Mercurial > repos > tomnl > mspurity_spectralmatching
diff spectralMatching.xml @ 12:e131f2fb0f97 draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
| author | tomnl |
|---|---|
| date | Fri, 13 Sep 2019 11:48:31 -0400 |
| parents | 103d2613b3a7 |
| children | 8dd98b0f83af |
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--- a/spectralMatching.xml Thu Jun 27 13:08:00 2019 -0400 +++ b/spectralMatching.xml Fri Sep 13 11:48:31 2019 -0400 @@ -18,55 +18,58 @@ spectralMatching.R --outDir=. --cores=\${GALAXY_SLOTS:-4} - - #if $Query.q_dbPth_con.q_dbPth_select == 'userdb' + #if $Query.q_dbPth_con.q_dbPth_select == 'msPurityData' + --q_defaultDb + #else if $Query.q_dbPth_con.q_dbPth_select == 'sqlite' --q_dbPth=$Query.q_dbPth_con.q_dbPth - #else - --q_defaultDb #end if - - #if $Library.l_dbPth_con.l_dbPth_select == 'userdb' + + #if $Library.l_dbPth_con.l_dbPth_select == 'msPurityData' + --l_defaultDb + #else if $Library.l_dbPth_con.l_dbPth_select == 'userdb_sqlite' --l_dbPth=$Library.l_dbPth_con.l_dbPth - #else - --l_defaultDb #end if - + + --l_dbType=$Library.l_dbPth_con.l_dbPth_select + --q_dbType=$Query.q_dbPth_con.q_dbPth_select + + --q_ppmPrec=$Query.q_filters.q_ppmPrec --l_ppmPrec=$Library.l_filters.l_ppmPrec - + --q_ppmProd=$Query.q_filters.q_ppmProd --l_ppmProd=$Library.l_filters.l_ppmProd - - + + #if $Query.q_filters.q_raThres_cond.q_raThres_bool --q_raThres=$Query.q_filters.q_raThres_cond.q_raThres #end if - + #if $Library.l_filters.l_raThres_cond.l_raThres_bool --l_raThres=$Library.l_filters.l_raThres_cond.l_raThres #end if - + #if $Query.q_filters.q_polarity_cond.q_polarity_bool --q_polarity=$Query.q_filters.q_polarity_cond.q_polarity #end if - + #if $Library.l_filters.l_polarity_cond.l_polarity_bool --l_polarity=$Library.l_filters.l_polarity_cond.l_polarity #end if - + #if $Query.q_filters.q_purity_cond.q_purity_bool --q_purity=$Query.q_filters.q_purity_cond.q_purity #end if - + #if $Library.l_filters.l_purity_cond.l_purity_bool --l_purity=$Library.l_filters.l_purity_cond.l_purity #end if - + #if $Query.q_filters.q_xcmsGroups_cond.q_xcmsGroups_bool --q_xcmsGroups=$Query.q_filters.q_xcmsGroups_cond.q_xcmsGroups #end if - + #if $Library.l_filters.l_xcmsGroups_cond.l_xcmsGroups_bool --l_xcmsGroups=$Library.l_filters.l_xcmsGroups_cond.l_xcmsGroups #end if @@ -74,54 +77,54 @@ #if $Query.q_filters.q_pids_cond.q_pids_bool --q_pids=$Query.q_filters.q_pids_cond.q_pids #end if - + #if $Library.l_filters.l_pids_cond.l_pids_bool --l_pids=$Library.l_filters.l_pids_cond.l_pids #end if - + #if $Query.q_filters.q_rtrange_cond.q_rtrange_bool --q_rtrangeMin=$Query.q_filters.q_rtrange_cond.q_rtrangeMin --q_rtrangeMax=$Query.q_filters.q_rtrange_cond.q_rtrangeMax #end if - + #if $Library.l_filters.l_rtrange_cond.l_rtrange_bool --l_rtrangeMin=$Library.l_filters.l_rtrange_cond.l_rtrangeMin --l_rtrangeMax=$Library.l_filters.l_rtrange_cond.l_rtrangeMax #end if - + #if $Query.q_filters.q_accessions_cond.q_accessions_bool --q_accessions=$Query.q_filters.q_accessions_cond.q_accessions #end if - + #if $Library.l_filters.l_accessions_cond.l_accessions_bool --l_accessions=$Library.l_filters.l_accessions_cond.l_accessions #end if - - + + #if $Query.q_filters.q_sources_cond.q_sources_bool --q_sources=$Query.q_filters.q_sources_cond.q_sources --q_sourcesUser=$Query.q_filters.q_sources_cond.q_sourcesUser #end if - + #if $Library.l_filters.l_sources_cond.l_sources_bool --l_sources=$Library.l_filters.l_sources_cond.l_sources --l_sourcesUser=$Library.l_filters.l_sources_cond.l_sourcesUser #end if - + #if $Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes_bool --q_instrumentTypes=$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes --q_instrumentTypesUser=$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypesUser #end if - + #if $Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes_bool --l_instrumentTypes=$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes --l_instrumentTypesUser=$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypesUser #end if - + #if $Query.q_filters.q_instruments_cond.q_instruments_bool --q_instruments=$Query.q_filters.q_instruments_cond.q_instruments #end if - + #if $Library.l_filters.l_instruments_cond.l_instruments_bool --l_instruments=$Library.l_filters.l_instruments_cond.l_instruments #end if @@ -129,7 +132,7 @@ #if $Query.q_filters.q_spectraTypes_cond.q_spectraTypes_bool --q_spectraTypes=$Query.q_filters.q_spectraTypes_cond.q_spectraTypes #end if - + #if $Library.l_filters.l_spectraTypes_cond.l_spectraTypes_bool --l_spectraTypes=$Library.l_filters.l_spectraTypes_cond.l_spectraTypes #end if @@ -137,7 +140,7 @@ #if $Query.q_filters.q_spectraFilter --q_spectraFilter #end if - + #if $Library.l_filters.l_spectraFilter --l_spectraFilter #end if @@ -145,80 +148,80 @@ #if $General.rttol_cond.rttol_bool --rttol=$General.rttol_cond.rttol #end if - + --raW=$General.raW --mzW=$General.mzW - + #if $General.updateDb_cond.updateDb --updateDb #if $General.updateDb_cond.copyDb --copyDb #end if #end if - + #if $General.usePrecursors --usePrecursors #end if - + ]]></command> <inputs> - + - + <section name="Query" title="Query spectra input and filters" expanded="True"> <expand macro="sm_input" ql='Query' ql_shrt = "q" user="True" mspuritydatalib="False" msp="False" help="Query SQLite database - in the standard XCMS msPurity workflow - the output - of msPurity.createDatabase should be used here. However any SQLite database + of msPurity.createDatabase should be used here. However any SQLite database following the schema of xxx can be used as input"/> <expand macro="filters" ql="Query" ql_shrt="q"/> </section> - + <section name="Library" title="Library spectra input and filters" expanded="True"> <expand macro="sm_input" ql='Library' ql_shrt = "l" user="False" mspuritydatalib="True" msp="False" - help="Library SQLite database - in the standard XCMS msPurity workflow - a default - database of MassBank, HMDB, LipidBlast and GNPS is used. However any SQLite + help="Library SQLite database - in the standard XCMS msPurity workflow - a default + database of MassBank, HMDB, LipidBlast and GNPS is used. However any SQLite database following the schema of xxx can be used as input"/> <expand macro="filters" ql="Library" ql_shrt="l"/> </section> - + <section name="General" title="General arguments" expanded="False"> <conditional name="rttol_cond"> - <param name="rttol_bool" type="boolean" label="Filter on retention time match?" + <param name="rttol_bool" type="boolean" label="Filter on retention time match?" help="" /> <when value="true"> - <param name="rttol" type="float" value="30" min="0" + <param name="rttol" type="float" value="30" min="0" label="Retention time tolerance (seconds)" help="Retention time tolerance in seconds to match precursors"/> </when> <when value="false"> </when> </conditional> - - - <param name="usePrecursors" type="boolean" checked="true" label="Filter on matching precursors?" - help="If True, spectra will be filtered by similarity of precursors based on + + + <param name="usePrecursors" type="boolean" checked="true" label="Filter on matching precursors?" + help="If True, spectra will be filtered by similarity of precursors based on the library and query ppm defined tolerance" /> - - <param name="raW" label="Weighting for relative abundance" + + <param name="raW" label="Weighting for relative abundance" type="float" value="0.5" help="Relative abundance weight for spectra (default to 0.5 as determined by massbank for ESI data)"/> - - <param name="mzW" label="Weighting for mz" + + <param name="mzW" label="Weighting for mz" type="float" value="2" help="mz weight for spectra (default to 2 as determined by massbank for ESI data)"/> - + <conditional name="updateDb_cond"> <param name="updateDb" type="boolean" checked="true" label="Update database with results?" help="" /> <when value="true"> - <param name="copyDb" type="boolean" checked="true" + <param name="copyDb" type="boolean" checked="true" label="Make a copy of the database?" - help="A copy will be made of the input SQLite target database and the - results will be added to this copy. When False, the input SQLite - database will be updated with the matching results. Use False if + help="A copy will be made of the input SQLite target database and the + results will be added to this copy. When False, the input SQLite + database will be updated with the matching results. Use False if you want to reduce storage space being used."