# HG changeset patch # User fgiacomoni # Date 1652971294 0 # Node ID d8e2ede293a64c85ca73a253e1dbc57b6cb9bb23 # Parent 2d8a310e86ceb33c6fb6bdd7e4e4b33e96707445 Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx diff -r 2d8a310e86ce -r d8e2ede293a6 conf_hmdb.cfg --- a/conf_hmdb.cfg Thu May 19 13:43:09 2022 +0000 +++ b/conf_hmdb.cfg Thu May 19 14:41:34 2022 +0000 @@ -1,7 +1,7 @@ ## Conf file for wsdl_hmdb.pl script # ## Version -- edited by F.Giacomoni -VERSION=1.6.0 +VERSION=1.7.1 # ## ARGVT # Hmdb limits per job (max is 700) @@ -14,4 +14,4 @@ # ## HTML OUTPUT : HTML_ENTRIES_PER_PAGE=4 -HMDB_METABOCARD_URL=http://www.hmdb.ca/metabolites/ +HMDB_METABOCARD_URL=https://hmdb.ca/metabolites/ diff -r 2d8a310e86ce -r d8e2ede293a6 lib/hmdb.pm --- a/lib/hmdb.pm Thu May 19 13:43:09 2022 +0000 +++ b/lib/hmdb.pm Thu May 19 14:41:34 2022 +0000 @@ -710,7 +710,7 @@ #query_mass,compound_id,compound_name,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,"delta(ppm),",ccs_value', if ( $line =~ /(\d+\.\d+),(\w+),(.*),(\w+),(\d+\.\d+),([\w|n\/a|\s+]+)\s*,(\+|\-),(\d+\.\d+),(\d+),(\d*)/ ) { - print "$line\n" ; + #print "$line\n" ; #if ( $line =~ /(\d+\.\d+),(\w+),(.*),([\w|n\/a|\s+]+)\s*,(\w+),(\d+\.\d+),(.*),(\+|\-),(\d+\.\d+),(\d+)/ ) { my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ; diff -r 2d8a310e86ce -r d8e2ede293a6 test-data/out_test02.html --- a/test-data/out_test02.html Thu May 19 13:43:09 2022 +0000 +++ b/test-data/out_test02.html Thu May 19 14:41:34 2022 +0000 @@ -1,1 +1,1 @@ -Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.001

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct typeAdduct MW (Da)Delta (ppm)InChI IdentifierPredicted LogP (ALOGPS)
mz_000017.02080998
BerylliumHMDB0002387Be9.012182135M+NH4-H2O+7.0203368NONEDATANONEDATA
mz_0000275.05547146
glycinamideHMDB0062472C2H6N2O74.048012824M+H+75.0552892NONEDATANONEDATA
N-NitrosodimethylamineHMDB0031419C2H6N2O74.048012824M+H+75.0552892NONEDATANONEDATA
AcetylhydrazineHMDB0060428C2H6N2O74.048012824M+H+75.0552892NONEDATANONEDATA
CreatineHMDB0000064C4H9N3O2131.069476547M+H+NH4+75.0552882NONEDATANONEDATA
Beta-Guanidinopropionic acidHMDB0013222C4H9N3O2131.069476547M+H+NH4+75.0552882NONEDATANONEDATA
mz_0000375.08059797
PyrophosphateHMDB0000250H4O7P2177.943225506M+H+2Na+75.0805990NONEDATANONEDATA
EthanolHMDB0000108C2H6O46.0418648142M+H-H2O+75.080531NONEDATANONEDATA
2-Methylpropan-2-olHMDB0031456C4H10O74.073164942M+H+75.0804412NONEDATANONEDATA
1-ButanolHMDB0004327C4H10O74.073164942M+H+75.0804412NONEDATANONEDATA
"1-hydroperoxy-8-carboxyoctyl 3,4-epoxynon-(2E)-enyl ether"HMDB0062326C4H10O74.073164942M+H+75.0804412NONEDATANONEDATA
mz_0000476.03942694
L-Aspartic acidHMDB0000191C4H7NO4133.037507717M+H+NH4+76.0393042NONEDATANONEDATA
Ethyl nitriteHMDB0031239C2H5NO275.032028409M+H+76.0393042NONEDATANONEDATA
Iminodiacetic acidHMDB0011753C4H7NO4133.037507717M+H+NH4+76.0393042NONEDATANONEDATA
GlycineHMDB0000123C2H5NO275.032028409M+H+76.0393042NONEDATANONEDATA
Acetohydroxamic AcidHMDB0014691C2H5NO275.032028409M+H+76.0393042NONEDATANONEDATA
mz_0000576.07584477
3-aminopropan-1-olHMDB0140038C3H9NO75.068413915M+H+76.075692NONEDATANONEDATA
N-monomethylethanolamineHMDB0142449C3H9NO75.068413914M+H+76.075692NONEDATANONEDATA
Trimethylamine N-oxideHMDB0000925C3H9NO75.068413915M+H+76.075692NONEDATANONEDATA
1-Amino-propan-2-olHMDB0012136C3H9NO75.068413915M+H+76.075692NONEDATANONEDATA
MethyloxiraneHMDB0031558C3H6O58.041864814M+NH4+76.0756882NONEDATANONEDATA
mz_0000676.07593168
3-aminopropan-1-olHMDB0140038C3H9NO75.068413915M+H+76.075693NONEDATANONEDATA
N-monomethylethanolamineHMDB0142449C3H9NO75.068413914M+H+76.075693NONEDATANONEDATA
Trimethylamine N-oxideHMDB0000925C3H9NO75.068413915M+H+76.075693NONEDATANONEDATA
1-Amino-propan-2-olHMDB0012136C3H9NO75.068413915M+H+76.075693NONEDATANONEDATA
MethyloxiraneHMDB0031558C3H6O58.041864814M+NH4+76.0756883NONEDATANONEDATA
\ No newline at end of file +Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.001

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct typeAdduct MW (Da)Delta (ppm)InChI IdentifierPredicted LogP (ALOGPS)
mz_000017.02080998
UNKNOWNNONEn/an/an/an/an/a0n/an/a
mz_0000275.05547146
O-MethylisoureaHMDB0255861C2H6N2O74.048012821M+H+75.0552892NONEDATANONEDATA
N-Propyl-N-nitrosoureaHMDB0255236C4H9N3O2131.069476542M+H+NH4+75.0552882NONEDATANONEDATA
N-METHYL-N-FORMYLHYDRAZINEHMDB0255179C2H6N2O74.048012821M+H+75.0552892NONEDATANONEDATA
AsparaginamideHMDB0248665C4H9N3O2131.069476542M+H+NH4+75.0552882NONEDATANONEDATA
N'-HydroxyethanimidamideHMDB0243752C2H6N2O74.048012821M+H+75.0552892NONEDATANONEDATA
mz_0000375.08059797
"Propan-2,2-diyl"HMDB0251402C3H642.046950193M+CH3OH+H+75.0804392NONEDATANONEDATA
MethyleneHMDB0249629CH214.015650064M+IsoProp+H+75.080995NONEDATANONEDATA
CyclopropaneHMDB0250673C3H642.046950193M+CH3OH+H+75.0804392NONEDATANONEDATA
PyrophosphateHMDB0000250H4O7P2177.943225506M+H+2Na+75.0805990NONEDATANONEDATA
