From 7a1b49277173d624f0cff18e8a8da0f6db60197c Mon Sep 17 00:00:00 2001 From: Steffen Neumann Date: Thu, 20 Sep 2018 21:53:16 +0200 Subject: [PATCH 1/6] First addition of MetFrag, planemo still failling --- tools/metfrag/metfrag-cli-batch.xml | 147 ++++++++++++++++++ ...00003_PE_PG_AutoMS_2-B_3_03_18583.mzML.txt | 12 ++ tools/metfrag/test-data/candidates.csv | 72 +++++++++ 3 files changed, 231 insertions(+) create mode 100644 tools/metfrag/metfrag-cli-batch.xml create mode 100644 tools/metfrag/test-data/1_746.022_716.5434_1569591.66000003_PE_PG_AutoMS_2-B_3_03_18583.mzML.txt create mode 100644 tools/metfrag/test-data/candidates.csv diff --git a/tools/metfrag/metfrag-cli-batch.xml b/tools/metfrag/metfrag-cli-batch.xml new file mode 100644 index 00000000000..bbd666a0fae --- /dev/null +++ b/tools/metfrag/metfrag-cli-batch.xml @@ -0,0 +1,147 @@ + + + + + + Run MetFrag with a given parameter set. + + metfrag + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +| **Tool update: See the 'NEWS' section at the bottom of the page** + +--------------------------------------------------- + +.. class:: infomark + +**Authors** + +| **Payam Emami (payam.emami@medsci.uu.se)** and **Christoph Ruttkies (christoph.ruttkies@ipb-halle.de)** wrote and maintain this wrapper for MetFrag batch mode processing. + +--------------------------------------------------- + +.. class:: infomark + +**Please cite** + +Ruttkies, C., Schymanski, E. L., Wolf, S., Hollender, J. and Neumann, S. MetFrag relaunched: incorporating strategies beyond in silico fragmentation. J Cheminform 8:3, (2016) DOI: 10.1186/s13321-016-0115-9 + +--------------------------------------------------- + +===================== +MetFrag CLI Batch +===================== + +----------- +Description +----------- + +| This module is used to run MetFrag on annotated MS/MS spectra for compound annotation. The parameters are set by **msms2metfrag**. + + +----------- +Input files +----------- + ++------------------------------+------------+ +| File | Format | ++==============================+============+ +| 1) File with MetFrag | txt | +| parameters | | ++------------------------------+------------+ +| 2) Database File (optional) | csv | ++------------------------------+------------+ + +---------- +Parameters +---------- + +File with MetFrag parameters + | File containing MetFrag parameters which is generated by **msms2metfrag** + | + +Additional Parameters + | Additional parameters that can be passed to MetFrag. This can include e.g. access information for a local MetChem database instance + | + +Database File + | File containing candidates used as database + | + +Additional MetFrag scores + | Add additional MetFrag scores used to score candidates + | + +------------ +Output files +------------ + +metfrag_cli_batch_output_1.csv + | A csv output file with scored candidates and properties + | + +--------------------------------------------------- + +---- +NEWS +---- + +CHANGES IN VERSION 0.3 +======================== + +- added support for additional MetFrag scores + +CHANGES IN VERSION 0.2 +======================== + +- added support for a local file database + + +CHANGES IN VERSION 0.1 +======================== + +First version + + + + 10.1186/s13321-016-0115-9 + + diff --git a/tools/metfrag/test-data/1_746.022_716.5434_1569591.66000003_PE_PG_AutoMS_2-B_3_03_18583.mzML.txt b/tools/metfrag/test-data/1_746.022_716.5434_1569591.66000003_PE_PG_AutoMS_2-B_3_03_18583.mzML.txt new file mode 100644 index 00000000000..484fcc0b849 --- /dev/null +++ b/tools/metfrag/test-data/1_746.022_716.5434_1569591.66000003_PE_PG_AutoMS_2-B_3_03_18583.mzML.txt @@ -0,0 +1,12 @@ +DatabaseSearchRelativeMassDeviation=10 +FragmentPeakMatchAbsoluteMassDeviation=0.01 +FragmentPeakMatchRelativeMassDeviation=10 +MetFragDatabaseType=LocalCSV +MetFragScoreTypes=FragmenterScore +NeutralPrecursorMass=715.534338937996 +IsPositiveIonMode=True +PrecursorIonType=[M+H]+ +MetFragPeakListReader=de.ipbhalle.metfraglib.peaklistreader.FilteredStringTandemMassPeakListReader +MetFragCandidateWriter=CSV +PeakListString=109.103311843742_768;121.103762723448_868;123.119465394337_900;135.120024070472_2640;137.135484671643_1468;149.136560151127_3224;151.152033162978_1164;153.130606018147_992;155.145526557257_548;163.152466697533_2148;165.167467997353_1420;167.146916027229_616;177.167441192232_1552;178.170771149042_548;179.182987576231_884;191.18490851056_688;195.177982692616_748;205.198339837553_744;216.069470315333_948;219.215462981816_6176;220.217798385165_1624;237.190849210659_548;237.226555173215_20256;238.22988426663_3684;247.247176465296_4812;248.251098120068_752;265.258280888417_20560;266.261749807278_3428;267.264596056284_768;280.269716583548_10068;281.273384026216_2556;293.250880662543_720;308.301601568872_4172;309.305542755894_768;311.264230896464_7848;312.266766070307_2700;321.285800876234_1032;322.291770256775_520;339.296880532298_7604;340.300925333769_1180;480.31958650958_760;575.516818987314_111508;576.519796680911_47012;577.522357809362_9092 +SampleName=outputfolder/1_746.022_716.5434_1569591.66000003_PE_PG_AutoMS_2-B_3_03_18583.mzML.txt diff --git a/tools/metfrag/test-data/candidates.csv b/tools/metfrag/test-data/candidates.csv new file mode 100644 index 00000000000..07b169804d2 --- /dev/null +++ b/tools/metfrag/test-data/candidates.csv @@ -0,0 +1,72 @@ +Score,MonoisotopicMass,SMILES,InChIKey,NoExplPeaks,NumberPeaksUsed,InChI,MaximumTreeDepth,Identifier,ExplPeaks,InChIKey2,InChIKey1,IUPACName,FragmenterScore,MolecularFormula,FragmenterScore_Values,FormulasOfExplPeaks,XlogP3 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b/tools/metfrag/metfrag-cli-batch.xml index bbd666a0fae..b766467e661 100644 --- a/tools/metfrag/metfrag-cli-batch.xml +++ b/tools/metfrag/metfrag-cli-batch.xml @@ -17,7 +17,7 @@ -s "$additional_metfrag_scores" #end if --> - Date: Fri, 21 Sep 2018 09:59:37 +0200 Subject: [PATCH 3/6] metFrag: added missing output file --- ...00003_PE_PG_AutoMS_2-B_3_03_18583.mzML.csv | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 tools/metfrag/test-data/1_746.022_716.5434_1569591.66000003_PE_PG_AutoMS_2-B_3_03_18583.mzML.csv diff --git a/tools/metfrag/test-data/1_746.022_716.5434_1569591.66000003_PE_PG_AutoMS_2-B_3_03_18583.mzML.csv b/tools/metfrag/test-data/1_746.022_716.5434_1569591.66000003_PE_PG_AutoMS_2-B_3_03_18583.mzML.csv new file mode 100644 index 00000000000..a2bbb5e03f2 --- /dev/null +++ b/tools/metfrag/test-data/1_746.022_716.5434_1569591.66000003_PE_PG_AutoMS_2-B_3_03_18583.mzML.csv @@ -0,0 +1,72 @@ 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+0.005336850057597394,715.539,CCCCOC(C)O[C@H]1C[C@H]([C@@H]([C@H]1C/C=C\CCCC(=O)NCC)/C=C/[C@H](CCC2=CC=CC=C2)OC(C)OCCCC)OC(C)OCCCC,BTUFLIXUGPFYQU-JKSDMFEPSA-N,2,44,"InChI=1S/C43H73NO7/c1-8-12-30-46-34(5)49-38(27-26-37-22-18-17-19-23-37)28-29-40-39(24-20-15-16-21-25-43(45)44-11-4)41(50-35(6)47-31-13-9-2)33-42(40)51-36(7)48-32-14-10-3/h15,17-20,22-23,28-29,34-36,38-42H,8-14,16,21,24-27,30-33H2,1-7H3,(H,44,45)/b20-15-,29-28+/t34?,35?,36?,38-,39+,40+,41-,42+/m0/s1",2,132014333,121.103762723448_7.8;237.190849210659_4.9,N,JKSDMFEPSA,BTUFLIXUGPFYQU,NA,1.6747288444828066,C43H73NO7,908.0;448.0,121.103762723448:[C9H10+2H]+H+;237.190849210659:[C15H23O2+H]+H+,9.3 From d2d148af8f7a98f2796f53f09b1b43734db2ea28 Mon Sep 17 00:00:00 2001 From: Steffen Neumann Date: Fri, 21 Sep 2018 13:01:35 +0200 Subject: [PATCH 4/6] Added shed.yml --- tools/metfrag/.shed.yml | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 tools/metfrag/.shed.yml diff --git a/tools/metfrag/.shed.yml b/tools/metfrag/.shed.yml new file mode 100644 index 00000000000..c0c90c5f8fe --- /dev/null +++ b/tools/metfrag/.shed.yml @@ -0,0 +1,7 @@ +categories: + - Metabolomics +description: MetFrag performs annotation of tandem mass spectra of metabolites. Candidate molecules of different databases are fragmented in silico and matched against mass MS/MS spectra. +homepage_url: http://c-ruttkies.github.io/MetFrag/ +name: metfrag +owner: iuc +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metfrag/ From b36bf3971a9807a79313675de3a9f7a68e23e0ee Mon Sep 17 00:00:00 2001 From: Steffen Neumann Date: Fri, 21 Sep 2018 22:14:35 +0200 Subject: [PATCH 5/6] Bunp tool version --- tools/metfrag/metfrag-cli-batch.