/> </when> <when value="false"> @@ -228,8 +231,8 @@ </section> - - + + </inputs> @@ -274,44 +277,44 @@ ----------- -Perform spectral matching to spectral libraries for an LC-MS/MS dataset. +Perform spectral matching to spectral libraries for an LC-MS/MS dataset. -The spectral matching is performed from a **Query** SQLite spectral-database against a **Library** SQLite spectral-database. +The spectral matching is performed from a **Query** SQLite spectral-database against a **Library** SQLite spectral-database. The SQLite schema of the spectral database here: spectral_database_schema_ -The query spectral-database in most cases should contain be the "unknown" spectra database generated the msPurity -function createDatabase as part of a msPurity-XCMS data processing workflow. +The query spectral-database in most cases should contain be the "unknown" spectra database generated the msPurity +function createDatabase as part of a msPurity-XCMS data processing workflow. -The library spectral-database in most cases should contain the "known" spectra from either public or user generated resources. -The library SQLite database by default contains data from MoNA including Massbank, HMDB, LipidBlast and GNPS. +The library spectral-database in most cases should contain the "known" spectra from either public or user generated resources. +The library SQLite database by default contains data from MoNA including Massbank, HMDB, LipidBlast and GNPS. A larger_database_ can be download and used from the msp2db github repository. -To create a user generated library SQLite database the following tool can be used to generate a SQLite database +To create a user generated library SQLite database the following tool can be used to generate a SQLite database from a collection of MSP files: msp2db_. -It should be noted though, that as long as the schema of the spectral-database is as described here, then any database can be used -for either the library or query - even allowing for the same database to be used. +It should be noted though, that as long as the schema of the spectral-database is as described here, then any database can be used +for either the library or query - even allowing for the same database to be used. -The spectral matching functionality has four main components, spectral filtering, spectral alignment, spectral matching, -and summarising the results. +The spectral matching functionality has four main components, spectral filtering, spectral alignment, spectral matching, +and summarising the results. -Spectral filtering is simply filtering both the library and query spectra to be search against (e.g. choosing -the library source, instrument, retention time, precursor PPM tolerance etc). +Spectral filtering is simply filtering both the library and query spectra to be search against (e.g. choosing +the library source, instrument, retention time, precursor PPM tolerance etc). -The spectral alignment stage involves aligning the query peaks to the library peaks. The approach used is similar -to modified pMatch algorithm described in Zhou et al 2015. +The spectral alignment stage involves aligning the query peaks to the library peaks. The approach used is similar +to modified pMatch algorithm described in Zhou et al 2015. -The spectral matching of the aligned spectra is performed against a combined intensity and m/z weighted vector - created for both -the query and library spectra (wq and