PropyleneHMDB0256839C3H642.046950192M+CH3OH+H+75.0804392NONEDATANONEDATA
mz_0000476.03942694
Glutamic acid diethyl esterHMDB0252807C9H17NO4203.115758031M+2H+Na+76.0398435NONEDATANONEDATA
MethylcarbonyloxyHMDB0249651C2H2O258.005479304M+NH4+76.0393022NONEDATANONEDATA
o-AcetylhydroxylamineHMDB0248304C2H5NO275.032028405M+H+76.0393042NONEDATANONEDATA
2-HydroxyacetamideHMDB0245149C2H5NO275.032028405M+H+76.0393042NONEDATANONEDATA
1-CarboxyethylisoleucineHMDB0242158C9H17NO4203.115758031M+2H+Na+76.0398435NONEDATANONEDATA
mz_0000576.07584477
2-(2-Hydroxypropan-2-ylamino)propan-2-olHMDB0257796C6H15NO2133.110278727M+H+NH4+76.0756892NONEDATANONEDATA
AminopropanolHMDB0248330C3H9NO75.068413914M+H+76.075692NONEDATANONEDATA
2-MethoxyethylamineHMDB0245205C3H9NO75.068413914M+H+76.075692NONEDATANONEDATA
(E)-1-PropenolHMDB0243637C3H6O58.041864813M+NH4+76.0756882NONEDATANONEDATA
Methyl vinyl etherHMDB0254619C3H6O58.041864813M+NH4+76.0756882NONEDATANONEDATA
mz_0000676.07593168
2-(2-Hydroxypropan-2-ylamino)propan-2-olHMDB0257796C6H15NO2133.110278727M+H+NH4+76.0756893NONEDATANONEDATA
AminopropanolHMDB0248330C3H9NO75.068413914M+H+76.075693NONEDATANONEDATA
2-MethoxyethylamineHMDB0245205C3H9NO75.068413914M+H+76.075693NONEDATANONEDATA
(E)-1-PropenolHMDB0243637C3H6O58.041864813M+NH4+76.0756883NONEDATANONEDATA
Methyl vinyl etherHMDB0254619C3H6O58.041864813M+NH4+76.0756883NONEDATANONEDATA
\ No newline at end of file diff -r 2d8a310e86ce -r d8e2ede293a6 test-data/out_test02.tabular --- a/test-data/out_test02.tabular Thu May 19 13:43:09 2022 +0000 +++ b/test-data/out_test02.tabular Thu May 19 14:41:34 2022 +0000 @@ -1,7 +1,7 @@ id mz rt hmdb(delta::name::mz::formula::adduct::id) -1 7.02080998 49.38210915 68::[Beryllium]::9.012182135::Be::[M+NH4-H2O]::HMDB0002387 -2 75.05547146 0.658528069 "2::[glycinamide]::74.048012824::C2H6N2O::[M+H]::HMDB0062472 | 2::[N-Nitrosodimethylamine]::74.048012824::C2H6N2O::[M+H]::HMDB0031419 | 2::[Acetylhydrazine]::74.048012824::C2H6N2O::[M+H]::HMDB0060428 | 2::[Creatine]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0000064 | 2::[Beta-Guanidinopropionic acid]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0013222" -3 75.08059797 1743.94267 "0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0000250 | 1::[Ethanol]::46.041864814::C2H6O::[2M+H-H2O]::HMDB0000108 | 2::[2-Methylpropan-2-ol]::74.073164942::C4H10O::[M+H]::HMDB0031456 | 2::[1-Butanol]::74.073164942::C4H10O::[M+H]::HMDB0004327 | 2::[""1-hydroperoxy-8-carboxyoctyl 3,4-epoxynon-(2E)-enyl ether""]::74.073164942::C4H10O::[M+H]::HMDB0062326" -4 76.03942694 51.23158899 "2::[L-Aspartic acid]::133.037507717::C4H7NO4::[M+H+NH4]::HMDB0000191 | 2::[Ethyl nitrite]::75.032028409::C2H5NO2::[M+H]::HMDB0031239 | 2::[Iminodiacetic acid]::133.037507717::C4H7NO4::[M+H+NH4]::HMDB0011753 | 2::[Glycine]::75.032028409::C2H5NO2::[M+H]::HMDB0000123 | 2::[Acetohydroxamic Acid]::75.032028409::C2H5NO2::[M+H]::HMDB0014691" -5 76.07584477 50.51249853 "2::[3-aminopropan-1-ol]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 2::[N-monomethylethanolamine]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 2::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 2::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 2::[Methyloxirane]::58.041864814::C3H6O::[M+NH4]::HMDB0031558" -6 76.07593168 0.149308136 "3::[3-aminopropan-1-ol]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 3::[N-monomethylethanolamine]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 3::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 3::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 3::[Methyloxirane]::58.041864814::C3H6O::[M+NH4]::HMDB0031558" +1 7.02080998 49.38210915 NONE +2 75.05547146 0.658528069 "2::[O-Methylisourea]::74.048012821::C2H6N2O::[M+H]::HMDB0255861 | 2::[N-Propyl-N-nitrosourea]::131.069476542::C4H9N3O2::[M+H+NH4]::HMDB0255236 | 2::[N-METHYL-N-FORMYLHYDRAZINE]::74.048012821::C2H6N2O::[M+H]::HMDB0255179 | 2::[Asparaginamide]::131.069476542::C4H9N3O2::[M+H+NH4]::HMDB0248665 | 2::[N'-Hydroxyethanimidamide]::74.048012821::C2H6N2O::[M+H]::HMDB0243752" +3 75.08059797 1743.94267 "2::[""Propan-2,2-diyl""]::42.046950193::C3H6::[M+CH3OH+H]::HMDB0251402 | 5::[Methylene]::14.015650064::CH2::[M+IsoProp+H]::HMDB0249629 | 2::[Cyclopropane]::42.046950193::C3H6::[M+CH3OH+H]::HMDB0250673 | 0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0000250 | 2::[Propylene]::42.046950192::C3H6::[M+CH3OH+H]::HMDB0256839" +4 76.03942694 51.23158899 "5::[Glutamic acid diethyl ester]::203.115758031::C9H17NO4::[M+2H+Na]::HMDB0252807 | 2::[Methylcarbonyloxy]::58.005479304::C2H2O2::[M+NH4]::HMDB0249651 | 2::[o-Acetylhydroxylamine]::75.032028405::C2H5NO2::[M+H]::HMDB0248304 | 2::[2-Hydroxyacetamide]::75.032028405::C2H5NO2::[M+H]::HMDB0245149 | 5::[1-Carboxyethylisoleucine]::203.115758031::C9H17NO4::[M+2H+Na]::HMDB0242158" +5 76.07584477 50.51249853 "2::[2-(2-Hydroxypropan-2-ylamino)propan-2-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0257796 | 2::[Aminopropanol]::75.068413914::C3H9NO::[M+H]::HMDB0248330 | 2::[2-Methoxyethylamine]::75.068413914::C3H9NO::[M+H]::HMDB0245205 | 2::[(E)-1-Propenol]::58.041864813::C3H6O::[M+NH4]::HMDB0243637 | 2::[Methyl vinyl ether]::58.041864813::C3H6O::[M+NH4]::HMDB0254619" +6 76.07593168 0.149308136 "3::[2-(2-Hydroxypropan-2-ylamino)propan-2-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0257796 | 3::[Aminopropanol]::75.068413914::C3H9NO::[M+H]::HMDB0248330 | 3::[2-Methoxyethylamine]::75.068413914::C3H9NO::[M+H]::HMDB0245205 | 3::[(E)-1-Propenol]::58.041864813::C3H6O::[M+NH4]::HMDB0243637 | 3::[Methyl vinyl ether]::58.041864813::C3H6O::[M+NH4]::HMDB0254619" diff -r 2d8a310e86ce -r d8e2ede293a6 test-data/out_test02.txt --- a/test-data/out_test02.txt Thu May 19 13:43:09 2022 +0000 +++ b/test-data/out_test02.txt Thu May 19 14:41:34 2022 +0000 @@ -1,27 +1,27 @@ ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID -mz_00001 7.02080998 68 [Beryllium] 9.012182135 Be [M+NH4-H2O] 7.02033 HMDB0002387 -mz_00002 75.05547146 2 [glycinamide] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0062472 -mz_00002 75.05547146 2 [N-Nitrosodimethylamine] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0031419 -mz_00002 75.05547146 2 [Acetylhydrazine] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0060428 -mz_00002 75.05547146 2 [Creatine] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0000064 -mz_00002 75.05547146 2 [Beta-Guanidinopropionic acid] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0013222 +mz_00001 7.02080998 0 UNKNOWN N/A N/A N/A N/A N/A +mz_00002 75.05547146 2 [O-Methylisourea] 74.048012821 C2H6N2O [M+H] 75.055289 HMDB0255861 +mz_00002 75.05547146 2 [N-Propyl-N-nitrosourea] 131.069476542 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0255236 +mz_00002 75.05547146 2 [N-METHYL-N-FORMYLHYDRAZINE] 74.048012821 C2H6N2O [M+H] 75.055289 HMDB0255179 +mz_00002 75.05547146 2 [Asparaginamide] 131.069476542 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0248665 +mz_00002 75.05547146 2 [N'-Hydroxyethanimidamide] 74.048012821 C2H6N2O [M+H] 75.055289 HMDB0243752 +mz_00003 75.08059797 2 ["Propan-2,2-diyl"] 42.046950193 C3H6 [M+CH3OH+H] 75.080439 HMDB0251402 +mz_00003 75.08059797 5 [Methylene] 14.015650064 CH2 [M+IsoProp+H] 75.08099 HMDB0249629 +mz_00003 75.08059797 2 [Cyclopropane] 42.046950193 C3H6 [M+CH3OH+H] 75.080439 HMDB0250673 mz_00003 75.08059797 0 [Pyrophosphate] 177.943225506 H4O7P2 [M+H+2Na] 75.080599 HMDB0000250 -mz_00003 75.08059797 1 [Ethanol] 46.041864814 C2H6O [2M+H-H2O] 75.08053 HMDB0000108 -mz_00003 75.08059797 2 [2-Methylpropan-2-ol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0031456 -mz_00003 75.08059797 2 [1-Butanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0004327 -mz_00003 75.08059797 2 ["1-hydroperoxy-8-carboxyoctyl 3,4-epoxynon-(2E)-enyl ether"] 74.073164942 C4H10O [M+H] 75.080441 HMDB0062326 -mz_00004 76.03942694 2 [L-Aspartic acid] 133.037507717 C4H7NO4 [M+H+NH4] 76.039304 HMDB0000191 -mz_00004 76.03942694 2 [Ethyl nitrite] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB0031239 -mz_00004 76.03942694 2 [Iminodiacetic acid] 133.037507717 C4H7NO4 [M+H+NH4] 76.039304 HMDB0011753 -mz_00004 76.03942694 2 [Glycine] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB0000123 -mz_00004 76.03942694 2 [Acetohydroxamic Acid] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB0014691 -mz_00005 76.07584477 2 [3-aminopropan-1-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038 -mz_00005 76.07584477 2 [N-monomethylethanolamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449 -mz_00005 76.07584477 2 [Trimethylamine N-oxide] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0000925 -mz_00005 76.07584477 2 [1-Amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136 -mz_00005 76.07584477 2 [Methyloxirane] 58.041864814 C3H6O [M+NH4] 76.075688 HMDB0031558 -mz_00006 76.07593168 3 [3-aminopropan-1-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038 -mz_00006 76.07593168 3 [N-monomethylethanolamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449 -mz_00006 76.07593168 3 [Trimethylamine N-oxide] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0000925 -mz_00006 76.07593168 3 [1-Amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136 -mz_00006 76.07593168 3 [Methyloxirane] 58.041864814 C3H6O [M+NH4] 76.075688 HMDB0031558 +mz_00003 75.08059797 2 [Propylene] 42.046950192 C3H6 [M+CH3OH+H] 75.080439 HMDB0256839 +mz_00004 76.03942694 5 [Glutamic acid diethyl ester] 203.115758031 C9H17NO4 [M+2H+Na] 76.039843 HMDB0252807 +mz_00004 76.03942694 2 [Methylcarbonyloxy] 58.005479304 C2H2O2 [M+NH4] 76.039302 HMDB0249651 +mz_00004 76.03942694 2 [o-Acetylhydroxylamine] 75.032028405 C2H5NO2 [M+H] 76.039304 HMDB0248304 +mz_00004 