# HG changeset patch # User fgiacomoni # Date 1657024755 0 # Node ID 8f7546d0b925f19e650b6e7fd8493f538013d428 # Parent d8e2ede293a64c85ca73a253e1dbc57b6cb9bb23 master branch Updating with tag :CI_COMMIT_TAG - - Fxx diff -r d8e2ede293a6 -r 8f7546d0b925 Dockerfile --- a/Dockerfile Thu May 19 14:41:34 2022 +0000 +++ b/Dockerfile Tue Jul 05 12:39:15 2022 +0000 @@ -1,53 +1,39 @@ -# ref install: ubuntu 20.04 -FROM ubuntu:20.04 - -# init var -ARG DEBIAN_FRONTEND=noninteractive +#FROM pfem/perlfull +FROM python:3.8-buster # set author -MAINTAINER Franck Giacomoni +LABEL maintainer="franck.giacomoni@inrae.fr" -### -### [CONTAINER CORE FUNCTIONS]: -### xxxx -### xxxx -### [NOTES] -### xxxx +ENV PLANEMO_VENV_LOCATION /planemo-venv +ENV CONDA /tmp/conda -ENV PATH /opt/conda/bin:$PATH -RUN apt-get -y update &&\ - apt-get -y install build-essential \ - cpanminus \ - gzip \ - wget \ - bzip2 \ - ca-certificates \ - libglib2.0-0 \ - libxext6 \ - libsm6 \ - libxrender1 \ - libtext-csv-perl \ - libxml-twig-perl \ - libfile-share-perl - -RUN wget --quiet https://repo.anaconda.com/archive/Anaconda3-5.3.0-Linux-x86_64.sh -O ~/anaconda.sh && \ - /bin/bash ~/anaconda.sh -b -p /opt/conda && \ - rm ~/anaconda.sh && \ - ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \ - echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \ - echo "conda activate base" >> ~/.bashrc - -RUN cpan install ExtUtils::MakeMaker && \ - cpan install File::ShareDir::Install && \ - cpan install Module::Release && \ - cpan install Archive::Zip && \ - apt -y install git &&\ - apt -y install python3 python3-pip && \ - apt -y install virtualenv && \ - pip install "pip>=7" && \ - pip install -U git+git://github.com/galaxyproject/planemo.git && \ +RUN apt-get update &&\ + apt-get upgrade -y &&\ + apt-get install --no-install-recommends --yes build-essential \ + git \ + libgl1-mesa-glx \ + libegl1-mesa \ + libxrandr2 \ + libxss1 \ + libxcursor1 \ + libxcomposite1 \ + libasound2 \ + libxi6 \ + libxtst6 \ + python-virtualenv && \ + pip install virtualenv && \ + python3 -m virtualenv "$PLANEMO_VENV_LOCATION" && \ + . "$PLANEMO_VENV_LOCATION"/bin/activate && \ + pip install --upgrade pip setuptools && \ + pip install planemo numpy && \ + pip install -U planemo && \ + #planemo conda_init --conda_prefix "$CONDA" && \ apt-get autoremove -y && \ apt-get clean && \ - rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* - + rm -rf /var/lib/apt/lists/* && \ + rm -rf /tmp/* && \ + rm -rf /var/tmp/* && \ + rm -rf /usr/bin/X11 ; + +CMD [] \ No newline at end of file diff -r d8e2ede293a6 -r 8f7546d0b925 README.txt --- a/README.txt Thu May 19 14:41:34 2022 +0000 +++ b/README.txt Tue Jul 05 12:39:15 2022 +0000 @@ -1,5 +1,5 @@ ## ****** HMDB environnemnt : ****** ## -# version Nov 2016 M Landi / F Giacomoni - INRA - METABOHUB - workflow4metabolomics.org core team +# version June 2022 M Landi / F Giacomoni - INRAE - METABOHUB - workflow4metabolomics.org core team ## --- PERL compilator / libraries : --- ## $ perl -v diff -r d8e2ede293a6 -r 8f7546d0b925 lib/hmdb.pm --- a/lib/hmdb.pm Thu May 19 14:41:34 2022 +0000 +++ b/lib/hmdb.pm Tue Jul 05 12:39:15 2022 +0000 @@ -709,10 +709,12 @@ if ($line !~ /query_mass,compound_id,compound_name,formula,monoisotopic_mass,adduct,adduct_type,adduct_m\/z,"delta\(ppm\),",ccs_value/) { #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" ; + #if ( $line =~ /(\d+\.\d+),(\w+),(.*),(\w+),(\d+\.