Mercurial > repos > kpbioteam > minfi_rset
changeset 1:1a8ad582820d draft
planemo upload for repository https://github.com/kpbioteam/minfi_rset commit d43c3e67fa72ca39cbd67d33b010ebed8e7420bf-dirty
| author | kpbioteam |
|---|---|
| date | Tue, 22 May 2018 09:19:03 -0400 |
| parents | c3b42276697a |
| children | 68e80e06e67b |
| files | README.md RSet.rdata minfi_rset.xml r_wrapper.sh stderr test.Rmd |
| diffstat | 6 files changed, 9 insertions(+), 94 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Tue May 22 09:19:03 2018 -0400 @@ -0,0 +1,1 @@ +# Create RSet objects contain respectively the Beta value matrix, M value matrix and the Copy Number matrix.
--- a/minfi_rset.xml Mon Feb 05 06:56:59 2018 -0500 +++ b/minfi_rset.xml Tue May 22 09:19:03 2018 -0400 @@ -7,7 +7,7 @@ Rscript ${__tool_directory__}/minfi_rset.R "$input1" "$output1" ]]></command> <inputs> - <param type="data" name="input1" format="rdata" /> + <param type="data" name="input1" format="rdata" label="Methylation Signals" /> </inputs> <outputs> <data name="output1" format="rdata" /> @@ -24,4 +24,4 @@ <citations> <citation type="doi">10.1093/bioinformatics/btu049</citation> </citations> -</tool> \ No newline at end of file +</tool>
--- a/r_wrapper.sh Mon Feb 05 06:56:59 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,25 +0,0 @@ -#!/bin/sh - -### Run R providing the R script in $1 as standard input and passing -### the remaining arguments on the command line - -BASEDIR=`dirname $0` - -# Function that writes a message to stderr and exits -fail() -{ - echo "$@" >&2 - exit 1 -} - -# Ensure R executable is found -which R > /dev/null || fail "'R' is required by this tool but was not found on path" - -# Extract first argument -infile=$BASEDIR/$1; shift - -# Ensure the file exists -test -f $infile || fail "R input file '$infile' does not exist" - -# Invoke R -R --vanilla --slave -f $infile --args $* 2> stderr || cat stderr 1>&2
--- a/stderr Mon Feb 05 06:56:59 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,67 +0,0 @@ - -Attaching package: ‘BiocGenerics’ - -The following objects are masked from ‘package:parallel’: - - clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, - clusterExport, clusterMap, parApply, parCapply, parLapply, - parLapplyLB, parRapply, parSapply, parSapplyLB - -The following objects are masked from ‘package:stats’: - - IQR, mad, sd, var, xtabs - -The following objects are masked from ‘package:base’: - - anyDuplicated, append, as.data.frame, cbind, colMeans, colnames, - colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep, - grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, - mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, - rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, - table, tapply, union, unique, unsplit, which, which.max, which.min - - -Attaching package: ‘S4Vectors’ - -The following object is masked from ‘package:base’: - - expand.grid - -Welcome to Bioconductor - - Vignettes contain introductory material; view with - 'browseVignettes()'. To cite Bioconductor, see - 'citation("Biobase")', and for packages 'citation("pkgname")'. - - -Attaching package: ‘matrixStats’ - -The following objects are masked from ‘package:Biobase’: - - anyMissing, rowMedians - - -Attaching package: ‘DelayedArray’ - -The following objects are masked from ‘package:matrixStats’: - - colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges - -The following object is masked from ‘package:base’: - - apply - - -Attaching package: ‘Biostrings’ - -The following object is masked from ‘package:DelayedArray’: - - type - -The following object is masked from ‘package:base’: - - strsplit - -locfit 1.5-9.1 2013-03-22 -Setting options('download.file.method.GEOquery'='auto') -Setting options('GEOquery.inmemory.gpl'=FALSE)