76.03942694 2 [2-Hydroxyacetamide] 75.032028405 C2H5NO2 [M+H] 76.039304 HMDB0245149 +mz_00004 76.03942694 5 [1-Carboxyethylisoleucine] 203.115758031 C9H17NO4 [M+2H+Na] 76.039843 HMDB0242158 +mz_00005 76.07584477 2 [2-(2-Hydroxypropan-2-ylamino)propan-2-ol] 133.110278727 C6H15NO2 [M+H+NH4] 76.075689 HMDB0257796 +mz_00005 76.07584477 2 [Aminopropanol] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0248330 +mz_00005 76.07584477 2 [2-Methoxyethylamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0245205 +mz_00005 76.07584477 2 [(E)-1-Propenol] 58.041864813 C3H6O [M+NH4] 76.075688 HMDB0243637 +mz_00005 76.07584477 2 [Methyl vinyl ether] 58.041864813 C3H6O [M+NH4] 76.075688 HMDB0254619 +mz_00006 76.07593168 3 [2-(2-Hydroxypropan-2-ylamino)propan-2-ol] 133.110278727 C6H15NO2 [M+H+NH4] 76.075689 HMDB0257796 +mz_00006 76.07593168 3 [Aminopropanol] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0248330 +mz_00006 76.07593168 3 [2-Methoxyethylamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0245205 +mz_00006 76.07593168 3 [(E)-1-Propenol] 58.041864813 C3H6O [M+NH4] 76.075688 HMDB0243637 +mz_00006 76.07593168 3 [Methyl vinyl ether] 58.041864813 C3H6O [M+NH4] 76.075688 HMDB0254619 diff -r 2d8a310e86ce -r d8e2ede293a6 test-data/out_test03.html --- a/test-data/out_test03.html Thu May 19 13:43:09 2022 +0000 +++ b/test-data/out_test03.html Thu May 19 14:41:34 2022 +0000 @@ -1,1 +1,1 @@ -Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.05

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct typeAdduct MW (Da)Delta (ppm)InChI IdentifierPredicted LogP (ALOGPS)
mz_00001175.01
Phenol sulphateHMDB0060015C6H6O4S173.99867937M+H+175.00595523NONEDATANONEDATA
trans-Aconitic acidHMDB0000958C6H6O6174.016437924M+H+175.02371478NONEDATANONEDATA
cis-Aconitic acidHMDB0000072C6H6O6174.016437924M+H+175.02371478NONEDATANONEDATA
Dehydroascorbic acidHMDB0001264C6H6O6174.016437924M+H+175.02371478NONEDATANONEDATA
dehydroascorbide(1-)HMDB0062706C6H6O6174.016437913M+H+175.02371478NONEDATANONEDATA
mz_00002238.19
UNKNOWNNONEn/an/an/an/an/a0n/an/a
mz_00003420.16
FenvalerateHMDB0031791C25H22ClNO3419.128821282M+H+420.13609757NONEDATANONEDATA
mz_00004780.32
3'-Sialyl-3-fucosyllactoseHMDB0006606C29H49NO23779.269536879M+H+780.27681355NONEDATANONEDATA
mz_00005956.25
UNKNOWNNONEn/an/an/an/an/a0n/an/a
mz_000061100.45
UNKNOWNNONEn/an/an/an/an/a0n/an/a
\ No newline at end of file +Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.05

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct typeAdduct MW (Da)Delta (ppm)InChI IdentifierPredicted LogP (ALOGPS)
mz_00001175.01
TrinitrosotrimethylenetriamineHMDB0259249C3H6N6O3174.050138077M+H+175.057414271NONEDATANONEDATA
"Naphthalene-1,2,4-trione"HMDB0257698C10H6O3174.031694053M+H+175.03897166NONEDATANONEDATA
Phenyl phosphonothioateHMDB0256424C6H7O2PS173.990437637M+H+174.99771470NONEDATANONEDATA
p-TOLUENESULFONYL FLUORIDEHMDB0256057C7H7FO2S174.015078802M+H+175.02235571NONEDATANONEDATA
Aconitic acidHMDB0247961C6H6O6174.016437913M+H+175.02371478NONEDATANONEDATA
mz_00002238.19
"N,N-di-n-propyldopamine"HMDB0255249C14H23NO2237.172878985M+H+238.18015541NONEDATANONEDATA
Ethoxybenzyl diethylenetriamineHMDB0252022C13H23N3O237.184112373M+H+238.1913886NONEDATANONEDATA
DeacetylmoxisylyteHMDB0250903C14H23NO2237.172878985M+H+238.18015541NONEDATANONEDATA
viloxazineHMDB0259807C13H19NO3237.136493476M+H+238.143769194NONEDATANONEDATA
mz_00003420.16
CligosibanHMDB0256366C19H19ClFN5O3419.1160454M+H+420.12332187NONEDATANONEDATA
Perphenazine sulfoxideHMDB0256352C21H26ClN3O2S419.143426M+H+420.15070222NONEDATANONEDATA
"Glycine, L-gamma-glutamyl-2-(1-methyl-4-(nitrosothio)-4-piperidinyl)glycyl-"HMDB0253933C15H25N5O7S419.147469339M+H+420.15474513NONEDATANONEDATA
DolutegravirHMDB0251580C20H19F2N3O5419.12927705M+H+420.13655356NONEDATANONEDATA
AcorafloxacinHMDB0247964C21H23F2N3O4419.165662559M+H+420.17293931NONEDATANONEDATA
mz_00004780.32
RavtansineHMDB0247402C38H54ClN3O10S779.3218438M+H+780.3291212NONEDATANONEDATA
3'-Sialyl-3-fucosyllactoseHMDB0006606C29H49NO23779.269536879M+H+780.27681355NONEDATANONEDATA
mz_00005956.25
jasmonoyl-CoAHMDB0304397C33H48N7O18P3S955.201134221M+H+956.2084143NONEDATANONEDATA
mz_000061100.45
UNKNOWNNONEn/an/an/an/an/a0n/an/a
