 Subject: [PATCH 11/19] Add write-summaries to sirius call (cmd) --- .../sirius_csifingerid/sirius_csifingerid.py | 21 ++++++++++--------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/tools/sirius_csifingerid/sirius_csifingerid.py b/tools/sirius_csifingerid/sirius_csifingerid.py index b7ea07f..213593d 100644 --- a/tools/sirius_csifingerid/sirius_csifingerid.py +++ b/tools/sirius_csifingerid/sirius_csifingerid.py @@ -232,16 +232,17 @@ def run_sirius(meta_info, peaklist, args, wd, spectrac): "formula -c {} --ppm-max {} --profile {} " \ "fingerprint " \ "structure --database {} " \ - "canopus".format(paramd["cli"]["--cores"], - paramd["cli"]["--ms2"], - adduct, - paramd["cli"]["--precursor"], - paramd["cli"]["--output"], - paramd["cli"]["--candidates"], - paramd["cli"]["--ppm-max"], - paramd["cli"]["--profile"], - paramd["cli"]["--database"] - ) + "canopus " \ + "write-summaries".format(paramd["cli"]["--cores"], + paramd["cli"]["--ms2"], + adduct, + paramd["cli"]["--precursor"], + paramd["cli"]["--output"], + paramd["cli"]["--candidates"], + paramd["cli"]["--ppm-max"], + paramd["cli"]["--profile"], + paramd["cli"]["--database"] + ) print(cmd) paramds[paramd["SampleName"]] = paramd From da0d081696c5ce4afa2832a9294bbf97dca323ce Mon Sep 17 00:00:00 2001 From: Ralf Weber Date: Wed, 17 Jul 2024 21:55:39 +0100 Subject: [PATCH 12/19] Add .tt_biocontainer_skip --- .tt_biocontainer_skip | 1 + 1 file changed, 1 insertion(+) create mode 100644 .tt_biocontainer_skip diff --git a/.tt_biocontainer_skip b/.tt_biocontainer_skip new file mode 100644 index 0000000..6a9de6a --- /dev/null +++ b/.tt_biocontainer_skip @@ -0,0 +1 @@ +tools/sirius_csifingerid From d8611a50223d5ab84d21d07960e30ba186d7c88a Mon Sep 17 00:00:00 2001 From: Ralf Weber Date: Wed, 17 Jul 2024 22:28:53 +0100 Subject: [PATCH 13/19] Update pr.yaml --- .github/workflows/pr.yaml | 103 ++++++++++++++++++++------------------ 1 file changed, 55 insertions(+), 48 deletions(-) diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index a52652f..3aab965 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -288,63 +288,70 @@ jobs: # to `|| true`) and create a global test report as json and html which # is provided as artifact # - check if any tool test actually failed (by lookup in the combined json) -# # and fail this step if this is the case -# SEEMS TO BE FAILING ON CONDA - UNABLE TO FIX -# combine_outputs: -# name: Combine chunked test results -# needs: [setup, test] -# if: ${{ needs.setup.outputs.repository-list != '' }} -# runs-on: ubuntu-latest -# strategy: -# matrix: -# python-version: ['3.11'] -# steps: -# - uses: actions/download-artifact@v2 -# with: -# path: artifacts -# - uses: actions/setup-python@v1 -# with: -# python-version: ${{ matrix.python-version }} -# - name: Cache .cache/pip -# uses: actions/cache@v2 -# id: cache-pip -# with: -# path: ~/.cache/pip -# key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} -# - name: Combine outputs -# uses: galaxyproject/planemo-ci-action@v1 -# id: combine -# with: -# mode: combine -# html-report: true -# - uses: actions/upload-artifact@v2 -# with: -# name: 'All tool test results' -# path: upload -# - name: Check outputs -# uses: galaxyproject/planemo-ci-action@v1 -# id: check -# with: -# mode: check + # and fail this step if this is the case + combine_outputs: + name: Combine chunked test results + needs: [setup, test] + if: ${{ always() && needs.setup.outputs.repository-list != '' }} + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ['3.11'] + steps: + - uses: actions/download-artifact@v4 + with: + path: artifacts + - uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + - name: Cache .cache/pip + uses: actions/cache@v4 + id: cache-pip + with: + path: ~/.cache/pip + key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} + - name: Combine outputs + uses: galaxyproject/planemo-ci-action@v1 + id: combine + with: + mode: combine + html-report: true + markdown-report: true + - uses: actions/upload-artifact@v4 + with: + name: 'All tool test results' + path: upload + - run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY + - name: Check outputs + uses: galaxyproject/planemo-ci-action@v1 + id: check + with: + mode: check + - name: Check if all test chunks succeeded + run: | + NFILES=$(ls artifacts/ | grep "Tool test output" | wc -l) + if [[ "${{ needs.setup.outputs.chunk-count }}" != "$NFILES" ]]; then + exit 1 + fi # deploy the tools to the toolsheds (first TTS for testing) deploy: name: Deploy - needs: [setup, lint, flake8, lintr] - if: ${{ (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'computational-metabolomics' }} + needs: [setup, lint, combine_outputs] + if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'computational-metabolomics' }} runs-on: ubuntu-latest strategy: matrix: python-version: ['3.11'] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 with: fetch-depth: 1 - - uses: actions/setup-python@v1 + - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Cache .cache/pip - uses: actions/cache@v2 + uses: actions/cache@v4 id: cache-pip with: path: ~/.cache/pip @@ -367,8 +374,8 @@ jobs: determine-success: name: Check workflow success - needs: [setup, lint, flake8, lintr, file_sizes] - if: ${{ always() && github.ref != 'refs/heads/main' && github.ref != 'refs/heads/main' }} + needs: [setup, lint, flake8, lintr, file_sizes, combine_outputs] + if: ${{ always() && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/main' }} runs-on: ubuntu-latest steps: - name: Check tool lint status @@ -383,6 +390,6 @@ jobs: - name: Indicate file size check status if: ${{ needs.file_sizes.result != 'success' && needs.file_sizes.result != 'skipped' }} run: exit 1 -# - name: Check tool test status -# if: ${{ needs.combine_outputs.result != 'success' && needs.combine_outputs.result != 'skipped' }} -# run: exit 1 + - name: Check tool test status + if: ${{ needs.combine_outputs.result != 'success' && needs.combine_outputs.result != 'skipped' }} + run: exit 1 From 98a88fe95be6dc0046818ba1ae151a1d43fef56c Mon Sep 17 00:00:00 2001 From: RJMW Date: Tue, 30 Jul 2024 13:54:45 +0100 Subject: [PATCH 14/19] Update job_config and ENVs --- .github/workflows/pr.yaml | 12 +++++++++ config/job_config_planemo.xml | 27 +++++++++++++++++++ .../sirius_csifingerid/sirius_csifingerid.xml | 10 +++++-- 3 files changed, 47 insertions(+), 2 deletions(-) create mode 100644 config/job_config_planemo.xml diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 3aab965..d99204f 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -269,9 +269,20 @@ jobs: with: path: ~/.planemo key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} + - name: Prepare specific job_conf for Sirius + uses: danielr1996/envsubst-action@1.0.0 + env: + USERNAME_SIRIUS: "${{ secrets.USERNAME_SIRIUS }}" + PASSWORD_SIRIUS: "${{ secrets.PASSWORD_SIRIUS }}" + with: + input: "${{ github.workspace }}/job_conf_planemo.xml" + output: "${{ github.workspace }}/job_conf_planemo_subst.xml" - name: Planemo test uses: galaxyproject/planemo-ci-action@v1 id: test + env: + USERNAME_SIRIUS: "${{ secrets.USERNAME_SIRIUS }}" + PASSWORD_SIRIUS: "${{ secrets.PASSWORD_SIRIUS }}" with: mode: test repository-list: ${{ needs.setup.outputs.repository-list }} @@ -279,6 +290,7 @@ jobs: galaxy-branch: ${{ env.GALAXY_BRANCH }} chunk: ${{ matrix.chunk }} chunk-count: ${{ needs.setup.outputs.chunk-count }} + additional-planemo-options: "format('--job_config_file {0}/config/job_conf_planemo_subst.xml', github.workspace)}}" - uses: actions/upload-artifact@v2 with: name: 'Tool test output ${{ matrix.chunk }}' diff --git a/config/job_config_planemo.xml b/config/job_config_planemo.xml new file mode 100644 index 0000000..6199cec --- /dev/null +++ b/config/job_config_planemo.