Mercurial > repos > prog > lcmsmatching
changeset 3:f61ce21ed17c draft
planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 476a081c0da66822f4e77070f5ce59d9f14511f4-dirty
author | prog |
---|---|
date | Thu, 02 Mar 2017 11:07:56 -0500 |
parents | 20d69a062da3 |
children | b34c14151f25 |
files | MsPeakForestDb.R lcmsmatching.xml |
diffstat | 2 files changed, 10 insertions(+), 8 deletions(-) [+] |
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--- a/MsPeakForestDb.R Thu Mar 02 08:55:00 2017 -0500 +++ b/MsPeakForestDb.R Thu Mar 02 11:07:56 2017 -0500 @@ -260,13 +260,15 @@ # 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()) - for (x in spectra) - 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$attribution), - stringsAsFactors = FALSE)) + for (x in spectra) { + if ('source' %in% names(x) && is.list(x$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)) + } # RT search if ( ! is.null(rt.low) && ! is.null(rt.high)) {
--- a/lcmsmatching.xml Thu Mar 02 08:55:00 2017 -0500 +++ b/lcmsmatching.xml Thu Mar 02 11:07:56 2017 -0500 @@ -1,4 +1,4 @@ -<tool id="lcmsmatching" name="LC/MS matching" version="3.1.7" profile="16.01"> +<tool id="lcmsmatching" name="LC/MS matching" version="3.1.8" profile="16.01"> <description>Annotation of MS peaks using matching on a spectra database.</description>