\ No newline at end of file diff -r 2d8a310e86ce -r d8e2ede293a6 test-data/out_test03.tabular --- a/test-data/out_test03.tabular Thu May 19 13:43:09 2022 +0000 +++ b/test-data/out_test03.tabular Thu May 19 14:41:34 2022 +0000 @@ -1,11 +1,19 @@ ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID -mz_00001 175.01 23 [Phenol sulphate] 173.99867937 C6H6O4S [M+H] 175.005955 HMDB0060015 -mz_00001 175.01 78 [trans-Aconitic acid] 174.016437924 C6H6O6 [M+H] 175.023714 HMDB0000958 -mz_00001 175.01 78 [cis-Aconitic acid] 174.016437924 C6H6O6 [M+H] 175.023714 HMDB0000072 -mz_00001 175.01 78 [Dehydroascorbic acid] 174.016437924 C6H6O6 [M+H] 175.023714 HMDB0001264 -mz_00001 175.01 78 [dehydroascorbide(1-)] 174.016437913 C6H6O6 [M+H] 175.023714 HMDB0062706 -mz_00002 238.19 0 UNKNOWN N/A N/A N/A N/A N/A -mz_00003 420.16 57 [Fenvalerate] 419.128821282 C25H22ClNO3 [M+H] 420.136097 HMDB0031791 +mz_00001 175.01 271 [Trinitrosotrimethylenetriamine] 174.050138077 C3H6N6O3 [M+H] 175.057414 HMDB0259249 +mz_00001 175.01 166 ["Naphthalene-1,2,4-trione"] 174.031694053 C10H6O3 [M+H] 175.03897 HMDB0257698 +mz_00001 175.01 70 [Phenyl phosphonothioate] 173.990437637 C6H7O2PS [M+H] 174.997714 HMDB0256424 +mz_00001 175.01 71 [p-TOLUENESULFONYL FLUORIDE] 174.015078802 C7H7FO2S [M+H] 175.022355 HMDB0256057 +mz_00001 175.01 78 [Aconitic acid] 174.016437913 C6H6O6 [M+H] 175.023714 HMDB0247961 +mz_00002 238.19 41 ["N,N-di-n-propyldopamine"] 237.172878985 C14H23NO2 [M+H] 238.180155 HMDB0255249 +mz_00002 238.19 6 [Ethoxybenzyl diethylenetriamine] 237.184112373 C13H23N3O [M+H] 238.191388 HMDB0252022 +mz_00002 238.19 41 [Deacetylmoxisylyte] 237.172878985 C14H23NO2 [M+H] 238.180155 HMDB0250903 +mz_00002 238.19 194 [viloxazine] 237.136493476 C13H19NO3 [M+H] 238.143769 HMDB0259807 +mz_00003 420.16 87 [Cligosiban] 419.1160454 C19H19ClFN5O3 [M+H] 420.123321 HMDB0256366 +mz_00003 420.16 22 [Perphenazine sulfoxide] 419.143426 C21H26ClN3O2S [M+H] 420.150702 HMDB0256352 +mz_00003 420.16 13 ["Glycine, L-gamma-glutamyl-2-(1-methyl-4-(nitrosothio)-4-piperidinyl)glycyl-"] 419.147469339 C15H25N5O7S [M+H] 420.154745 HMDB0253933 +mz_00003 420.16 56 [Dolutegravir] 419.12927705 C20H19F2N3O5 [M+H] 420.136553 HMDB0251580 +mz_00003 420.16 31 [Acorafloxacin] 419.165662559 C21H23F2N3O4 [M+H] 420.172939 HMDB0247964 +mz_00004 780.32 12 [Ravtansine] 779.3218438 C38H54ClN3O10S [M+H] 780.32912 HMDB0247402 mz_00004 780.32 55 [3'-Sialyl-3-fucosyllactose] 779.269536879 C29H49NO23 [M+H] 780.276813 HMDB0006606 -mz_00005 956.25 0 UNKNOWN N/A N/A N/A N/A N/A +mz_00005 956.25 43 [jasmonoyl-CoA] 955.201134221 C33H48N7O18P3S [M+H] 956.20841 HMDB0304397 mz_00006 1100.45 0 UNKNOWN N/A N/A N/A N/A N/A diff -r 2d8a310e86ce -r d8e2ede293a6 test-data/out_test03.txt --- a/test-data/out_test03.txt Thu May 19 13:43:09 2022 +0000 +++ b/test-data/out_test03.txt Thu May 19 14:41:34 2022 +0000 @@ -1,11 +1,19 @@ ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID -mz_00001 175.01 23 [Phenol sulphate] 173.99867937 C6H6O4S [M+H] 175.005955 HMDB0060015 -mz_00001 175.01 78 [trans-Aconitic acid] 174.016437924 C6H6O6 [M+H] 175.023714 HMDB0000958 -mz_00001 175.01 78 [cis-Aconitic acid] 174.016437924 C6H6O6 [M+H] 175.023714 HMDB0000072 -mz_00001 175.01 78 [Dehydroascorbic acid] 174.016437924 C6H6O6 [M+H] 175.023714 HMDB0001264 -mz_00001 175.01 78 [dehydroascorbide(1-)] 174.016437913 C6H6O6 [M+H] 175.023714 HMDB0062706 -mz_00002 238.19 0 UNKNOWN N/A N/A N/A N/A N/A -mz_00003 420.16 57 [Fenvalerate] 419.128821282 C25H22ClNO3 [M+H] 420.136097 HMDB0031791 +mz_00001 175.01 271 [Trinitrosotrimethylenetriamine] 174.050138077 C3H6N6O3 [M+H] 175.057414 HMDB0259249 +mz_00001 175.01 166 ["Naphthalene-1,2,4-trione"] 174.031694053 C10H6O3 [M+H] 175.03897 HMDB0257698 +mz_00001 175.01 70 [Phenyl phosphonothioate] 173.990437637 C6H7O2PS [M+H] 174.997714 HMDB0256424 +mz_00001 175.01 71 [p-TOLUENESULFONYL FLUORIDE] 174.015078802 C7H7FO2S [M+H] 175.022355 HMDB0256057 +mz_00001 175.01 78 [Aconitic acid] 174.016437913 C6H6O6 [M+H] 175.023714 HMDB0247961 +mz_00002 238.19 41 ["N,N-di-n-propyldopamine"] 237.172878985 C14H23NO2 [M+H] 238.180155 HMDB0255249 +mz_00002 238.19 6 [Ethoxybenzyl diethylenetriamine] 237.184112373 C13H23N3O [M+H] 238.191388 HMDB0252022 +mz_00002 238.19 41 [Deacetylmoxisylyte] 237.172878985 C14H23NO2 [M+H] 238.180155 HMDB0250903 +mz_00002 238.19 194 [viloxazine] 237.136493476 C13H19NO3 [M+H] 238.143769 HMDB0259807 +mz_00003 420.16 87 [Cligosiban] 419.1160454 C19H19ClFN5O3 [M+H] 420.123321 HMDB0256366 +mz_00003 420.16 22 [Perphenazine sulfoxide] 419.143426 C21H26ClN3O2S [M+H] 420.150702 HMDB0256352 +mz_00003 420.16 13 ["Glycine, L-gamma-glutamyl-2-(1-methyl-4-(nitrosothio)-4-piperidinyl)glycyl-"] 419.147469339 C15H25N5O7S [M+H] 420.154745 HMDB0253933 +mz_00003 420.16 56 [Dolutegravir] 419.12927705 C20H19F2N3O5 [M+H] 420.136553 HMDB0251580 +mz_00003 420.16 31 [Acorafloxacin] 419.165662559 C21H23F2N3O4 [M+H] 420.172939 HMDB0247964 +mz_00004 780.32 12 [Ravtansine] 779.3218438 C38H54ClN3O10S [M+H] 780.32912 HMDB0247402 mz_00004 780.32 55 [3'-Sialyl-3-fucosyllactose] 779.269536879 C29H49NO23 [M+H] 780.276813 HMDB0006606 -mz_00005 956.25 0 UNKNOWN N/A N/A N/A N/A N/A +mz_00005 956.25 43 [jasmonoyl-CoA] 955.201134221 C33H48N7O18P3S [M+H] 956.20841 HMDB0304397 mz_00006 1100.45 0 UNKNOWN N/A N/A N/A N/A N/A diff -r 2d8a310e86ce -r d8e2ede293a6 test-data/out_test04.html --- a/test-data/out_test04.html Thu May 19 13:43:09 2022 +0000 +++ b/test-data/out_test04.html Thu May 19 14:41:34 2022 +0000 @@ -1,1 +1,1 @@ -Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.05

