# HG changeset patch
# User prog
# Date 1489666511 14400
# Node ID 18254e8d1b72194cf7f28b42d1987cac8b1ef408
# Parent  1ba222315fd5985ff3db4fb86470e41e54f26d74
planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb-dirty

diff -r 1ba222315fd5 -r 18254e8d1b72 MsPeakForestDb.R
--- 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)
diff -r 1ba222315fd5 -r 18254e8d1b72 lcmsmatching.xml
--- 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>
 
diff -r 1ba222315fd5 -r 18254e8d1b72 search-mz
--- 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)) {
diff -r 1ba222315fd5 -r 18254e8d1b72 test-data/filedb.tsv
--- 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"