\d+),([\+|\-|\w|n\/a|\s+]+)\s*,(\+|\-),(\d+\.\d+),(\d+),(\d*)/ ) { + if ( $line =~ /(\d+\.\d+),(\w+),(.*),(\w+),(\d+\.\d+),([\+|\-|\w|n\/a|\s+]+)\s*,(\+|\-),(\d+\.\d+),(\d+),.*/ ) { # works on NEG AND POS results + print "$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") ; + my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9") ; + #my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ; if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; } diff -r d8e2ede293a6 -r 8f7546d0b925 test-data/out_test02.html --- a/test-data/out_test02.html Thu May 19 14:41:34 2022 +0000 +++ b/test-data/out_test02.html Tue Jul 05 12:39:15 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
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

Copyright © INRA, N Paulhe, F Giacomoni 2014

\ 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
BerylliumHMDB0002387Be9.012182135M+NH4-H2O+7.0203368NONEDATANONEDATA
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
o-AcetylhydroxylamineHMDB0248304C2H5NO275.032028405M+NH4-H2O+75.05472810NONEDATANONEDATA
mz_0000375.08059797
"Propan-2,2-diyl"HMDB0251402C3H642.046950193M+CH3OH+H+75.0804392NONEDATANONEDATA
MethyleneHMDB0249629CH214.015650064M+IsoProp+H+75.080995NONEDATANONEDATA
EthanolHMDB0000108C2H6O46.0418648142M+H-H2O+75.080531NONEDATANONEDATA
CyclopropaneHMDB0250673C3H642.046950193M+CH3OH+H+75.0804392NONEDATANONEDATA
PyrophosphateHMDB0000250H4O7P2177.943225506M+H+2Na+75.0805990NONEDATANONEDATA
mz_0000476.03942694
Tri-hydroxymethylaminomethaneHMDB0259134C2H7NO393.042593089M+H-H2O+76.0398936NONEDATANONEDATA
Glutamic acid diethyl esterHMDB0252807C9H17NO4203.115758031M+2H+Na+76.0398435NONEDATANONEDATA
MethylcarbonyloxyHMDB0249651C2H2O258.005479304M+NH4+76.0393022NONEDATANONEDATA
o-AcetylhydroxylamineHMDB0248304C2H5NO275.032028405M+H+76.0393042NONEDATANONEDATA
"2-Aminoethane-1,1,1-triol"HMDB0247334C2H7NO393.042593089M+H-H2O+76.0398936NONEDATANONEDATA
mz_0000576.07584477
2-(2-Hydroxypropan-2-ylamino)propan-2-olHMDB0257796C6H15NO2133.110278727M+H+NH4+76.0756892NONEDATANONEDATA
PropanediolHMDB0256813C3H8O276.052429498M+NH4-H2O+76.0751299NONEDATANONEDATA
AminopropanolHMDB0248330C3H9NO75.068413914M+H+76.075692NONEDATANONEDATA
2-MethoxyethylamineHMDB0245205C3H9NO75.068413914M+H+76.075692NONEDATANONEDATA
(E)-1-PropenolHMDB0243637C3H6O58.041864813M+NH4+76.0756882NONEDATANONEDATA
mz_0000676.07593168
2-(2-Hydroxypropan-2-ylamino)propan-2-olHMDB0257796C6H15NO2133.110278727M+H+NH4+76.0756893NONEDATANONEDATA
PropanediolHMDB0256813C3H8O276.052429498M+NH4-H2O+76.07512911NONEDATANONEDATA
AminopropanolHMDB0248330C3H9NO75.068413914M+H+76.075693NONEDATANONEDATA
2-MethoxyethylamineHMDB0245205C3H9NO75.068413914M+H+76.075693NONEDATANONEDATA
(E)-1-PropenolHMDB0243637C3H6O58.041864813M+NH4+76.0756883NONEDATANONEDATA

Copyright © INRA, N Paulhe, F Giacomoni 2014

\ No newline at end of file diff -r d8e2ede293a6 -r 8f7546d0b925 test-data/out_test02.tabular --- a/test-data/out_test02.tabular Thu May 19 14:41:34 2022 +0000 +++ b/test-data/out_test02.tabular Tue Jul 05 12:39:15 2022 +0000 @@ -1,7 +1,7 @@ id mz rt hmdb(delta::name::mz::formula::adduct::id) -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" +1 7.02080998 49.38210915 68::[Beryllium]::9.012182135::Be::[M+NH4-H2O]::HMDB0002387 +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 | 10::[o-Acetylhydroxylamine]::75.032028405::C2H5NO2::[M+NH4-H2O]::HMDB0248304" +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 | 