# HG changeset patch # User computational-metabolomics # Date 1644328652 0 # Node ID 942e676515feac0555c123d09403cac28381f3d6 # Parent 6b9a83e0846789dd1fbee42819e32dd128aa12c4 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240" diff -r 6b9a83e08467 -r 942e676515fe README.rst --- a/README.rst Thu Mar 04 12:25:25 2021 +0000 +++ b/README.rst Tue Feb 08 13:57:32 2022 +0000 @@ -3,13 +3,13 @@ |Build Status (Travis)| |Git| |Bioconda| |License| -Version v1.16.2+galaxy0 +Version v1.16.2+galaxy1 ------------------------ - msPurity - bioconductor-mspurity v1.16.2 - Galaxy tools - - v0 + - v1 About ------ @@ -32,8 +32,6 @@ * Conda (dev and testing): https://anaconda.org/tomnl/bioconductor-mspurity - - Dependencies ------------------ Dependencies for these Galaxy tools should be handled by CONDA. @@ -53,8 +51,13 @@ - Julien Saint-Vanne (jsaintvanne) - `ABiMS (France) `_ - Simon Bray (sbray@informatik.uni-freiburg.de) - `University of Freiburg (Germany) `_ + Changes ------------------------- +v1.16.2-galaxy1 + - Fix for "scan" option for spectral matching + - Add allfrag option for filterFragSpectra + v1.16.2-galaxy0 - Version bump - Fix for intra spectral matching diff -r 6b9a83e08467 -r 942e676515fe filterFragSpectra.R --- a/filterFragSpectra.R Thu Mar 04 12:25:25 2021 +0000 +++ b/filterFragSpectra.R Tue Feb 08 13:57:32 2022 +0000 @@ -17,7 +17,8 @@ make_option("--snr", default = 0.0), make_option("--rmp", action = "store_true"), - make_option("--snmeth", default = "median", type = "character") + make_option("--snmeth", default = "median", type = "character"), + make_option("--allfrag", action = "store_true") ) opt <- parse_args(OptionParser(option_list = option_list)) @@ -39,12 +40,19 @@ opt$rmp <- TRUE } +if (is.null(opt$allfrag)) { + opt$allfrag <- FALSE +}else{ + opt$allfrag <- TRUE +} + pa <- filterFragSpectra(pa, ilim = opt$ilim, plim = opt$plim, ra = opt$ra, snr = opt$snr, rmp = opt$rmp, + allfrag = opt$allfrag, snmeth = opt$snmeth) print(pa) diff -r 6b9a83e08467 -r 942e676515fe macros.xml --- a/macros.xml Thu Mar 04 12:25:25 2021 +0000 +++ b/macros.xml Tue Feb 08 13:57:32 2022 +0000 @@ -1,7 +1,7 @@ 1.16.2 - 0 + 1 @@ -271,7 +271,7 @@ - + @@ -333,13 +333,14 @@ + help="Note that when using 'scan' spectra types the spectraFilter option may need to be FALSE + if 'allfrag' was not selecting when performing filterFragSpectra or if no filtering was performed at all" /> - +