| Previous changeset 3:f61ce21ed17c (2017-03-02) Next changeset 5:fb9c0409d85c (2017-04-19) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 494194bb501d1d7033613131865f7bd68976041c |
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modified:
MsPeakForestDb.R lcmsmatching.xml |
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| diff -r f61ce21ed17c -r b34c14151f25 MsPeakForestDb.R --- a/MsPeakForestDb.R Thu Mar 02 11:07:56 2017 -0500 +++ b/MsPeakForestDb.R Tue Mar 14 12:40:22 2017 -0400 |
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| @@ -259,15 +259,27 @@ spectra <- .self$.get.url(url = url) # Build result data frame - results <- data.frame(MSDB.TAG.MOLID = character(), MSDB.TAG.MOLNAMES = character(), MSDB.TAG.MZTHEO = numeric(), MSDB.TAG.COMP = character(), MSDB.TAG.ATTR = character()) + results <- data.frame(MSDB.TAG.MOLID = character(), MSDB.TAG.MOLNAMES = character(), MSDB.TAG.MOLMASS = numeric(), MSDB.TAG.MZTHEO = numeric(), MSDB.TAG.COMP = character(), MSDB.TAG.ATTR = character(), MSDB.TAG.INCHI = character(), MSDB.TAG.INCHIKEY = character(), MSDB.TAG.CHEBI = character(), MSDB.TAG.HMDB = character(), MSDB.TAG.KEGG = character(), MSDB.TAG.PUBCHEM = character()) for (x in spectra) { if ('source' %in% names(x) && is.list(x$source)) - results <- rbind(results, data.frame(MSDB.TAG.MOLID = vapply(x$source$listOfCompounds, function(c) as.character(c$id), FUN.VALUE = ''), - MSDB.TAG.MOLNAMES = vapply(x$source$listOfCompounds, function(c) paste(c$names, collapse = MSDB.MULTIVAL.FIELD.SEP), FUN.VALUE = ''), - MSDB.TAG.MZTHEO = as.numeric(x$theoricalMass), - MSDB.TAG.COMP = as.character(x$composition), - MSDB.TAG.ATTR = as.character(x$attribution), - stringsAsFactors = FALSE)) + mztheo <- if ('theoricalMass' %in% names(x)) as.numeric(x$theoricalMass) else NA_real_ + comp <- if ('composition' %in% names(x)) x$composition else NA_character_ + attr <- if ('attribution' %in% names(x)) x$attribution else NA_character_ + if ('listOfCompounds' %in% names(x$source)) { + molids <- vapply(x$source$listOfCompounds, function(c) as.character(c$id), FUN.VALUE = '') + molnames <- vapply(x$source$listOfCompounds, function(c) paste(c$names, collapse = MSDB.MULTIVAL.FIELD.SEP), FUN.VALUE = '') + mass <- vapply(x$source$listOfCompounds, function(c) as.character(c$averageMass), FUN.VALUE = '') + inchi <- vapply(x$source$listOfCompounds, function(c) as.character(c$inChI), FUN.VALUE = '') + inchikey <- vapply(x$source$listOfCompounds, function(c) as.character(c$inChIKey), FUN.VALUE = '') + chebi <- vapply(x$source$listOfCompounds, function(c) as.character(c$ChEBI), FUN.VALUE = '') + chebi[chebi == 'CHEBI:null'] <- NA_character_ + hmdb <- vapply(x$source$listOfCompounds, function(c) as.character(c$HMDB), FUN.VALUE = '') + hmdb[hmdb == 'HMDBnull'] <- NA_character_ + kegg <- vapply(x$source$listOfCompounds, function(c) as.character(c$KEGG), FUN.VALUE = '') + pubchem <- vapply(x$source$listOfCompounds, function(c) as.character(c$PubChemCID), FUN.VALUE = '') + if (length(molids) > 0 && length(molids) == length(molnames)) + results <- rbind(results, data.frame(MSDB.TAG.MOLID = molids, MSDB.TAG.MOLNAMES = molnames, MSDB.TAG.MOLMASS = mass, MSDB.TAG.MZTHEO = mztheo, MSDB.TAG.COMP = comp, MSDB.TAG.ATTR = attr, MSDB.TAG.INCHI = inchi, MSDB.TAG.INCHIKEY = inchikey, MSDB.TAG.CHEBI = chebi, MSDB.TAG.HMDB = hmdb, MSDB.TAG.KEGG = kegg, MSDB.TAG.PUBCHEM = pubchem, stringsAsFactors = FALSE)) + } } # RT search |
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| diff -r f61ce21ed17c -r b34c14151f25 lcmsmatching.xml --- a/lcmsmatching.xml Thu Mar 02 11:07:56 2017 -0500 +++ b/lcmsmatching.xml Tue Mar 14 12:40:22 2017 -0400 |
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| @@ -1,9 +1,8 @@ -<tool id="lcmsmatching" name="LC/MS matching" version="3.1.8" profile="16.01"> +<tool id="lcmsmatching" name="LC/MS matching" version="3.2.0" profile="16.01"> <description>Annotation of MS peaks using matching on a spectra database.</description> <requirements> - <requirement type="package" version="3.2.2">R</requirement> <requirement type="package" version="1.20.0">r-getopt</requirement> <requirement type="package" version="1.0.0">r-stringr</requirement> <requirement type="package" version="1.8.3">r-plyr</requirement> |