Mercurial > repos > czouaoui > gc_cover_data
changeset 23:8a780635d8b4 draft
Deleted selected files
| author | czouaoui |
|---|---|
| date | Wed, 16 May 2018 10:23:10 -0400 |
| parents | a1f6c322aa26 |
| children | 07176cd5b79d |
| files | gc_cover_data/gc_cover_data.xml gc_cover_data/getGCCoverData.R |
| diffstat | 2 files changed, 0 insertions(+), 42 deletions(-) [+] |
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--- a/gc_cover_data/gc_cover_data.xml Wed May 16 10:12:05 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -<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="2.46.0">bioconductor-biostrings</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - Rscript $__tool_directory__/getGCCoverData.R $input1 $input2 "$input1.name" - ]]></command> - <inputs> - <param type="data" name="input1" format="fasta" label="DNA Sequence"/> - <param type="data" name="input2" format="txt" label="Coverage (Imagesmajik file)"/> - </inputs> - <outputs> - <data name= "output" format="rdata" label="${input1.name} - GCCover" from_work_dir="gcCover.RData"/> - </outputs> - <tests> - <test> - <param name="input1" format="fasta" value="sequence.fasta"/> - <param name="input2" format="txt" value="covFile"/> - <output name="output" format="rdata" file="gcCover.RData"/> - </test> - </tests> - <help><![CDATA[ - This tool is used to generate a R Data file from Fasta and Imagesmajik files. The data inside this file are used - to start the GC Cover Shiny application from Galaxy. - ]]></help> -</tool>
--- a/gc_cover_data/getGCCoverData.R Wed May 16 10:12:05 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -#!/usr/bin/env Rscript -args = commandArgs(trailingOnly=TRUE) -sessionInfo() -library(Biostrings) -sessionInfo() -# test if there is at least one argument: if not, return an error -if (length(args) != 3) { - stop("At least 3 arguments must be supplied (Fasta file, Coverage file, Fasta file name)", call.=FALSE) -} - -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")