Mercurial > repos > czouaoui > gc_cover_data
changeset 31:ec0d59a927e2 draft default tip
Uploaded
| author | czouaoui |
|---|---|
| date | Thu, 17 May 2018 03:10:57 -0400 |
| parents | 55f4ada53e50 |
| children | |
| files | gc_cover_data/gc_cover_data.xml gc_cover_data/getGCCoverData.R |
| diffstat | 2 files changed, 1 insertions(+), 5 deletions(-) [+] |
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--- a/gc_cover_data/gc_cover_data.xml Thu May 17 03:02:16 2018 -0400 +++ b/gc_cover_data/gc_cover_data.xml Thu May 17 03:10:57 2018 -0400 @@ -1,7 +1,5 @@ <tool id="gc_cover_data" name="Generating R Data to run GC Cover Shiny app inside Galaxy" version="0.1.0"> <requirements> - <requirement type="package" version="2.12.0">bioconductor-iranges</requirement> - <requirement type="package" version="2.46.0">bioconductor-biostrings</requirement> <requirement type="package" version="3.4_5">r-seqinr</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[
--- a/gc_cover_data/getGCCoverData.R Thu May 17 03:02:16 2018 -0400 +++ b/gc_cover_data/getGCCoverData.R Thu May 17 03:10:57 2018 -0400 @@ -1,7 +1,6 @@ #!/usr/bin/env Rscript args = commandArgs(trailingOnly=TRUE) library(seqinr) -library(Biostrings) # test if there is at least one argument: if not, return an error if (length(args) != 3) { @@ -9,8 +8,7 @@ } seqString <- read.fasta(args[1], seqonly=TRUE) -sequence <- DNAString(seqString[[1]]) covData <- scan(args[2], integer(), sep =",", skip = 1) seqName <- strsplit(args[3], '[.].*') -save(sequence, covData, seqName, file="gcCover.RData") +save(seqString, covData, seqName, file="gcCover.RData")