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct typeAdduct MW (Da)Delta (ppm)InChI IdentifierPredicted LogP (ALOGPS)
mz_00001175.01
MercaptopurineHMDB0015167C5H4N4S152.015666838M+Na+175.00488529NONEDATANONEDATA
S-Methyl benzenecarbothioateHMDB0029694C8H8OS152.029585568M+Na+175.01880450NONEDATANONEDATA
"6,8-Dihydroxypurine"HMDB0001182C5H4N4O2152.033425392M+Na+175.02264372NONEDATANONEDATA
OxypurinolHMDB0000786C5H4N4O2152.033425392M+Na+175.02264372NONEDATANONEDATA
XanthineHMDB0000292C5H4N4O2152.033425392M+Na+175.02264372NONEDATANONEDATA
mz_00002238.19
HeptanoylcholineHMDB0013239C12H26NO2216.196354081M+Na+238.17829649NONEDATANONEDATA
FencamfamineHMDB0015508C15H21N215.167399677M+Na+238.156618140NONEDATANONEDATA
SolamineHMDB0031202C12H29N3215.236147943M+Na+238.225366148NONEDATANONEDATA
Diethylcarbamazine N-oxideHMDB0060817C10H21N3O2215.163376931M+Na+238.152595157NONEDATANONEDATA
N-NonanoylglycineHMDB0013279C11H21NO3215.152143543M+Na+238.141362204NONEDATANONEDATA
mz_00003420.16
SimulansamideHMDB0030435C22H23NO6397.152537473M+Na+420.14175543NONEDATANONEDATA
mz_00004780.32
UNKNOWNNONEn/an/an/an/an/a0n/an/a
mz_00005956.25
"(2S,3S,4R,5R,6R)-6-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-{[(3R,4R,5R)-4,5,6-trihydroxyoxan-3-yl]oxy}oxan-4-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-4,5-dihydroxy-3-{[(2R,3R,4R,5R,6R)-5-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)-4-(sulfooxy)oxan-2-yl]oxy}oxane-2-carboxylic acid"HMDB0062476C31H51NO29S933.2267458M+Na+956.21596436NONEDATANONEDATA
(3S)-3-isopropenyl-6-oxoheptanoyl-CoAHMDB0062370C31H50N7O18P3S933.214589966M+Na+956.20380848NONEDATANONEDATA
mz_000061100.45
UNKNOWNNONEn/an/an/an/an/a0n/an/a
\ No newline at end of file +Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.05

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct typeAdduct MW (Da)Delta (ppm)InChI IdentifierPredicted LogP (ALOGPS)
mz_00001175.01
4-Hydrazinylpyridine-3-carboxamideHMDB0258083C6H8N4O152.069810894M+Na+175.059029280NONEDATANONEDATA
9-SulfanylpurineHMDB0257842C5H4N4S152.015667319M+Na+175.00488529NONEDATANONEDATA
S-Phenyl thioacetateHMDB0257424C8H8OS152.029586052M+Na+175.01880450NONEDATANONEDATA
"n-methyl-6-oxo-1,6-dihydropyridine-3-carboxamide"HMDB0255171C7H8N2O2152.058577506M+Na+175.047796216NONEDATANONEDATA
Methyl pyridone carboxamideHMDB0254609C7H8N2O2152.058577506M+Na+175.047796216NONEDATANONEDATA
mz_00002238.19
Ethyl butylacetylaminopropionateHMDB0246904C11H21NO3215.15214354M+Na+238.141362204NONEDATANONEDATA
HexaminolevulinateHMDB0253144C11H21NO3215.15214354M+Na+238.141362204NONEDATANONEDATA
ω-hydroxylaurateHMDB0304547C12H23O3215.165268181M+Na+238.154486149NONEDATANONEDATA
Diethylcarbamazine N-oxideHMDB0060817C10H21N3O2215.163376931M+Na+238.152595157NONEDATANONEDATA
N-NonanoylglycineHMDB0013279C11H21NO3215.152143543M+Na+238.141362204NONEDATANONEDATA
mz_00003420.16
"N-Acetyl-9-aminominocycline, (4R)-"HMDB0259457C20H31NO7397.210052342M+Na+420.1992793NONEDATANONEDATA
Reduced ketanserinHMDB0257133C22H24FN3O3397.180169808M+Na+420.16938822NONEDATANONEDATA
"1,2,4-Triazolo(4,3-b)pyridazine, 7-cyclobutyl-3-(2,6-difluorophenyl)-6-((1-methyl-1H-1,2,4-triazol-5-yl)methoxy)-"HMDB0254773C19H17F2N7O397.146264521M+Na+420.13548358NONEDATANONEDATA
6-[[3-Fluoro-5-(4-methoxyoxan-4-yl)phenoxy]methyl]-1-methylquinolin-2-oneHMDB0253359C23H24FNO4397.16893642M+Na+420.1581544NONEDATANONEDATA
CI-1044HMDB0250223C23H19N5O2397.153874872M+Na+420.14309340NONEDATANONEDATA
mz_00004780.32
VaniprevirHMDB0259762C38H55N5O9S757.372049545M+Na+780.36126853NONEDATANONEDATA
mz_00005956.25
undec-10-enoyl-CoAHMDB0300959C32H54N7O17P3S933.250975475M+Na+956.24019310NONEDATANONEDATA
Undec-8-enoyl-CoAHMDB0300958C32H54N7O17P3S933.250975475M+Na+956.24019310NONEDATANONEDATA
Undec-9-enoyl-CoAHMDB0300957C32H54N7O17P3S933.250975475M+Na+956.24019310NONEDATANONEDATA
Undec-3-enoyl-CoAHMDB0300956C32H54N7O17P3S933.250975475M+Na+956.24019310NONEDATANONEDATA
(7E)-Undec-7-enoyl-CoAHMDB0300955C32H54N7O17P3S933.250975475M+Na+956.24019310NONEDATANONEDATA
mz_000061100.45
UNKNOWNNONEn/an/an/an/an/a0n/an/a
\ No newline at end of file diff -r 2d8a310e86ce -r d8e2ede293a6 test-data/out_test04.tabular --- a/test-data/out_test04.tabular Thu May 19 13:43:09 2022 +0000 +++ b/test-data/out_test04.tabular Thu May 19 14:41:34 2022 +0000 @@ -1,16 +1,23 @@ ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID -mz_00001 175.01 29 [Mercaptopurine] 152.015666838 C5H4N4S [M+Na] 175.004885 HMDB0015167 -mz_00001 175.01 50 [S-Methyl benzenecarbothioate] 152.029585568 C8H8OS [M+Na] 175.018804 HMDB0029694 -mz_00001 175.01 72 ["6,8-Dihydroxypurine"] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0001182 -mz_00001 175.01 72 [Oxypurinol] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0000786 -mz_00001 175.01 72 [Xanthine] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0000292 -mz_00002 238.19 49 [Heptanoylcholine] 216.196354081 C12H26NO2 [M+Na] 238.178296 HMDB0013239 -mz_00002 238.19 140 [Fencamfamine] 215.167399677 C15H21N [M+Na] 238.156618 HMDB0015508 -mz_00002 238.19 148 [Solamine] 215.236147943 C12H29N3 [M+Na] 238.225366 HMDB0031202 +mz_00001 175.01 280 [4-Hydrazinylpyridine-3-carboxamide] 152.069810894 C6H8N4O [M+Na] 175.059029 HMDB0258083 +mz_00001 175.01 29 [9-Sulfanylpurine] 152.015667319 C5H4N4S [M+Na] 175.004885 HMDB0257842 +mz_00001 175.01 50 [S-Phenyl thioacetate] 152.029586052 C8H8OS [M+Na] 175.018804 HMDB0257424 +mz_00001 175.01 216 ["n-methyl-6-oxo-1,6-dihydropyridine-3-carboxamide"] 152.058577506 C7H8N2O2 [M+Na] 175.047796 HMDB0255171 +mz_00001 175.01 216 [Methyl pyridone carboxamide] 152.058577506 C7H8N2O2 [M+Na] 175.047796 HMDB0254609 +mz_00002 238.19 204 [Ethyl butylacetylaminopropionate] 215.15214354 C11H21NO3 [M+Na] 238.141362 HMDB0246904 +mz_00002 238.19 204 [Hexaminolevulinate] 215.15214354 C11H21NO3 [M+Na] 238.141362 HMDB0253144 +mz_00002 238.19 149 [ω-hydroxylaurate] 215.165268181 C12H23O3 [M+Na] 238.154486 HMDB0304547 mz_00002 238.19 157 [Diethylcarbamazine N-oxide] 215.163376931 C10H21N3O2 [M+Na] 238.152595 HMDB0060817 mz_00002 238.19 204 [N-Nonanoylglycine] 215.152143543 C11H21NO3 [M+Na] 238.141362 HMDB0013279 -mz_00003 420.16 43 [Simulansamide] 397.152537473 C22H23NO6 [M+Na] 420.141755 HMDB0030435 -mz_00004 780.32 0 UNKNOWN N/A N/A N/A N/A N/A -mz_00005 956.25 36 ["(2S,3S,4R,5R,6R)-6-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-{[(3R,4R,5R)-4,5,6-trihydroxyoxan-3-yl]oxy}oxan-4-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-4,5-dihydroxy-3-{[(2R,3R,4R,5R,6R)-5-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)-4-(sulfooxy)oxan-2-yl]oxy}oxane-2-carboxylic acid"] 933.2267458 C31H51NO29S [M+Na] 956.215964 HMDB0062476 -mz_00005 956.25 48 [(3S)-3-isopropenyl-6-oxoheptanoyl-CoA] 933.214589966 C31H50N7O18P3S [M+Na] 956.203808 HMDB0062370 +mz_00003 420.16 93 ["N-Acetyl-9-aminominocycline, (4R)-"] 397.210052342 C20H31NO7 [M+Na] 420.19927 HMDB0259457 +mz_00003 420.16 22 [Reduced ketanserin] 397.180169808 C22H24FN3O3 [M+Na] 420.169388 HMDB0257133 +mz_00003 420.16 58 ["1,2,4-Triazolo(4,3-b)pyridazine, 7-cyclobutyl-3-(2,6-difluorophenyl)-6-((1-methyl-1H-1,2,4-triazol-5-yl)methoxy)-"] 397.146264521 C19H17F2N7O [M+Na] 420.135483 HMDB0254773 +mz_00003 420.16 4 [6-[[3-Fluoro-5-(4-methoxyoxan-4-yl)phenoxy]methyl]-1-methylquinolin-2-one] 397.16893642 C23H24FNO4 [M+Na] 420.158154 HMDB0253359 +mz_00003 420.16 40 [CI-1044] 397.153874872 C23H19N5O2 [M+Na] 420.143093 HMDB0250223 +mz_00004 780.32 53 [Vaniprevir] 757.372049545 C38H55N5O9S [M+Na] 780.361268 HMDB0259762 +mz_00005 956.25 10 [undec-10-enoyl-CoA] 933.250975475 C32H54N7O17P3S [M+Na] 956.240193 HMDB0300959 +mz_00005 956.25 10 [Undec-8-enoyl-CoA] 933.250975475 C32H54N7O17P3S [M+Na] 956.240193 HMDB0300958 +mz_00005 956.25 10 [Undec-9-enoyl-CoA] 933.250975475 C32H54N7O17P3S [M+Na] 956.240193 HMDB0300957 +mz_00005 956.25 10 [Undec-3-enoyl-CoA] 933.250975475 C32H54N7O17P3S [M+Na] 956.240193 HMDB0300956 +mz_00005 956.25 10 [(7E)-Undec-7-enoyl-CoA] 933.250975475 C32H54N7O17P3S [M+Na] 956.240193 HMDB0300955 mz_00006 1100.45 0 UNKNOWN N/A N/A N/A N/A N/A diff -r 2d8a310e86ce -r d8e2ede293a6 test-data/out_test04.txt --- a/test-data/out_test04.txt Thu May 19 13:43:09 2022 +0000 +++ b/test-data/out_test04.txt Thu May 19 14:41:34 2022 +0000 @@ -1,16 +1,23 @@ ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID -mz_00001 175.01 29 [Mercaptopurine] 152.015666838 C5H4N4S [M+Na] 175.004885 HMDB0015167 -mz_00001 175.01 50 [S-Methyl benzenecarbothioate] 152.029585568 C8H8OS [M+Na] 175.018804 HMDB0029694 -mz_00001 175.01 72 ["6,8-Dihydroxypurine"] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0001182 -mz_00001 175.01 72 [Oxypurinol] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0000786 -mz_00001 175.01 72 [Xanthine] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0000292 -mz_00002 238.19 49 [Heptanoylcholine] 216.196354081 C12H26NO2 [M+Na] 238.178296 HMDB0013239 -mz_00002 238.19 140 [Fencamfamine] 215.167399677 C15H21N [M+Na] 238.156618 HMDB0015508 -mz_00002 238.19 148 [Solamine] 215.236147943 C12H29N3 [M+Na] 238.225366 HMDB0031202 +mz_00001 175.01 280 [4-Hydrazinylpyridine-3-carboxamide] 152.069810894 C6H8N4O [M+Na] 175.059029 HMDB0258083 +mz_00001 175.01 29 [9-Sulfanylpurine] 152.015667319 C5H4N4S [M+Na] 175.004885 HMDB0257842 +mz_00001 175.01 50 [S-Phenyl thioacetate] 152.029586052 C8H8OS [M+Na] 175.018804 HMDB0257424 +mz_00001 175.01 216 ["n-methyl-6-oxo-1,6-dihydropyridine-3-carboxamide"] 152.058577506 C7H8N2O2 [M+Na] 175.047796 HMDB0255171 +mz_00001 175.01 216 [Methyl pyridone carboxamide] 152.058577506 C7H8N2O2 [M+Na] 175.047796 HMDB0254609 +mz_00002 238.19 204 [Ethyl butylacetylaminopropionate] 215.15214354 C11H21NO3 [M+Na] 238.141362 HMDB0246904 +mz_00002 238.19 204 [Hexaminolevulinate] 215.15214354 C11H21NO3 [M+Na] 238.141362 HMDB0253144 +mz_00002 238.19 149 [ω-hydroxylaurate] 215.165268181 C12H23O3 [M+Na] 238.154486 HMDB0304547 mz_00002 238.19 157 [Diethylcarbamazine N-oxide] 215.163376931 C10H21N3O2 [M+Na] 238.152595 HMDB0060817 mz_00002 238.19 204 [N-Nonanoylglycine] 215.152143543 C11H21NO3 [M+Na] 238.141362 HMDB0013279 -mz_00003 420.16 43 [Simulansamide] 397.152537473 C22H23NO6 [M+Na] 420.141755 HMDB0030435 -mz_00004 780.32 0 UNKNOWN N/A N/A N/A N/A N/A -mz_00005 956.25 36 ["(2S,3S,4R,5R,6R)-6-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-{[(3R,4R,5R)-4,5,6-trihydroxyoxan-3-yl]oxy}oxan-4-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-4,5-dihydroxy-3-{[(2R,3R,4R,5R,6R)-5-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)-4-(sulfooxy)oxan-2-yl]oxy}oxane-2-carboxylic acid"] 933.2267458 C31H51NO29S [M+Na] 956.215964 HMDB0062476 -mz_00005 956.25 48 [(3S)-3-isopropenyl-6-oxoheptanoyl-CoA] 933.214589966 C31H50N7O18P3S [M+Na] 956.203808 HMDB0062370 +mz_00003 420.16 93 ["N-Acetyl-9-aminominocycline, (4R)-"] 397.210052342 C20H31NO7 [M+Na] 420.19927 HMDB0259457 +mz_00003 420.16 22 [Reduced ketanserin] 397.180169808 C22H24FN3O3 [M+Na] 420.169388 HMDB0257133 +mz_00003 420.16 58 ["1,2,4-Triazolo(4,3-b)pyridazine, 7-cyclobutyl-3-(2,6-difluorophenyl)-6-((1-methyl-1H-1,2,4-triazol-5-yl)methoxy)-"] 397.146264521 C19H17F2N7O [M+Na] 420.135483 HMDB0254773 +mz_00003 420.16 4 [6-[[3-Fluoro-5-(4-methoxyoxan-4-yl)phenoxy]methyl]-1-methylquinolin-2-one] 397.16893642 C23H24FNO4 [M+Na] 420.158154 HMDB0253359 +mz_00003 420.16 40 [CI-1044] 397.153874872 C23H19N5O2 [M+Na] 420.143093 HMDB0250223 +mz_00004 780.32 53 [Vaniprevir] 757.372049545 C38H55N5O9S [M+Na] 780.361268 HMDB0259762 +mz_00005 956.25 10 [undec-10-enoyl-CoA] 933.250975475 C32H54N7O17P3S [M+Na] 956.240193 HMDB0300959 +mz_00005 956.25 10 [Undec-8-enoyl-CoA] 933.250975475 C32H54N7O17P3S [M+Na] 956.240193 HMDB0300958 +mz_00005 956.25 10 [Undec-9-enoyl-CoA] 933.250975475 C32H54N7O17P3S [M+Na] 956.240193 HMDB0300957 +mz_00005 956.25 10 [Undec-3-enoyl-CoA] 933.250975475 C32H54N7O17P3S [M+Na] 956.240193 HMDB0300956 +mz_00005 956.25 10 [(7E)-Undec-7-enoyl-CoA] 933.250975475 C32H54N7O17P3S [M+Na] 956.240193 HMDB0300955 mz_00006 1100.45 0 UNKNOWN N/A N/A N/A N/A N/A diff -r 2d8a310e86ce -r d8e2ede293a6 wsdl_hmdb.pl --- a/wsdl_hmdb.pl Thu May 19 13:43:09 2022 +0000 +++ b/wsdl_hmdb.pl Thu May 19 14:41:34 2022 +0000 @@ -49,7 +49,7 @@ "output_tabular:s" => \$out_tab, ## option : path to the ouput (tabular : input+results ) "output_html|v:s" => \$out_html, ## option : path to the results view (output2) "output_xlsx:s" => \$out_xls, ## option : path to the xls-like format output - #"advancedFeatures:i"=> \$advancedFeatures, ## option : set to 1 to get advanced options or 0 to get first level only. + "advancedFeatures:i"=> \$advancedFeatures, ## option : set to 1 to get advanced options or 0 to get first level only. "verbose:i" => \$VERBOSE, ## VERBOSE Of the tool ) ; @@ -160,7 +160,7 @@ ## hard modification with $max_query fixed at 1000 !!! Need to be refactoring ## Cutof will be done in next method after URI check - ($result) = $oHmdb->getMatchesFromHmdb5WithUA($hmdb_pages, $mzs, 1000) ; ## hash format result + ($result) = $oHmdb->parseHmdb5CSVResults($hmdb_pages, $mzs, 1000) ; ## hash format result ## This previous step return results with cutoff on the number of entries returned ! @@ -216,7 +216,7 @@ ($tbody_object) = $oHtml->add_mz_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $ids) ; ($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $results) ; - print Dumper $tbody_object ; + # print Dumper $tbody_object ; my $output_html = $oHtml->write_html_skel(\$out_html, $tbody_object, $nb_pages_for_html_out, $search_condition, $CONF->{'HTML_TEMPLATE'}, $CONF->{'JS_GALAXY_PATH'}, $CONF->{'CSS_GALAXY_PATH'}) ; diff -r 2d8a310e86ce -r d8e2ede293a6 wsdl_hmdb.xml --- a/wsdl_hmdb.xml Thu May 19 13:43:09 2022 +0000 +++ b/wsdl_hmdb.xml Thu May 19 14:41:34 2022 +0000 @@ -1,6 +1,6 @@ - + - search by masses on HMDB online LCMS bank + search by masses on HMDB v5 online LCMS bank @@ -29,10 +29,10 @@ -nblineheader "${$input_type.header.nbHeader}" #end if -colfactor "${input_type.colfactor}" - -output_tabular "$variableMetadata" -output_html "$HmdbOutWeb" -output_xls "$HmdbOutXlsx" + -output_tabular "$variableMetadata" -output_html "$HmdbOutWeb" -output_xlsx "$HmdbOutXlsx" #else: -mass "${input_type.mass}" - -output_tabular "$variableMetadata2" -output_html "$HmdbOutWeb2" -output_xls "$HmdbOutXlsx2" + -output_tabular "$variableMetadata2" -output_html "$HmdbOutWeb2" -output_xlsx "$HmdbOutXlsx2" #end if -mode "${mode_type.mode}" @@ -377,7 +377,7 @@ .. class:: warningmark -And their "W4M courses 2021": +And their "W4M courses 2022": | Using Galaxy4Metabolomics - W4M table format for Galaxy | Annotation Banks - Annotation