Mercurial > repos > prog > lcmsmatching
changeset 5:18254e8d1b72 draft
planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb-dirty
| author | prog |
|---|---|
| date | Thu, 16 Mar 2017 08:15:11 -0400 |
| parents | 1ba222315fd5 |
| children | b8f70d8216b3 |
| files | MsPeakForestDb.R lcmsmatching.xml search-mz test-data/filedb.tsv |
| diffstat | 4 files changed, 5 insertions(+), 3 deletions(-) [+] |
line wrap: on
line diff
--- a/MsPeakForestDb.R Thu Mar 16 05:05:55 2017 -0400 +++ b/MsPeakForestDb.R Thu Mar 16 08:15:11 2017 -0400 @@ -291,7 +291,7 @@ url <- paste0('spectra/lcms/range-rt-min/', rt.low, '/', rt.high) params <- NULL if ( ! is.null(col)) - params <- c(columns = paste(col[['id']], collapse = ',')) + params <- c(columns = paste(col, collapse = ',')) # Run query rtspectra <- .self$.get.url(url = url, params = params)
--- a/lcmsmatching.xml Thu Mar 16 05:05:55 2017 -0400 +++ b/lcmsmatching.xml Thu Mar 16 08:15:11 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="lcmsmatching" name="LC/MS matching" version="3.2.1" profile="16.01"> +<tool id="lcmsmatching" name="LC/MS matching" version="3.2.2" profile="16.01"> <description>Annotation of MS peaks using matching on a spectra database.</description>
--- a/search-mz Thu Mar 16 05:05:55 2017 -0400 +++ b/search-mz Thu Mar 16 08:15:11 2017 -0400 @@ -530,7 +530,7 @@ # Set columns 'all-cols' specified if ( ! is.null(opt[['all-cols']])) - opt$rtcol <- db$getChromCol() + opt$rtcol <- db$getChromCol()[['id']] # Check chrom columns if ( ! is.null(opt[['check-cols']]) && ! is.null(opt$rtcol)) {
--- a/test-data/filedb.tsv Thu Mar 16 05:05:55 2017 -0400 +++ b/test-data/filedb.tsv Thu Mar 16 08:15:11 2017 -0400 @@ -1,7 +1,9 @@ "compoundid" "msmode" "mztheo" "peakcomp" "peakattr" "chromcol" "chromcolrt" "compoundcomp" "compoundmass" "fullnames" A10 "POS" 112.07569 "P9Z6W410 O" "[(M+H)-(H2O)-(NH3)]+" "colzz" 5.69 "J114L6M62O2" 146.10553 Blablaine' +A10 "POS" 112.07569 "P9Z6W410 O" "[(M+H)-(H2O)-(NH3)]+" "colAA" 1.58 "J114L6M62O2" 146.10553 Blablaine' A10 "POS" 112.07569 "P9Z6W410 O" "[(M+H)-(H2O)-(NH3)]+" "col12" 0.8 "J114L6M62O2" 146.10553 "Blablaine" A10 "POS" 112.07569 "P9Z6W410 O" "[(M+H)-(H2O)-(NH3)]+" "somecol" 8.97 "J114L6M62O2" 146.10553 "Blablaine" +A10 "POS" 112.07569 "P9Z6W410 O" "[(M+H)-(H2O)-(NH3)]+" "colzz2" 4.08 "J114L6M62O2" 146.10553 Blablaine' A10 "POS" 191.076694 "P92Z6W413 Na2 O2" "[(M-H+2Na)]+" "colAA" 1.58 "J114L6M62O2" 146.10553 "Blablaine" A10 "POS" 191.076694 "P92Z6W413 Na2 O2" "[(M-H+2Na)]+" "colzz2" 4.08 "J114L6M62O2" 146.10553 "Blablaine" A10 "POS" 294.221687 "U1113P94ZW429 O4" "[(2M+H)]+ (13C)" "somecol" 8.97 "J114L6M62O2" 146.10553 "Blablaine"