wl). See below: +The spectral matching of the aligned spectra is performed against a combined intensity and m/z weighted vector - created for both +the query and library spectra (wq and wl). See below: .. math:: w=intensity^x \cdot mz^y -Where x and y represent weight factors and can be adjusted with the parameters raW and mzW. +Where x and y represent weight factors and can be adjusted with the parameters raW and mzW. Defaults to x=0.5 and y=2 as per MassBank for ESI based mass spectrometry data. The aligned weighted vectors are then matched using dot product cosine, reverse dot product cosine and the composite dot product. @@ -343,49 +346,39 @@ The updated query database (this will have been updated with the annotation results if updateDb argument used) -**matchedResults** - -All matched results from the query spectra to the library spectra. Contains the following columns - -* dpc - dot product cosine of the match -* rdpc - reverse dot product cosine of the match -* cdpc - composite dot product cosine of the match -* mcount - number of matching peaks -* allcount - total number of peaks across both query and library spectra -* mpercent - percentage of matching peaks across both query and library spectra -* accession - accession of library match -* name - name of library match -* inchikey - inchikey of library match -* lpid - pid in database of library match -* qpid - pid in database of query match -* mid - id of the match **xcmsMatchedResults** If the qeury spectra had XCMS based chromotographic peaks tables (e.g c_peak_groups, c_peaks) in the sqlite database - it will be possible to summarise the matches for each XCMS grouped feature. The dataframe contains the following columns -* pid - pid in database of query match -* grpid - grpid of the XCMS grouped feature for query match -* mz - derived from XCMS grouped feature -* mzmin - derived from XCMS grouped feature -* mzmax - derived from XCMS grouped feature -* rt - derived from XCMS grouped feature -* rtmin - derived from XCMS grouped feature -* rtmax - derived from XCMS grouped feature -* npeaks - derived from XCMS grouped feature -* grp_name - derived from XCMS grouped feature +* lpid - id in database of library spectra +* qpid - id in database of query spectra * dpc - dot product cosine of the match * rdpc - reverse dot product cosine of the match * cdpc - composite dot product cosine of the match * mcount - number of matching peaks * allcount - total number of peaks across both query and library spectra * mpercent - percentage of matching peaks across both query and library spectra -* accession - accession of library match -* name - name of library match -* inchikey - inchikey of library match -* lpid - pid in database of library match -* mid - id of the match +* library_rt - retention time of library spectra +* query_rt - retention time of query spectra +* rtdiff - difference between library and query retention time +* library_precursor_mz - library precursor mz +* query_precursor_mz - query precursor mz +* library_precursor_ion_purity - library precursor ion purity +* query_precursor_ion_purity - query precursor ion purity +* library_accession - library accession value (unique string or number given to eith MoNA or Massbank data entires) +* library_precursor_type - library precursor type (i.e. adduct) +* library_entry_name - Name given to the library spectra +* inchikey - inchikey of the matched library spectra +* library_source_name - source of the spectra (e.g. massbank, gnps) +* library_compound_name - name of compound spectra was obtained from + +**matchedResults** + +All matched results from the query spectra to the library spectra. Contains the same as above +without the XCMS details. This table is useful to observe spectral matching results +for all MS/MS spectra irrespective of if they are linked to XCMS MS1 features. .. _spectral_database_schema: https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-datatabase-schema.html