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + false + true + false + sudo + docker + -e USERNAME_SIRIUS='${USERNAME_SIRIUS}' -e PASSWORD_SIRIUS='${PASSWORD_SIRIUS}' + ${USERNAME_SIRIUS} + ${PASSWORD_SIRIUS} + + + false + + + + + + diff --git a/tools/sirius_csifingerid/sirius_csifingerid.xml b/tools/sirius_csifingerid/sirius_csifingerid.xml index 3ca11c9..8b4f349 100644 --- a/tools/sirius_csifingerid/sirius_csifingerid.xml +++ b/tools/sirius_csifingerid/sirius_csifingerid.xml @@ -7,10 +7,15 @@ Preferences -> Manage Information" - #end if + #else: echo "Running Sirius as user: $username" && export _JAVA_OPTIONS=-Duser.home=$__new_file_path__ && python '$__tool_directory__/sirius_csifingerid.py' @@ -53,6 +58,7 @@ --adducts [M+CH3COO]- #end if #end if + #end if ]]> Date: Tue, 30 Jul 2024 13:59:48 +0100 Subject: [PATCH 15/19] Update .tt_biocontainer_skip --- .tt_biocontainer_skip | 1 - 1 file changed, 1 deletion(-) diff --git a/.tt_biocontainer_skip b/.tt_biocontainer_skip index 6a9de6a..e69de29 100644 --- a/.tt_biocontainer_skip +++ b/.tt_biocontainer_skip @@ -1 +0,0 @@ -tools/sirius_csifingerid From d5761fe7050e8a9bbe5a75c3f91f647df5ef4303 Mon Sep 17 00:00:00 2001 From: RJMW Date: Tue, 30 Jul 2024 14:17:33 +0100 Subject: [PATCH 16/19] Update github workflow --- .github/workflows/pr.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index d99204f..2d4f0f0 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -275,8 +275,8 @@ jobs: USERNAME_SIRIUS: "${{ secrets.USERNAME_SIRIUS }}" PASSWORD_SIRIUS: "${{ secrets.PASSWORD_SIRIUS }}" with: - input: "${{ github.workspace }}/job_conf_planemo.xml" - output: "${{ github.workspace }}/job_conf_planemo_subst.xml" + input: "${{ github.workspace }}/config/job_conf_planemo.xml" + output: "${{ github.workspace }}/config/job_conf_planemo_subst.xml" - name: Planemo test uses: galaxyproject/planemo-ci-action@v1 id: test @@ -290,7 +290,7 @@ jobs: galaxy-branch: ${{ env.GALAXY_BRANCH }} chunk: ${{ matrix.chunk }} chunk-count: ${{ needs.setup.outputs.chunk-count }} - additional-planemo-options: "format('--job_config_file {0}/config/job_conf_planemo_subst.xml', github.workspace)}}" + additional-planemo-options: "format('--job_config_file {0}/config/job_conf_planemo_subst.xml', github.workspace)" - uses: actions/upload-artifact@v2 with: name: 'Tool test output ${{ matrix.chunk }}' From 54d97b97ebaca1cc5c4885093984122ccb9106e5 Mon Sep 17 00:00:00 2001 From: RJMW Date: Tue, 30 Jul 2024 14:26:53 +0100 Subject: [PATCH 17/19] Rename job config --- config/{job_config_planemo.xml => job_conf_planemo.xml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename config/{job_config_planemo.xml => job_conf_planemo.xml} (100%) diff --git a/config/job_config_planemo.xml b/config/job_conf_planemo.xml similarity index 100% rename from config/job_config_planemo.xml rename to config/job_conf_planemo.xml From abcb97f3d518741f56ff86afa712baad2269b08b Mon Sep 17 00:00:00 2001 From: RJMW Date: Tue, 30 Jul 2024 14:49:25 +0100 Subject: [PATCH 18/19] Update additional-planemo-options --- .github/workflows/pr.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 2d4f0f0..5b248e2 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -290,7 +290,7 @@ jobs: galaxy-branch: ${{ env.GALAXY_BRANCH }} chunk: ${{ matrix.chunk }} chunk-count: ${{ needs.setup.outputs.chunk-count }} - additional-planemo-options: "format('--job_config_file {0}/config/job_conf_planemo_subst.xml', github.workspace)" + additional-planemo-options: --job_config_file "${{ github.workspace }}/config/job_conf_planemo_subst.xml" - uses: actions/upload-artifact@v2 with: name: 'Tool test output ${{ matrix.chunk }}' From 778685e33b28b481c5ecc1f0653defb4705d12d1 Mon Sep 17 00:00:00 2001 From: Ralf Weber Date: Wed, 31 Jul 2024 10:18:01 +0100 Subject: [PATCH 19/19] Update pr.yaml (additional-planemo-options) --- .github/workflows/pr.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 5b248e2..8fcb834 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -290,7 +290,7 @@ jobs: galaxy-branch: ${{ env.GALAXY_BRANCH }} chunk: ${{ matrix.chunk }} chunk-count: ${{ needs.setup.outputs.chunk-count }} - additional-planemo-options: --job_config_file "${{ github.workspace }}/config/job_conf_planemo_subst.xml" + additional-planemo-options: --job_config_file ${{ github.workspace }}/config/job_conf_planemo_subst.xml - uses: actions/upload-artifact@v2 with: name: 'Tool test output ${{ matrix.chunk }}'