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/metfrag/metfrag-cli-batch.xml b/tools/metfrag/metfrag-cli-batch.xml index b766467e661..1ab49bdad7e 100644 --- a/tools/metfrag/metfrag-cli-batch.xml +++ b/tools/metfrag/metfrag-cli-batch.xml @@ -1,7 +1,7 @@ - + From 87543bda3ab588d7d2622289933d9eb8cc011a27 Mon Sep 17 00:00:00 2001 From: Steffen Neumann Date: Fri, 21 Sep 2018 22:30:58 +0200 Subject: [PATCH 6/6] Re-indent to 4 spaces --- tools/metfrag/metfrag-cli-batch.xml | 192 ++++++++++++++-------------- 1 file changed, 97 insertions(+), 95 deletions(-) diff --git a/tools/metfrag/metfrag-cli-batch.xml b/tools/metfrag/metfrag-cli-batch.xml index 1ab49bdad7e..6dbcfe36ac8 100644 --- a/tools/metfrag/metfrag-cli-batch.xml +++ b/tools/metfrag/metfrag-cli-batch.xml @@ -2,146 +2,148 @@ - - Run MetFrag with a given parameter set. - - metfrag - - + - - - - - - - - - - - - - - - - - - - - - + ]]> + + + + + + + + + + + + + + + + + + + + -.. class:: infomark + .. class:: infomark -| **Tool update: See the 'NEWS' section at the bottom of the page** + | **Tool update: See the 'NEWS' section at the bottom of the page** ---------------------------------------------------- + --------------------------------------------------- -.. class:: infomark + .. class:: infomark -**Authors** + **Authors** -| **Payam Emami (payam.emami@medsci.uu.se)** and **Christoph Ruttkies (christoph.ruttkies@ipb-halle.de)** wrote and maintain this wrapper for MetFrag batch mode processing. + | **Payam Emami (payam.emami@medsci.uu.se)** and **Christoph Ruttkies (christoph.ruttkies@ipb-halle.de)** wrote and maintain this wrapper for MetFrag batch mode processing. ---------------------------------------------------- + --------------------------------------------------- -.. class:: infomark + .. class:: infomark -**Please cite** + **Please cite** -Ruttkies, C., Schymanski, E. L., Wolf, S., Hollender, J. and Neumann, S. MetFrag relaunched: incorporating strategies beyond in silico fragmentation. J Cheminform 8:3, (2016) DOI: 10.1186/s13321-016-0115-9 + Ruttkies, C., Schymanski, E. L., Wolf, S., Hollender, J. and Neumann, S. MetFrag relaunched: incorporating strategies beyond in silico fragmentation. J Cheminform 8:3, (2016) DOI: 10.1186/s13321-016-0115-9 ---------------------------------------------------- + --------------------------------------------------- -===================== -MetFrag CLI Batch -===================== + ===================== + MetFrag CLI Batch + ===================== ------------ -Description ------------ + ----------- + Description + ----------- -| This module is used to run MetFrag on annotated MS/MS spectra for compound annotation. The parameters are set by **msms2metfrag**. + | This module is used to run MetFrag on annotated MS/MS spectra for compound annotation. The parameters are set by **msms2metfrag**. ------------ -Input files ------------ + ----------- + Input files + ----------- -+------------------------------+------------+ -| File | Format | -+==============================+============+ -| 1) File with MetFrag | txt | -| parameters | | -+------------------------------+------------+ -| 2) Database File (optional) | csv | -+------------------------------+------------+ + +------------------------------+------------+ + | File | Format | + +==============================+============+ + | 1) File with MetFrag | txt | + | parameters | | + +------------------------------+------------+ + | 2) Database File (optional) | csv | + +------------------------------+------------+ ----------- -Parameters ----------- + ---------- + Parameters + ---------- -File with MetFrag parameters + File with MetFrag parameters | File containing MetFrag parameters which is generated by **msms2metfrag** | -Additional Parameters + Additional Parameters | Additional parameters that can be passed to MetFrag. This can include e.g. access information for a local MetChem database instance | -Database File + Database File | File containing candidates used as database | -Additional MetFrag scores + Additional MetFrag scores | Add additional MetFrag scores used to score candidates | ------------- -Output files ------------- + ------------ + Output files + ------------ -metfrag_cli_batch_output_1.csv + metfrag_cli_batch_output_1.csv | A csv output file with scored candidates and properties | ---------------------------------------------------- + --------------------------------------------------- ----- -NEWS ----- + ---- + NEWS + ---- -CHANGES IN VERSION 0.3 -======================== + CHANGES IN VERSION 0.3 + ======================== -- added support for additional MetFrag scores + - added support for additional MetFrag scores -CHANGES IN VERSION 0.2 -======================== + CHANGES IN VERSION 0.2 + ======================== -- added support for a local file database + - added support for a local file database -CHANGES IN VERSION 0.1 -======================== + CHANGES IN VERSION 0.1 + ======================== -First version + First version - - - 10.1186/s13321-016-0115-9 - + + + 10.1186/s13321-016-0115-9 + + + + + +