1::[Ethanol]::46.041864814::C2H6O::[2M+H-H2O]::HMDB0000108 | 2::[Cyclopropane]::42.046950193::C3H6::[M+CH3OH+H]::HMDB0250673 | 0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0000250" +4 76.03942694 51.23158899 "6::[Tri-hydroxymethylaminomethane]::93.042593089::C2H7NO3::[M+H-H2O]::HMDB0259134 | 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 | 6::[""2-Aminoethane-1,1,1-triol""]::93.042593089::C2H7NO3::[M+H-H2O]::HMDB0247334" +5 76.07584477 50.51249853 "2::[2-(2-Hydroxypropan-2-ylamino)propan-2-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0257796 | 9::[Propanediol]::76.052429498::C3H8O2::[M+NH4-H2O]::HMDB0256813 | 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" +6 76.07593168 0.149308136 "3::[2-(2-Hydroxypropan-2-ylamino)propan-2-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0257796 | 11::[Propanediol]::76.052429498::C3H8O2::[M+NH4-H2O]::HMDB0256813 | 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" diff -r d8e2ede293a6 -r 8f7546d0b925 test-data/out_test02.txt --- a/test-data/out_test02.txt Thu May 19 14:41:34 2022 +0000 +++ b/test-data/out_test02.txt Tue Jul 05 12:39:15 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 0 UNKNOWN N/A N/A N/A N/A N/A +mz_00001 7.02080998 68 [Beryllium] 9.012182135 Be [M+NH4-H2O] 7.02033 HMDB0002387 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_00002 75.05547146 10 [o-Acetylhydroxylamine] 75.032028405 C2H5NO2 [M+NH4-H2O] 75.054728 HMDB0248304 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 1 [Ethanol] 46.041864814 C2H6O [2M+H-H2O] 75.08053 HMDB0000108 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 2 [Propylene] 42.046950192 C3H6 [M+CH3OH+H] 75.080439 HMDB0256839 +mz_00004 76.03942694 6 [Tri-hydroxymethylaminomethane] 93.042593089 C2H7NO3 [M+H-H2O] 76.039893 HMDB0259134 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_00004 76.03942694 6 ["2-Aminoethane-1,1,1-triol"] 93.042593089 C2H7NO3 [M+H-H2O] 76.039893 HMDB0247334 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 9 [Propanediol] 76.052429498 C3H8O2 [M+NH4-H2O] 76.075129 HMDB0256813 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 11 [Propanediol] 76.052429498 C3H8O2 [M+NH4-H2O] 76.075129 HMDB0256813 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 d8e2ede293a6 -r 8f7546d0b925 wsdl_hmdb.pl --- a/wsdl_hmdb.pl Thu May 19 14:41:34 2022 +0000 +++ b/wsdl_hmdb.pl Tue Jul 05 12:39:15 2022 +0000 @@ -162,6 +162,8 @@ ## Cutof will be done in next method after URI check ($result) = $oHmdb->parseHmdb5CSVResults($hmdb_pages, $mzs, 1000) ; ## hash format result +# print Dumper $result ; + ## This previous step return results with cutoff on the number of entries returned ! ## clean/max result by testing each HMDB_ID page in HMDB @@ -275,7 +277,7 @@ # Email : fgiacomoni\@inra.fr # Version : 1.6 # Created : 08/07/2012 -# Updated : 23/01/2019 - 1.6 +# Updated : 22/06/2022 - 1.7.2 USAGE : wsdl_hmdb.pl -mass [one mass or a string list of exact masses] -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file] @@ -349,4 +351,6 @@ version 1.7.0 : 19/ 05 / 2022 - Update HMDB API client - compliant with HMDB 5.0 web portal +version 1.7.2 : 22/ 06 / 2022 - Fix issue with neg result parsing + =cut \ No newline at end of file diff -r d8e2ede293a6 -r 8f7546d0b925 wsdl_hmdb.xml --- a/wsdl_hmdb.xml Thu May 19 14:41:34 2022 +0000 +++ b/wsdl_hmdb.xml Tue Jul 05 12:39:15 2022 +0000 @@ -1,4 +1,4 @@ - + search by masses on HMDB v5 online LCMS bank